ThermoFisher.CommonCore.Data

Encapsulates information about AnalogInstrument.

Initializes a new instance of the class.

Defines the analog instrument data header for analog devices

Gets or sets the number of channels.

Gets or sets the start time.

Gets or sets the tic.

Specifies how positive and negative values are handled

Return all data

Return strictly positive data (not zero)

Return zero and above

Class to get various statistics from raw data. Intended to gather data for bar charts.

Gets or sets the scan filter string (sets "ScanFilter").

Gets or sets the compound names, for filtering chromatograms.

Gets or sets the maximum number of unique strings which are shown as a bar category, for "text string" diagnostic items. Any additional strings are displayed as a bar labeled "Other". Valid range: 3-1000 Default: 10

Create an analyzer for raw data.

the (open) raw file

Calculate the band size (bin size) needed to divide all data values into a given number of bands. The bands would usually represent "bars on a histogram".

Data to analyze Number of bands needed The width of each band

Gets the common average (mean) of a set of values, defined as 0 for "null or empty" data sets

The data to analyze the average

Gets the modal band of a set of data, by grouping into a fixed number of bands.

data to analyze The number of bands (groups) used to split the data the center of the modal band (from 0 to bands-1). 0 for null or empty data

Find the average delta between values in an array.

the data The average of the delta (d[x+1]-d[x])

Find the deltas between values in an array.

the data The average of the delta (d[x+1]-d[x])

Find the average delta between start times of scans matching a filter (minutes).

The average of the delta (d[x+1]-d[x]) in the start times

Find the delta between start times of scans matching a filter (minutes).

The the deltas (d[x+1]-d[x]) in the start times

Gets the scan number and start time of scans matching a filter

All scans which match this filter and their times.

Get a chromatogram from a filter

The chromatogram

Find the RT of all scans

the RT of every scan in a raw file

Find scan durations,in seconds.

the set of durations, in seconds. returns "new double[0] if there is no MS data

Find scan durations, for files which do not have "ElapsedKey"

the set of durations

Find scan durations, for files which do have "ElapsedKey"

scan filter index into trailer extra for time key the set of durations in seconds

Determine if this is a data type which needs banding. Small types (such as byte) can be mapped to a small array of results. For example: "unsigned byte" has only 256 states, so: we can collect data about each state. But: Float has infinite states, so must be banded. Note that "int" sometimes can handle all states, depending on the range of values, so is not considered "large" here

true if this is a large numeric type

Find a trend for the given trailer item

Find a trend for the given status item. Calling code should select a device with a status log first.

index into status log for required item Determines how positive, zero and negative data are handled. the set of values. Items which are (True, false) or (On,Off)or (yes,no) return 1 for true/on/yes and 0 for false/off/no

Find a trend for the given status item. Calling code should select a device with a status log first.

index into status log for required item Determines how positive, zero and negative data are handled. First record in the log to inspect. This is intended for incremental log reading (real time data). The value is updated to the next needed record number, such that repeated calls get new information as it arrives. the set of values. Items which are (True, false) or (On,Off)or (yes,no) return 1 for true/on/yes and 0 for false/off/no. If there are no further records after "startRecord" or all records are "NaN" the result will be an empty array.

Find a trend for the given trailer item

Find a trend for the given status item. Calling code should select a device with a status log first.

index into trailer extra for required item Determines how positive, zero and negative data are handled. the set of values. Items which are (True, false) or (On,Off)or (yes,no) return 1 for true/on/yes and 0 for false/off/no. If there are no further records after "startRecord" or all records are "NaN" the result will be an empty array. the set of values. Items which are (True, false) or (On,Off)or (yes,no) return 1 for true/on/yes and 0 for fasle/off/no

Find a trend for the given status item. Calling code should select a device with a status log first.

index into trailer extra for required item Determines how positive, zero and negative data are handled. First record in the log to inspect. This is intended for incremental log reading (real time data). The value is updated to the next needed record number, such that repeated calls get new information as it arrives. the set of values. Items which are (True, false) or (On,Off)or (yes,no) return 1 for true/on/yes and 0 for false/off/no. If there are no further records after "startRecord" or all records are "NaN" the result will be an empty array. the set of values. Items which are (True, false) or (On,Off)or (yes,no) return 1 for true/on/yes and 0 for fasle/off/no

Get a status numeric value from a status log

Index of the item in status log header status log format for this item stats log record index Time of this log entry list of names for "string" items The max number of unique strings accepted The numeric value for this log entry

Get a status numeric value from a sorted status log

Return a numeric value from any generic data type. Numeric types (double,int etc.) return the encoded number. String types "count unique string states" and return a state number.

generic record format data to decode For string data: unique strings found so far Max unique strings to accept the value from this log entry

Return a numeric value from any countable generic data type. Numeric types (short, byte etc.) return the encoded number. String types "count unique string states" and return a state number.

data to decode For string data: unique strings found so far Max unique strings to accept the value from this log entry

Silently ensure MaxTextCategories is in bounds, and fix if not

the fixed max

Get names for know "enum" formats.

format of this field string version of values

Find a trend for the given status log item. Calling code should select a device with a status log first.

Find a trend for the given trailer item

Decode only small (countable) values from logs.

Format of this field Value to decode Categories found so far maximum number of categories The log value

Get a small (countable state) status log value trend, based on index into the status log fields.

Index of field to read Filtering rule Format of the log The log value

Ensure that all trend items have a valid value. Assign values with "no saved name" as a category "other", valued 1 above the known names.

The set of names found (categories) in the log The data for the trend plot The names for the numbered categories.

Find the durations of scans, and bin them into a number of "millisecond" bands, ready for a histogram plot.

number of bands analysis of scan times (milliseconds)

Get banded data for a bar chart.

data to map into bands requested number of bands banded data for a bar chart

Get banded data for a chart (histogram). If the data has a small enough range of values, then all values have their own bar. Each bar represents "the count of values within a given band".

Data to band If there are too many unique data values (> maxBands) then the data becomes banded (grouped) into this many bands The maximum number of unique categories before that data must be banded The banded data

Class to keep trace of numeric value (bar number) for each text string found in a log

Name found in the log

Assigned bar number

Autofilter extenions for raw files

Create an enhanced autofilter for this raw file

raw file enhanced auto filter

Create an enhanced autofilter for this raw file, uing cans over a specific time range.

raw file start retention time end retention time enhanced auto filter

This class extends the functions of "auto filter". On construction, the "auto filter" list is obtained from the MS detector. methods are then called to construct a list of filters based on this data. The list can be searched for "items matching a given filter rule".

Adds the "empty filter" to the list.

Searches for the activation types used. Adds "Activation type" to the list, for MS/MS data (MS2 or above). This can find CID, HCD, ETD, UVPD

Creates a filter from a string and adds it

Adds "ms order filters" to the list this includes ms, ms2 etc up to ms10 if any ms/ms is found msn is also added.

When true (default): if any ms/ms is found "MSn" is also added.

Gets or sets a value indicating whether compound names shoud be included. This only has an effect if the "Name" property is set for at least one filter. Results which have names are shown in sorted (alpha) order. Any other filters, which do not have a name, are then added after the named items, in the original "auto filter" order. If a name appaers for more than one filter, then an entry is created which only contains a compound name, such that a chromatogram can be created based on all data identified for that compound. Note that this "name only" list is excluded when a "unique filter list" is requested with a specific subset filter.

Gets or sets a separator which appears between a compound name and a filter.

Add all unique filter groups (auto filter).

If this is not empty: The filters must all contan this sub-filter. For example "d" for "only return data dependent"

Remove "CV" from filters, such that filters which have CV at different values are merged.

Create am emhaced auto filter for a raw file

indicates whether time limits are used for the "auto filter" request from the raw file. If this is true: Only scans from minTime to maxTime are used else: all scans are used the minimum retention time for getting a set of filters from the raw file. Only applied when applyTimeLimits is set. the maximum retention time for getting a set of filters from the raw file. Only applied when applyTimeLimits is set.

remove "CV" from all filters

Filter to consolidate Updated list

The auto sampler information.

Gets or sets the tray index, -1 for "not recorded"

Gets or sets the vial index, -1 for "not recorded"

Gets or sets the number of vials (or wells) per tray. -1 for "not recorded"

Gets or sets the number of vials (or wells) per tray, across the tray. -1 for "not recorded"

Gets or sets the number of vials (or wells) per tray, down the tray. -1 for "not recorded"

Gets or sets the shape. If this property returns "Invalid", no other values in this object contain usable information. Invalid data can occur for older raw file formats, before auto sampler data was added.

Gets the tray shape as a string

Gets or sets the tray name.

Parameters for the Avalon integrator

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class.

Integrator events to copy

Results of banding algorithm. Data for a bar chart

Gets or sets the number of bands.

Gets or sets the width of a band.

Calculates the range of a given band

band whose range is needed The range of value in this band

Gets or sets the center of each band

Gets or sets the data (height of the bar) for each band

Gets or sets a value indicating whether this data got banded. For example: If a data set was integer, and contained "charges 1 to 7" then all 7 original data categories can be returned. If data is "double from 1..02-9000.6" then there are no fixed categories, and the data will be "sampled" into bands.

The cached scan provider.

Initializes a new instance of the class.

The capacity.

Get scan from a scan number.

The raw data. The scan number. The scan at that scan number, or null if the scan number is out of range.

The get scan at time.

The raw file. The time. The scan nearest the given time. Thrown on null raw file

Data for the calibration curve. Included and excluded points, fitted curve and equation text. This is designed to help creating calibration curve plots.

The _excluded.

The _external excluded.

The _external included.

The included.

The points.

The equation.

The percent cv.

The coefficient of determination (R squared).

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class.

The regression. The current calibration levels. The historic calibration levels. The is internal standard.

Gets or sets the equation text from the regression calculation.

Gets the excluded replicates from current sequence data

Covert points to read only.

The points. The collection of points

Gets the excluded replicates from current sequence data

Gets the excluded replicates from previously acquired data

Gets the included replicates from previously acquired data

Gets the fitted line

Gets the included replicates from current sequence data

Gets or sets a value indicating whether the fitted line is empty The curve data needs to be plotted as appropriate for an internal standard: Centered on the set of points,

Gets or sets the percentage coefficient of variance from the first calibration level.

Gets or sets the percentage relative standard deviation from the first calibration level.

Gets the fitted line

Gets or sets the RSquared value from the regression calculation (-1 if not valid)

Create data for a calibration curve report from a replicate table.

The replicates for one component Calibration replicates from the current sequence If set: the data is for an internal standard, and does not contain a line of fit X,Y points for included, excluded and fitted line

Create data for a calibration curve report from a replicate table.

The replicates for one component Calibration replicates from the current sequence X,Y points for included, excluded and fitted line

Create data for a calibration curve report from a replicate table.

The replicates for one component Calibration replicates from the current sequence Calibration replicates from previous sequences X,Y points for included, excluded and fitted line

Create data for a calibration curve report from a replicate table.

The replicates for one component Calibration replicates from the current sequence Calibration replicates from previous sequences If set: the data is for an internal standard, and does not contain a line of fit X,Y points for included, excluded and fitted line

Create data for a calibration curve report from a replicate table. This version does not support "stats" for ISTD curves.

The replicates for one component Calibration replicates from the current sequence X,Y points for included, excluded and fitted line

Create data for a calibration curve report from a replicate table. This version does not support "stats" for ISTD curves.

Create a table of points to draw on a calibration curve

Replicate table to convert into points if true, create points for the included data, else create points for the excluded data The list of points to plot

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Find the max amount in the supplied points

The points. The max amount.

Find the relative standard deviation

The calibration levels. The RSD.

class to represent calibration data, as may be drawn on a plot.

Gets or sets the amount (x) on calibration curve

Gets or sets the response (y) for the amount

Gets or sets the a key to identify this point. For example, a file name.

Gets or sets the a second key to identify this point. For example, a compound name.

Test that two points are equal

first point to compare second point to compare true if they have the same contents

Test that two spec points are not equal

first point to compare second point to compare true if they do not have the same contents

Test two points for equality

point to compare true if they are equal

Gets a hash code Object.GetHashCode

The has code Object.GetHashCode

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Defines interfaces for a calibration level.

Gets or sets the name for this calibration level

Gets or sets the amount of calibration compound (usually a concentration) for this level

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current level.

This class defines a calibration level. Each level has an amount BaseAmount and a name

A values very close to zero

Anticipated amount of target compound in calibration of QC standard.

Name for this calibration level

Gets or sets the name for this calibration level

Gets or sets the amount of calibration compound (usually a concentration) for this level

Initializes a new instance of the class. Create a copy of a calibration level

Level to copy

Initializes a new instance of the class. Default construction of calibration level

Initializes a new instance of the class.

A name associated with the level The amount of calibration compound (usually a concentration) for this level

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current level.

Centroid data making a second stream with profile scan.

this allows base peak mass and base peak intensity to search for the base value on first use

Intensity of largest peak (valid when _basePeakFound)

Mass of largest peak

Noise of largest peak (valid when _basePeakFound)

Resolution of largest peak (valid when _basePeakFound)

Mass calibration coefficients

Creates a new instance of CentroidStream

Deep copy constructor

Gets or sets the list of baseline at each peak

Gets the intensity of most intense peak

Gets the mass of most intense peak

Gets the noise of most intense peak

Gets the resolution of most intense peak

Gets or sets the list of charge calculated for peak

Gets or sets the calibration Coefficients

Gets or sets the coefficients count.

Gets or sets the flags for the peaks (such as reference)

Gets or sets the list of Intensities for each centroid

Gets or sets the number of centroids

Gets or sets the list of masses of each centroid

Gets or sets the list of noise level near peak

Gets or sets resolution of each peak

Gets or sets the scan Number

Return the largest intensity (base value) in the ranges supplies

Ranges of masses If the ranges have equal mass values, then are used to determine a band subtracted from low and added to high to search for matching masses Largest intensity in all ranges

Clears all the data.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Make a deep clone of this object.

An object containing all data in this, and no shared references

Get the list centroids.

The centroids in the scan

Convert the data for a given peak in this stream into a LabelPeak

The index of the peak to convert. Extracted data for the selected peak

Convert the data into LabelPeak objects

An array of LabelsPeaks, converted from this class

Forces re-computation of Base peaks , intensities.

Convert data into this object from an array of LabelPeaks

Data to populate the class true on success. False if the labels peaks are null or empty

Sum all masses within the ranges

List of ranges to sum If the ranges have equal mass values, then are used to determine a band subtracted from low and added to high to search for matching masses Sum of intensities in all ranges

Sum all masses within the ranges

List of ranges to sum If the ranges have equal mass values, then tolerance is subtracted from low and added to high to search for matching masses Sum of intensities in all ranges

Convert to simple scan. Even though this class implements ISimpleScanAccess, there can be an advantage in doing this conversion, as when this object goes out of scope the converted object only holds the mass and intensity refs, and will need less memory.

The .

Convert to segmented scan. This feature is intended for use where an application or algorithm in "SegmentedScan" format, such as typical centroid data from ITMS, but the data in this scan came from an FTMS detector, which would have the profile data in "SegmentedScan" and the centroid data in this object. Data from this object is duplicated (deep copy), such that changing values in the returned object will not affect data in this object.

The .

Convert to Scan. This feature is intended for use where an application or algorithm needs data in "Scan" format, with centroid information in the "SegmentedScan" property of the Scan. (such as typical centroid data from ITMS), but the data in this scan came from an FTMS detector, which would have the profile data in "SegmentedScan" and the centroid data in this object. The data is first converted to SegmentedScan format (using ToSegmentedScan) then a new Scan is made containing that data (with no data in "CentroidStream). Data from this object is duplicated (deep copy), such that changing values in the returned object will not affect data in this object. This initializes the returned scan's "ScanStatistics" based on the returned mass and intensity data. If the (optional) originalScanStats parameter is included, information from that is used to initialize RT, scan number and other fields which cannot be calculated from this data. The only values updated in the scan statistics are "BasePeakMass" and "BasePeakIntenity". All other values are either as copied from the supplied parameter, or defaults. Application should set any other values needed in the Scan, such as "ScansCombined, ToleranceUnit, MassResolution", which cannot be determined from the supplied parameters.

If this is supplied, the scan statistics are initialized as a deep clone of the supplied object (so that RT etc. get preserved) then the values of BasePeakMass and BasePeakIntensity are updated from this object The .

Find the mass limits of this data

Test if this is a valid object (all streams are not null. All data has same length)

true if the object has valid data in it.

Test if this is a valid object (all streams are not null. All data has same length)

is thrown if this instance does not contain valid data.

Internal method, used to truncate long arrays

The size to "resize" to

Change the size of an array. This exists because "Array.Resize" cannot be directly called on an array property.

The original data. The new size. The resized options

Change the size of an array. This exists because "Array.Resize" cannot be directly called on an array property.

The original data. The new size. The resized array.

Find the most intense peak

Find the largest value in a given mass range, and combine with the value passed in.

The mass range to analyze The base value so far. The largest of the base value passed in, and the base value in this mass range.

Create a label peak from data at a given index.

The label index. The .

Calculate the sum of intensities, for peaks within a mass range, and add to previous sum

The sum so far The mass range. This sum passed in, plus the sum of intensities of all peaks in range.

slice the data, using a set of mass ranges.

Ranges of data to include sA scan which only has data in the requested ranges

The chromatogram aggregator. This can join together chromatograms form batches of scans, and return to caller when complete

Gets or sets the number of batches of scans, that sub-divide this chromatogram.

Gets the generator.

Initializes a new instance of the class.

The tool to create chromatograms. The scan numbers and retention times Method called when the chromatogram is complete

Get the aggregator ready to hold result for "Batches" of data

Called when a signal is ready. That is: A set of scans has been combined to make a chromatogram. When the final batch is delivered, the chromatogram is sent to the client.

The batch number (which part of the overall chromatogram is this?). The signal.

Collate the signals

The joined signals

The chromatogram batch generator. This provides any number of chromatograms to a caller, using multiple threads.

Gets or sets the available scans.

Gets or sets the scan reader. Given a scan number, Return the spectral data and scan event

Gets or sets the scan reader, for multiple scans Given a scan number array, Return the spectral data and scan event. Note: May be null, in which case "ScanReader" will be used.

Gets or sets the scans in chromatogram batch. An optimal value will depend on the experiment type. For example: for SRM, with 20 or less centroid peaks per scan, this can be larger. For full scan experiments, with 500 or more centroids per scan, this may need to be smaller, especially on a 32 bit process. Default 400 for 32 bit, 1600 for 64 bit. Suggested range 100 to 3000. Setting this larger may increase efficiency (fewer small tasks to perform, in raw data with 100k scans), but is at the cost of possible increased memory usage for scans. This is intentionally "short". Values above 10,000 for this are discouraged, as that could lead to significant memory overheads, and possibly less efficient thread management.

Gets or sets a value indicating whether the chromatograms have a strict time range. By default, the retention time range of a chromatogram is considered as a "display range", such that the first value before the range, and the first value after the range is included in the data, permitting a continuous line, if plotted, to the edge of the time window. If this property is true, then only points which are within the supplied RT range are returned.

The minimum permitted number of threads to work on generating chromatograms.

Gets or sets the maximum number of consumer threads to make. In other words: The maximum number of chromatograms the caller will be given to process in parallel. Default: Environment.ProcessorCount. Minimum : MinConsumerThreads

Gets or sets the maximum work backlog, which controls how much work is kept in the pipeline, waiting for threads to become available. Default: 5 for 32 bit process, 20 for 64 bit. Setting a larger value may cause data reading from a raw file to be completed earlier, but at the expense of more memory overheads.

Gets or sets a value indicating whether accurate precursor mass testing is done. If not: a tolerance of 0.4 AMU is used. All data dependent tests are done with 0.4 AMU tolerance.

Gets or sets the precision (decimal places)

Initializes a new instance of the class.

Generate chromatograms, returning the in progress tasks, which are processing the chromatograms. This permits async generation of chromatograms. This method returns after all required scan data has been read, and all work to process the chromatograms is queued. (The implied raw data file can be closed, as ScanReader will not be called again).

The chromatogram deliveries. These define the chromatogram settings, and a callback which will occur as soon as the data for that chromatogram is ready. The in progress tasks. Assuming the result is saved as "taskList" Use "Task.WaitAll(taskList)" to wait for processing of these chromatograms to complete.

Process all items in a work list.

The work item list.

Add work to the work list. If there are insufficient background workers, assign more.

Collection of work New job to add

Add a worker thread.

The work.

Create partial chromatogram definitions, ordered by start scan.

requested chromatograms Ordered partial chromatograms

Create work items.

The work request list, ordered by start scan. The target work list.

Publish pending list of work, which has the same scan range

The pending item list. The work.

Generate the chromatogram chunks, for all work items that this thread sees.

The work items.

The work item. This consists of: The requested chromatogram. The set of scans needed to make a chromatogram.

Initializes a new instance of the class. Create a work item, ready to make chromatograms from scans

The tool to read scans The parameters for the chromatogram chunk

Gets the fragment.

Gets or sets the scans.

Process this work

Gets or sets the scan events interface, which can be used to optimize filtering, if provided. This interface may be obtained from IRawDataPlus (ScanEvents property).

Class to find which scans belong in the RT range of a chromatogram. This includes the feature that scans may be "entirely within" a given range, or go one scan beyond, such that the range is extended allowing a chromatogram plot can be generated over the entire range.

Gets or sets the available scans.

Find scan index for a given retention time.

The time. The index into the scan table for this time.

Find the scan index range for chromatogram, based on the retention time range.

The RT range of the chromatogram. The start and end index (items 1 and 2).

Class to analyze chromatogram requests, creating an ordered table of partial chromatograms, which can be used to optimize data reading for chromatogram generation.

Gets or sets a value indicating whether accurate precursor mass testing is done. If not: a tolerance of 0.4 AMU is used. All data dependent tests are done with 0.4 AMU tolerance.

Gets or sets the precision (decimal places)

Gets or sets the scan events interface, which can be used to optimize filtering, if provided. This interface may be obtained from IRawDataPlus (ScanEvents property).

Create ordered chromatograms. Creates a "time ordered" set of partial chromatogram requests, which can then be used for efficient chromatogram generation, by making a single pass over raw data.

The chromatograms to be delivered. The ordered set of chromatogram requests.

Create requests for one chromatogram.

The requests. The delivery.

Add a batch of scans.

The requests. The aggregator. The start scan index. The end scan index. Set if this is the final batch for a chromatogram

The chromatogram fragment request. A request to make a section of the overall chromatogram.

Gets or sets a value indicating whether this is empty. Empty implies that the raw file has no scans in the RT range.

Gets or sets the aggregator, which collates a set of partial chromatograms.

Gets or sets the batch. This is the batch index with the results table of the aggregator

Gets or sets the start scan index.

Gets or sets the end scan index.

Gets or sets a value indicating whether this is a final section of a chromatogram.

Make a chromatogram from a batch of scans

The scans

The SignalConvert interface. Defines an object which can be converted to signal

Convert to signal. The object implementing this would have the required intensity information, but limited other data (such as RT values) which can be pulled from "scans".

The scans. The .

Gets the number of points in this data

The chromatogram generator factory.

Create a chromatogram generator. This configures the generator for optimal performance in checking scans. as there may be over 1000 components over 100k scans, that is 10m or more scan filtering tests (most of which fail). So: optimize that test use "for" and arrays (not foreach and IEnumerable) etc.

The request. In this mode a tolerance matching for precursors is "accurate" (based on the precision value), except for data dependent scans. For all "non accurate" precursor selections, and for all data dependent scans a default (wide) tolerance is used. number of decimal places for masses in filter scan events interface, which can be used to optimize filtering, if provided. This interface may be obtained from IRawDataPlus (ScanEvents property). The .

The compressed chromatogram. This holds a "double intensity" and a "shot index offset" for each scan in the chromatogram, that is 10 bytes. Al alternative (scan number 4 bytes. plus RT 8 bytes, plus intensity 8 bytes is twice as much memory 20bytes). The data is expanded up on request. With 1k unfiltered chromatograms, over 100k scans, this saves 1k*100k*10=1GB ram.

Convert to signal. The object implementing this would have the required intensity information, but limited other data (such as RT values) which can be pulled from "scans".

The scans. The .

Gets the length.

Initializes a new instance of the class.

The first index. The index offsets. The intensities.

Create a chromatogram from a set of scans, with no filtering

Initializes a new instance of the class.

The request.

Create a chromatogram.

The scans. An interface to create a signal from the intensities which are calculated. Null if no scans.

Create a chromatogram from a set of scans

Initializes a new instance of the class.

The request.

Create a chromatogram.

The scans. An interface to create a signal from the intensities which are calculated. Null if no scans passed the filter.

Create a chromatogram from a set of scans, where a filter is used for scan selection.

Initializes a new instance of the class.

Create a chromatogram.

The scans. An interface to create a signal from the intensities which are calculated. Null if no scans passed the filter.

The ChromatogramGenerator interface.

Create a chromatogram.

The scans. An interface to create a signal from the intensities which are calculated. Null if no scans passed the filter.

Class to create objects to efficiently generate chromatogram points.

create an object to efficiently generate chromatogram points. This analyzes the given arguments, and returns an interface which can most efficiently generate the chromatograms

Retention time range for this chromatogram Method of selecting scans to be included Methods to generate points from scans Object to make chromatogram points

Standard properties for chromatogram point builders

Gets or sets the retention time range. Only scans within this range are included.

Gets or sets the scan selector, which determines if a scan is in the chromatogram, or not

Implementation of IChromatogramRequest, which can generate chromatogram points for mass ranges. Version which supports multiple mass ranges. This version sums values for the listed ranges

Gets a value indicating whether this point type needs "scan data". Always true for this type.

Gets or sets the point requests. These determine how chromatogram points are created from a scan, by adding or subtracting data form multiple mass ranges.

Gets the value for scan. This function returns the chromatogram value for a scan. For example: An XIC from the scan data.

The scan. The chromatogram value of this scan.

create an object to efficiently generate chromatogram points. This analyzes the given arguments, and returns an interface which can most efficiently generate the chromatograms. This version will find the "max value" from each of the supplied point requests (base peak)

Retention time range for this chromatogram Method of selecting scans to be included Methods to generate points from scans Object to make chromatogram points

This chromatogram request finds base peak mass and intensity data. It can return data for the full file or a mass range

Gets or sets a value indicating whether all data in the scan is used

Get os sets the mass range analyzed, when not "AllData"

Finds the Mass and Intsenty of the base peak

touple containin mass, intensity

Create a request to make an "base peak" mass chromatogram, based on a mass range. That is: returns the mass of most intense peak over a given range.

The low mass. The high mass. The .

Retention time range for this chromatogram Method of selecting scans to be included Methods to generate points from scans Object to make chromatogram points

Implementation of IChromatogramRequest, which can generate chromatogram points for mass ranges. Version which supports multiple mass ranges. This version finds the Max of the values for all range (base peak)

Gets a value indicating whether this point type needs "scan data". Always true for this type.

Gets or sets the point requests. These determine how chromatogram points are created from a scan, by adding or subtracting data form multiple mass ranges.

Gets the value for scan. This function returns the chromatogram value for a scan. For example: An XIC from the scan data.

The scan. The chromatogram value of this scan.

Gets a value indicating whether this point type needs "scan data". Always true for this type.

Gets or sets the point requests. These determine how chromatogram points are created from a scan, by adding or subtracting data form multiple mass ranges.

Gets the value for scan. This function returns the chromatogram value for a scan. For example: An XIC from the scan data.

The scan. The chromatogram value of this scan.

Implementation of IChromatogramRequest, which can generate chromatogram points for mass ranges. Simplified version for one mass range.

Gets a value indicating whether this point type needs "scan data". Always true for this type.

Gets or sets the point requests Determine how a chromatogram point is created from a scan.

Gets the value for scan. This function returns the chromatogram value for a scan. For example: An XIC from the scan data.

The scan. The chromatogram value of this scan.

Implementation of IChromatogramRequest, which can generate chromatogram points for mass ranges. Simplified version for one mass range, and no scaling

Gets a value indicating whether this point type needs "scan data". Always true for this type.

Gets or sets the point requests Determine how a chromatogram point is created from a scan.

Gets the value for scan. This function returns the chromatogram value for a scan. For example: An XIC from the scan data.

The scan. The chromatogram value of this scan.

Request to create a point in a chromatogram, based on mass/intensity data in a scan. Use the static methods to make common chromatogram types.

Gets or sets a value indicating whether all data in the scan is used, or just a mass range.

Gets or sets the scale. This can be 1 to "add data in a mass range" or -1 to "subtract data a mass range", or any other value to apply scaling to a range.

Gets or sets the mass range. If an application has a center mass +/ tolerance, then the static method may be useful to format the range.

Gets or sets the rule for how a chromatogram point is created from a mass range.

Create a request to make an "XIC" chromatogram, based on one ion plus mass tolerance.

The mass. The tolerance. The tolerance mode. The .

Create a request to make an "XIC" chromatogram, based on a mass range

The low mass. The high mass. The .

Create a request to make a "TIC" chromatogram.

The .

Create a request to make a "base peak in scan" chromatogram.

The .

Create a request to make an "base peak" chromatogram, based on a mass range. That is: returns the most intense peak over a given range.

The low mass. The high mass. The .

Create a request to make an "base peak" mass chromatogram, based on a mass range. That is: returns the mass of most intense peak over a given range.

The low mass. The high mass. The .

Create a request to make a "mass of base peak in scan" chromatogram.

The .

Initializes a new instance of the class.

Calculate tolerance factor, applied to supplied tolerance value, based on mode.

The mass. The mode. The factor to apply.

Create a request to make a "neutral fragment" chromatogram. If this is a "fixed fragment" based on a given MS/MS scan filter, the lowMass is positive, and the range is assumed to be "filter MS/MS mass - neutral mass". If the chromatogram has no MS/MS mass, then the lowMass = -neural -0.5 and the highMass is -neutral +0.5 To get amass range for a given scan, the MS/MS mass from that scan's event must be added to both low and high masses

Low mass of range High mass of range Mass tolerance (applied to precursor in target scan). Defaults to 0.5 amu when null Interface to generate a neural fragment chromatogram point

This represents the data for a chromatogram

Convert chromatogram signals to ChromatogramDataPlus interface

An array of signals interface to chromatogram data

Create a Chromatogram signal, from time and intensity arrays

array of retention times array of intensities at each time The constructed signal, or null if either of the inputs are null, or the inputs are not the same length

Create a Chromatogram signal, from time, intensity and scan arrays

array of retention times array of intensities at each time array of scan numbers for each time The constructed signal, or null if either of the inputs are null, or the inputs are not the same length

Create a Chromatogram signal, from time, intensity, scan and base peak arrays

array of retention times array of intensities at each time array of scan numbers for each time Array of base peak masses for each time The constructed signal, or null if either of the inputs are null, or the inputs are not the same length

Create an array of signals from . The Interface describes data read from a file (if using IRawData). This constructor converts to an array of type Signal, simplifying use of individual chromatograms with Peak integration.

data (usually read from file) to convert into signals The constructed signals, or null if the input is null

Create chromatogram data interface from . The Interface describes data read from a file (if using IRawData).

data (usually read from file) to convert into signals The constructed signals, or null if the input is null

The wrapped chromatogram data.

Initializes a new instance of the class.

The data to wrap

Gets the base peak array.

Gets the intensities array.

Gets the length.

Gets the positions array.

Gets the scan numbers array.

The signal times.

The signal base peak masses.

The signal intensities.

The signal scans.

Gets or sets the signal times.

The signal times.

Gets the times.

Gets or sets the signal intensities.

The signal intensities.

Gets the intensities.

The signal intensities.

Gets or sets the signal scans.

The signal scans.

Gets the signal scans.

The signal scans.

Gets or sets the signal base peak masses.

The signal times.

Gets the signal base peak masses.

The signal base peak masses. May be null (should not be used) when HasBasePeakData returns false

Gets the time at the end of the signal

Gets the time at the start of the signal

Gets the time range.

Gets the number of points in the signal

Gets a value indicating whether there is any base peak data in this signal

Creates a new object that is a (deep) copy of the current instance.

A new object that is a copy of this instance.

covert array to multi dimension.

The data. The converted array.

covert array to multi dimension.

The data. The converted array.

Gets times in minutes for each chromatogram

Gets the scan numbers for data points in each chromatogram

Gets the intensities for each chromatogram

Gets the number of chromatograms in this object

Test if the signal is valid

True if both times and intensities have been set, and are the same length

Initializes a new instance of the class.

Clone from this interface

Initializes a new instance of the class.

The times. The intensities.

Initializes a new instance of the class.

The times. The intensities. The scans.

Initializes a new instance of the class.

The times. The intensities. The scans. The base peaks.

Initializes a new instance of the class.

Test if the data is contained in valid arrays of the same size

The times. The intensities. True if both times and intensities have been set, and are the same length

Test if the data is contained in valid arrays of the same size

The times. The intensities. The scans. True if all of times intensities and scans have been set, and are the same length

Test if the data is contained in valid arrays of the same size

The times. The intensities. The scans. The base Peaks. True if all of times intensities and scans have been set, and are the same length

Add a delay to all times. This is intended to support "detector delays" where multiple detector see the same sample at different times.

The delay.

Setting to define a chromatogram Trace.

The delay in minutes.

The scan filter.

The fragment mass.

Flag for including reference and exception peaks.

The mass ranges.

The trace.

Initializes a new instance of the class. Default constructor creates a new instance of ChromatogramSettings

Initializes a new instance of the class. Constructor creates a new instance of ChromatogramSettings and sets the type of trace to construct.

The type of trace to construct; see for possible values

Initializes a new instance of the class. Constructor creates a new instance of ChromatogramSettings based on a read only interface

Access to the read only parameters

Initializes a new instance of the class. Initialize settings for a mass chromatogram. Makes "TraceType.MassRange"

scan filter The mass range(s)

Initializes a new instance of the class. Initialize settings for a mass chromatogram. Makes "TraceType.MassRange"

scan filter The mass range(s)

Initializes a new instance of the class. Clones available data from the supplied interface.

The chromatogram settings.

copy range.

from (old value). The index.

Gets or sets the compound names.

Gets or sets the delay in minutes.

Floating point delay in minutes

Gets or sets the filter used in searching scans during trace build

Gets or sets the fragment mass for neutral fragment filters.

Floating point fragment mass for neutral fragment filters

Gets or sets a value indicating whether reference and exception peaks are included in this chromatogram trace

Gets or sets the number of mass ranges, or wavelength ranges for PDA.

If is MassRange then mass range values are used to build trace. Numeric count of mass ranges

Gets or sets the mass ranges.

If is MassRange then mass range values are used to build trace. Array of mass ranges

Gets or sets the type of trace to construct

see for more details

Convert from interface chromatogram settings. Note: This method is available as static converter, not a constructor overload, to avoid ambiguity with exiting overloads.

The settings. The .

Copies all of the items to from this object into the returned object.

The clone.

Gets a range value at 0-based index.

Use to find out the count of mass ranges. If is MassRange then mass range values are used to build trace. Index at which to retrieve the range value at give index

Sets a range value at 0-based index.

Set count of mass ranges using before setting any mass ranges. If is MassRange then mass range values are used to build trace. Index at which new range value is to be set New value to be set

Defines the definitions required to reading the data files.

Low Resolution spectrum packet type.

Low Resolution spectrum packet type2.

High Resolution spectrum packet type.

Spectrum profileIndex type.

FTMS data type (centroids)

FTMS data type (profiles)

Compressed profile format for MAT95

Compressed profile format for MAT95 (high-res)

LowResolution Spectrum Type (early quantum version). Also referred to as LR_SP_TYPE3 in some parts of FileIO. Used for centroid data from quantum about 2000, 2001 instruments.

LowResolution Spectrum Type. Also referred to as LR_SP_TYPE4 in some parts of FileIO. Used for centroid data from quantum and some other post 2002 instruments.

Profile Spectrum Type

Profile Spectrum Type2

Profile Spectrum Type3

Mass profile scan type

PDA UV discrete channel packet type

PDA UV discrete channel index header type

PDA UV scanned spectrum header packet type

PDA UV scanned spectrum header index header type

UV channel packet type

LT combined data type (profiles).

LT Combined Centroids.

Bitwise left shift operator, to get high 16 bits.

Number to shift the high 16 bits of a 32 bit value

Get the low 16 bits of a 32 bit value.

Number to mask The low 16 bits

Helper function to identifying the profile scan based on the given packet type.

packet type True if this is a profile packet type

EH - The reason for the separation of packet type into profile/centroid and scan type is to support legacy LCQ code that utilized the packet type to determine whether or not a scan is profile or centroid. This becomes a problem with data converted from ICIS, for example, which may store profile data in the centroid packet format. Setting this value is only necessary where profile or centroid is written to a packet type that is not assumed to be of that data type.

default is to use the packet type to determine profile/centroid

Centroid type

profile type.

The default scan provider.

Get a scan from a scan number.

The raw data. The scan number. The scan at "scan number"

The get scan at time.

The raw file. The time. The scan nearest to the given time.

This static factory class provides method to create a device method for an instrument method.

Creates the device method.

Optional: Data for the device The IDeviceMethod instance. name;Device method name cannot be empty.

Creates the device method factory.

Device method writer factory object.

IsotopeConsolidation - which function will be used for isotope consolidation

RemoveAllIsotopes - use function that strips all the isotopes during processing

KeepNonBaseIsotopes - use function that keeps non-base isotopes in the formula

Settings for the elemental compositions (formula searching) algorithm

Gets or sets a value indicating whether all features of elemental composition should be used. When false, all other settings are ignored and results of searches should be returned as an empty collection.

Gets or sets the Lowest mass for use in mono isotopic mass searching

Gets or sets the Highest mass for mono isotopic mass searching

Gets or sets a value indicating whether to use the calculated mono isotopic mass, otherwise use the mass passed in. Applies when "CalculateCompositionForMass" is called.

Gets or sets the minimum percentage threshold from the base peak for the mono isotopic mass

Gets or sets the tolerance (in amu) around the value to set limits when searching for mono isotopic mass. Mass of mono isotopic peak must be within a limit of: -MonoIsotopicSearchMassThreshold to +MonoIsotopicSearchMassThreshold from the mass of a spectral peak.

Gets or sets the center of search range for mono isotopic mass as a delta from the mass of a peak being analyzed

Gets or sets a string representation of the centroiding algorithm (for use on the UI)

Gets or sets a string representation of Missing Penalty Mode (for use in UI)

Gets or sets String representation of the SpectralFitNormalizationMode (for use in UI)

Gets or sets a string representation of (for use in UI)

Gets or sets a value which determines how the masses are compared.

Gets or sets a value which determines the maximum error in mass for something to pass tolerance, in the selected units.

Gets or sets a value which determines how the fragment masses are compared.

Gets or sets a value which determines the maximum error in MSMS mass for something to pass tolerance, in the selected units.

Gets or sets the charge state of the fragmented ion

Gets or sets the String representation of (for use in UI)

Gets or sets a collection of elemental isotopes, and mix/max expected counts in formulae

Gets or sets a value indicating whether the element abundance table "Representative" should be use. If it is not set, the "Protein" abundance table should be used.

Gets or sets a value indicating whether elemental compositions to be based on fitting against the supplied scan

Gets or sets a value indicating whether calibration reference data should be included in the scan.

Gets or sets the penalty (in units of spectral distance) that is applied to a missing packet. A packet is missing if it exists in the theoretical pattern (above threshold) but is not found in the measured spectrum (or too far away)

Gets or sets a value indicating whether the distances are normalized to have a max of 1.0 per packet (TrueDistance=false) or of 1.414 (sqrt(2.0) per packet (TrueDistance=true)

Gets or sets a threshold which determines the smallest packets that are processed. It is applied to the theoretical isotope pattern of an elemental composition candidate. Note that it is not applied to the input spectrum. Therefore a small pattern (BPI of pattern is smaller than 100% of input pattern intensity) may still give good fits.

Gets or sets a value indicating whether the intensity error is taken absolute. This means that an intensity that is expected to be 10% but is 9% has an error of 1%. If false, the intensity error is taken relative. This means that an intensity that is expected to be 10% but is 9% has an error of 10%.

Gets or sets a value indicating whether the spectral distance of an isotope packet is scaled with its intensity. I.e: the intensity deviation of a small packet counts less than the same deviation of a large packet. see also WeightMassErrorByAbundance property.

Gets or sets a value indicating whether the spectral distance of an isotope packet is scaled with its intensity. I.e: the mass deviation of a small packet counts less than the same deviation of a large packet. See also WeightIntensityErrorByAbundance property.

Gets or sets the error in units of standard deviation that is defined to give a 100% Spectral Identity value. Together with the property ZeroFitExpectedError, these two values define the scale of a 0 to 100 % error.

Gets or sets the error in units of standard deviation that is defined to give a 0% Spectral Identity value. Together with the property HundredFitExpectedError, these two values define the scale of a 0 to 100 % error.

Gets or sets The expected intensity error in units of standard deviation. A standard deviation is defined such that 68% of all events are in the range X ± stddev. 95% of all events are in the range X± 2*stddev

Gets or sets the expected mass error in units of standard deviation. A standard deviation is defined such that 68% of all events are in the range X ± stddev. 95% of all events are in the range X± 2*stddev.

Gets or sets the charge of the mass for which an elemental composition is to be calculated.

Gets or sets the number of elemental compositions that are to be saved. If the number of fits found is bigger than "Best", only the best "Best" ( judged by their deviation from the specified mass) are saved in the result array.

Gets or sets the centroid algorithm that is used to calculate isotope pattern masses from their isotopic distribution

Gets or sets The lowest acceptable RDB for a formula Note that this property returns the RDB value for instances that contain absolute RDB values. It returns RDB / 100 amu for instances that contain relative values. Rather use GetRDB_LimitLow(). That one works for both absolute and relative limits

Gets or sets maximum RDB (ring double bond equivalence) for returned formulae.

Validates the ElementalCompositionParameters values

if parameters are invalid

Gets or sets the resolution that is used to calculate the theoretical isotope patterns. This should be the same resolution with which the measured spectrum was acquired.

Gets or sets a value which determines if the nitrogen rule should be used. NitrogenRule enum for details

Gets or sets the theoretical and measured isotope for the Spectral Distance calculation, patterns must be normalized. There are three different normalization modes available.

Gets or sets a value indicating whether to use auto dynamic range, for spectral distance isotope simulations. If this is true (default) then the property "DynamicRange" is automatically adjusted, each time spectral distance is calculated, based on the value of the theoretical peak intensity threshold, which may also be auto calculated, or set to depending on the value of .

Gets or sets a value indicating whether to apply dynamic A0 recalibration for spectral distance. It is set to false by default.

Gets or sets MSMS SignalToNoise threshold for MSMS spectral processing

Gets or sets SpectralFit score cutoff for which formulas MSMS ranking will not be computed - will be set as 1

Gets or sets which function will be used for isotope consolidation - 0 - RemoveAllIsotopes, 1 -KeepNonBaseIsotopes

Gets or sets the weight applied to Spectral Fit in the re-ranking algorithm

Gets or sets the weight applied to MsCoverage in the re-ranking algorithm

Gets or sets the weight applied to MsMsCoverage in the re-ranking algorithm

Gets or sets the weight applied to PatternCoverageWeight in the re-ranking algorithm

Gets or sets the weight applied to MsMsShiftMeasure in the re-ranking algorithm

Gets or sets a value indicating whether or not re-ranking will be performed

Creates a default list of elements for searching

A single possible result (formula) for elemental composition of a mass

The _mass.

The _combined fit.

The _delta mass.

The _formula.

The _pattern fit.

The RDB equivalents.

The _spectral distance.

The _mass deviation.

The _score.

The _composition.

The _isotopePackets

Gets or sets the fit value in percent.

Gets or sets the Elemental composition formula, with subscript style digits for elemental quantities. This formula defines the istope of the peak which was matched with the sample.

Gets or sets the Elemental composition formula, with subscript style digits for elemental quantities. This is the formula which contains the peak from the sample as one of it's istopes. It can be used to redraw the isotope plot.

Gets or sets the mass of Composition (the mass of the calculated formula)

Gets or sets the combined fit factor [range from 0% to 100%]. This is a linear combination between pattern fit and mass deviation.

Gets or sets the difference between the mass of the formula and the mass being searched. This is the mass difference in amu "mass to search for" - "mass of this formula".

Gets or sets the elemental formula (plain text)

Gets or sets the fit factor [range from 0% to 100%] that indicates fit between theoretical and measured isotope pattern.

Gets or sets the calculated RDB for the found formula

Gets or sets the Spectral Distance. This is the distance between a theoretical and a measured isotope pattern of n packets in an n-dimensional space.

Gets or sets the deviation in mass, using the same tolerance mode used when searching

Gets or sets the IsotopePackets.

Gets or sets the number of peaks matched to an isotope by spectral distance algorithm, that is: All peaks which contributed to the scoring (even if the peak was out of mass and intensity tolerance box).

Gets or sets the number of isotopes in the pattern tested for match against sample peaks

Gets or sets the number of isotopes in the pattern which were matched against a sample peak, and were within mass/intensity tolerance limits

Gets or sets the number of isotopes where there is at least one sample peak within 10* mass tolerance

Gets or sets the coverage of experimental spectrum by isotopic pattern

Gets or sets the coverage of theoretical spectrum by isotopic pattern

Gets or sets the computed coverage of MsMs spectrum

Gets or sets the computed measure of matches with average shift comparing to the precursor shift

Gets or sets the number of matched peaks in MSMS spectrum

Gets or sets the list of matched fragments

Gets or sets Combined score used for re-ranking results based on supplied weights

Gets or sets Rank of the candidate formula based on Combined score

isotope packet

Gets or sets Mass of theoretical isotope

Gets or sets Mass of measured centroid

Gets or sets Intensity of theoretical isotope

Gets or sets Intensity of measured centroid

Gets or sets the index into the original scan for the matched peak

Gets or sets a value indicating whether Theory has a close match with Measured

Gets or sets the match mode. Defines the quality of the match.

Initializes a new instance of the class. default constructor

Initializes a new instance of the class. constructor

The intensityMeasured The intensityTheory The massMeasured The massTheory The matched

Class containing assignments of formulas to masses to the fragmentation spectrum

Gets or sets mass in fragmentation spectrum

Gets or sets formula matched to the Mass in the fragmentation spectrum

Gets or sets DeltaMass of assigned formula from the observed m/z

Gets or sets Intensity of the fragment

Gets or sets Signal to noise ratio of the fragment

Initializes a new instance of the class.

Initializes a new instance of the class

assigned mass assigned formula

Initializes a new instance of the class

assigned mass assigned formula observed delta mass observed intensity observed signal to noise

Initializes a new instance of the class. default constructor

Initializes a new instance of the class. Construct from values. (Faster than constructing and setting properties, as property setters in this class may be instrumented with change notification).

Sets CombinedFit property Sets DeltaMass property Sets Formula property Sets Mass property Sets MassDeviation property Sets PatternFit property Sets RdbEquivalents property Sets SpectralDistance property Sets Score property Sets MatchedPeaks property Sets NoPenaltyPeaks property Sets BroadSearchMatches property Sets IsotopesTested property Sets Composition property. The is the isotope composition matched to the experminal peak

Add isotope packet into the ElementalCompositionResult

The intensityMeasured The intensityTheory The massMeasured The massTheory The matched How the isotope was matched (within the mass and intensity limits) Index of the matched peak in the original scan

Compares only the formula for equality

The Result who's formula is compared. True if equal

A collection of element subsets. Used to supply data to the elemental composition algorithm.

Add an element to the end of the collection.

Element to add

Add an element, keeping the list in nominal mass order.

Element to add

Remove all element subsets with a given sign

If the subset has this sign, it is removed

Reset the "UseRatio" flag for all subsets in the collection to a given value.

Value to set all "UseRatio" flags.

Test if there is any in the collection with a given sign

Sign to look for true if at least one in this collection has the given Sign

Reset the "in use" flag for all subsets in the collection to a given value.

Value to set all "in use" flags.

Defines an isotope of an element, and quantity limits of that isotope. This is an input parameter to elemental composition searching.

The chemical symbol.

The min abs count of this isotope.

The max abs count of this isotope

The min relative count of this isotope.

The max relative count of this isotope

If "relative" values (ratios) should be used.

Is this isotope used?

The nominal mass

The isotope mass.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct from all possible settings (Obsolete form, use initializer, as many of the values have the same type, and this is not "order safe").

The sign. The mass. The nominal. The min Abs. The max Abs. The min Relative. The max Relative. The use Ratio. The in Use.

Gets or sets the chemical symbol for the element

Gets or sets the maximum count of this isotope in returned formula

Gets or sets the maximum count of this element in the returned formula

Gets or sets the maximum count of this isotope in returned formulae

Gets or sets the minimum count of this isotope in returned formulae

Gets or sets the minimum relative amount of this isotope

Gets or sets the maximum relative amount of this isotope

Gets or sets the nominal mass of this isotope

Gets the isotope including its nominal mass. For example "12 C" or "13 C".

Gets or sets the exact mass of the isotope

Gets or sets a value indicating whether this element is used for searching.

Gets or sets a value indicating whether the "Relative" min and max count of isotopes is used.

Enumeration of possible bar code status values

NotRead status.

Read status.

Unreadable status.

Error status.

Wait status.

Enumeration of sample types

Unknown sample

Blank sample

QC sample

Standard Clear (None) sample

Standard Update (None) sample

Standard Bracket (Open) sample

Standard Bracket Start (multiple brackets) sample

Standard Bracket End (multiple brackets) sample

Program sample

A sample which only contains solvent

Blank which includes internal standard only.

Matrix sample with known amounts of surrogates

Matrix sample with known amounts of target.

Data acquisition device

No instrument

Mass spectrometer

Data collected from an analog input connected to a mass spectrometer.

An A to D device

UV/Vis detector

PDA (UV detector)

Unknown detector type or instrument which collects only status

Enumeration of trace types, for chromatograms. Note: legacy C++ file reader does not support analog trace numbers above "4" or UV above "channel D". Traces are organized in blocks of 10 For example: StartAnalogChromatogramTraces=10 (not a valid trace type, just a limit) Analog1 to Analog8 = 11 to 18 EndAnalogChromatogramTraces =19 (not a valid trace type, just a limit) Next block: StartPDAChromatogramTraces = 20 Etc.

Marks the start of the MS trace types (this enum value +1)

Chromatogram summing between two masses

Total Ion Current

Largest peak in scan (or mass range in scan)

Neutral fragment

Marks the end of the MS trace types (this enum value -1)

Marks the start of the Analog trace types (this enum value +1)

Analog channel 1

Analog channel 2

Analog channel 3

Analog channel 4

Analog channel 5

Analog channel 6

Marks the end of the Analog trace types (this enum value -1)

Marks the start of the PDA trace types (this enum value +1)

Sum of values over a range of wavelengths

Average of all values in PDA scan

Largest value in scan (or wavelength range in scan)

Marks the end of the PDA trace types (this enum value -1)

Marks the start of the UV trace types (this enum value +1)

UV Channel A

UV Channel B

UV Channel C

UV Channel D

UV Channel E

UV Channel F

UV Channel G

UV Channel H

Marks the end of the UV trace types (this enum value -1)

A to D converter channels start at this +1

A to D channel 1

A to D channel 2

A to D channel 3

A to D channel 3 (old naming convention) use "A2DChannel3" in new code

A to D channel 4

A to D channel 4 (old naming convention) use "A2DChannel4" in new code

A to D channel 5

A to D channel 6

A to D channel 7

A to D channel 8

A to D converter channels end at this -1

Marks the start of all trace types (this enum value -1)

enumeration for data type for the fields used by records of TuneData, StatusLog, TrailerExtra These are upper case names, so that they don't clash with standard type names.

Null data type. No data is available (just a label)

character data type (1 byte)

true/false data type/ Similar to boolean, 1 byte of data displayed as True or False

Yes/No data type. 1 byte of data displayed as Yes or No

ON/OFF data type. 1 byte of data displayed as On or Off

unsigned char data type

short data type

unsigned short data type

long data type Note: this is referred as a long (4-byte) in C++. It's not the same size as long in C#.

unsigned log data type Note: this is referred as an unsigned long (4-byte) in C++. It's not the same size as unsigned long in C#.

float data type

double data type

string data type (single byte chars)

string data type (wide chars, unicode)

enumeration of all initial and Timed events. Note. The Threshold and Bunch Factor parameters are the most important ones in controlling peak detection.

No peak detector event

Directly related to the RMS noise in the chromatogram, this is Threshold, the fundamental control used for peak detection. Set the threshold at the start of a peak

Directly related to the RMS noise in the chromatogram, this is Threshold, the fundamental control used for peak detection. Set the threshold at the end of a peak.

Controls the area cutoff. Any peaks with a final area less than the area threshold will not be detected. This control is in units of area for the data.

The peak to peak resolution threshold controls how much peak overlap must be present before two or more adjacent peaks create a peak cluster. Peak clusters will have a baseline drop instead of valley to valley baselines. This is specified as a percent of peak height overlap.

Permit detection of a negative going peak. Automatically resets after a negative peak has been found.

The Bunch Factor is the number of points grouped together during peak detection. It controls the bunching of chromatographic points during integration and does not affect the final area calculation of the peak. The Bunch Factor must be an integer between 1 and 6; a high bunch factor groups peaks into clusters.

Controls how closely the baseline should follow the overall shape of the chromatogram. A lower tension traces the baseline to follow changes in the chromatogram more closely. A high baseline tension follows the baseline less closely, over longer time intervals. Set in minutes.

Using this event, you can tangent skim any peak clusters. By default, it chooses the tallest peak in a cluster as the parent. You can also identify which peak in the cluster is the parent. Tangent skim peaks are detected on either side (or both sides) of the parent peak. Tangent skim automatically resets at the end of the peak cluster.

Allows peak shoulders to be detected (peaks which are separated by an inflection rather than a valley) Sets a threshold for the derivative.

Disables peak shoulder detection.

Stop detecting peaks, until the next on event.

Start detecting peaks again.

Force the following peaks to be treated as a cluster (single peak).

End the forced clustering of peaks.

Prevent any peaks from being clustered.

Permit clusters to occur again.

Determines if ion ratio checks are based on an absolute or relative window, from the expected percentage.

Window is an absolute % range. For example: 50% +/- absolute 10% gives 40-60%

Window is a relative range, for example: 50% +/ relative 10% gives 45%-55%.

Defines electrical polarity

Positive charge

Negative charge

Specifies how the valley between resolved peaks is measured (in what units)

Peaks are measured at full with half maximum. This implies that two close peaks will both hit half maximum at the valley, and is equivalent to 100% valley height (no valley), or just starting to be resolved.

Valley between two resolved peaks is 10% of peak height. Used for most accurate mass instruments.

The shape of the peaks to simulate, when making a profile out of an isotope pattern.

Create Profile with a Gaussian peak shape. (Legacy mode, as used in common core 2.0)

Create profile with a cosine peak shape

Create profile with a triangular peak shape

Create profile with a Lorentzian peaks shape

Use: Updated Gaussian table This table is designed to allow slightly higher precision in simulation and higher performance

Specifies a method of calculation centroids from a profile.

used in LCQ, TSQ, Quantum

Austin tweaking of TSQ algorithm

used in MAT95 and DFS products

used in Orbitrap and FT analyzers

Specifies units for measuring mass tolerance. Tolerance is used to determine if a results should be kept, in formula search. If the exact mass of a formula is not within tolerance of a measured mass from an instrument, then the formula is not considered a valid result.

No tolerance mode

Atomic mass units (or Daltons)

Milli Mass Units (1/1000 Dalton)

Parts Per Million

If a packet of a theoretical pattern is not found in the measured pattern, this causes a penalty. This enum defines the magnitude of the penalty

The penalty is one standard deviation

The penalty is four standard deviations

The penalty is sixteen standard deviations

The penalty is the spectral distance to the closest packet

The penalty is selected automatically. According to S/N

The penalty is selected automatically. According to S/N and ion statistic

For the Spectral Distance calculation, the theoretical and measured isotope patterns must be normalized. There are three different normalization modes available.

Base peak normalization means that base peak intensities are assumed to be identical.

If the mode is LINEAR, both theoretical and measured spectrum are normalized such that the sum of their intensity differences is minimized.

If the mode is QUADRATIC, both theoretical and measured spectrum are normalized such that the sum of their squared intensity differences is minimized.

The N-Rule builds on the fact that any compound containing C,H,O,N,S elements has an even number of N atoms if its molecular weight is even and has an odd number of N atoms if its molecular weight is odd. So if you want possible elemental compositions for an molecular ion that has an even mass, it makes no sense to display elemental composition candidates with an odd number of N-atoms.

No limitations are imposed on results based on this rule.

For the EvenElectronIons mode, elemental compositions containing N-atoms are only displayed if their RDB ( Ring and double bond equivalent ) has an integer value ( -1.0 0.0 1.0 2.0 … ); compositions containing N-atoms with an RDB value of -0.5 0.5 1.5.. are not displayed.

For the OddElectronIons mode, elemental compositions containing N-atoms are only displayed if their RDB ( Ring and double bond equivalent ) has an non-integer value ( -0.5 0.5 1.5.. ); compositions containing N-atoms with an RDB value of -1.0 0.0 1.0 2.0 … are not displayed.

Units of data from a UV or analog devices (if known).

No units or unknown units

straight AU

Milli AU

micro AU

Units are Volts

Units are Millivolts

micro volts

Gives orientation whether or not a packet is inside the expected mass and intensity window (= Expectation rectangle) If it is outside: it tells where the packet lies: North: intensity too big. South: Intensity too small West: Mass too low. East: Mass too big.

Unknown or not initialized yet

Packet has lower mass and higher intensity than expected

Packet has lower mass than expected but correct intensity

Packet has lower mass and lower intensity than expected

Packet has correct mass but lower intensity than expected

Packet has higher mass and lower intensity than expected

Packet has correct intensity but mass but higher mass than expected

Packet has higher mass and higher intensity than expected

Packet has correct mass and higher intensity than expected

Packet is inside expected error limits

The spectrum packet types. Internally, within raw files, these are defined simply as "a short integer packet type" These are then mapped to "constants". It is possible that types may be returned by from raw data, or other transmissions, which are outside of this range. These types define original compression formats from instruments. Note that most data values are returned as "double", when using IRawDataPlus regardless of the compressed file format used.

No packet type is being specified. This can be used as a method parameter to mean "use default". This value is not valid when in a data record within a raw file.

Format for basic profiles (especially: 1990s San Jose instruments). Packet Type 0.

Format for low resolution centroids (especially: 1990s San Jose instruments). Packet Type 1.

Format for high resolution centroids (especially: 1990s San Jose instruments). Packet Type 2.

Profile index. Index into multiple segment profile data. Legacy flag, not returned within scans. Packet Type 3.

Compressed accurate mass spectrum, legacy mass lab instruments. Packet type 4

Standard accurate mass spectrum, legacy mass lab instruments. Packet type 5

Standard uncalibrated spectrum, legacy mass lab instruments. Packet type 6

Accurate Mass Profile Spectrum, legacy mass lab instruments. Packet type 7

PDA UV discrete channel packet type. Packet type 8

PDA UV discrete channel index header type. (Typical for multi channel UV) Packet type 9

PDA UV scanned spectrum header packet type (Typical diode array detector format) Packet type 10

PDA UV scanned spectrum header index header type Packet type 11.

UV channel packet type Packet type 12

MS Analog channel packet type Packet type 13

Profile spectrum type 2. Older San Jose instruments (LCQ) format. Packet type 14.

Low resolution spectrum type 2. Older San Jose instruments (LCQ) format. Packet type 15.

Profile spectrum type 2. Quantum format. Packet type 16.

Low resolution spectrum type 3. Quantum format. Packet type 17.

Linear Trap (centroids). This format may also return extended data from "Centroid stream". Packet type 18.

Linear Trap (profiles). This format may also return extended data from "Centroid stream". Packet type 19.

FTMS data type (centroids) This format may also return extended data from "Centroid stream". Packet type 20.

FTMS data type (profiles) This format may also return extended data from "Centroid stream". Packet type 21.

Compressed profile format for MAT95 (high-res) Packet type 22.

Compressed profile format for MAT95 Packet type 23.

Low Resolution Packet type 4 (Quantum) Centroid + Flags Packet type 24.

Not a known type

Specifies a sequence bracket type. This determines which groups of samples use the same calibration curve.

No bracket type specified.

Standards are Overlapped with adjacent brackets.

There is no bracketing. All samples in a sequence are a single group with one calibration curve.

Multiple groups which are not overlapped (do not share standards).

Groups of samples are automatically determined, based on sample types of each row.

Event list, includes both initial events and timed events. Initial events are similar to properties of the peak detector. They are always at the start of the list, and are not time triggered. Timed events modify the initial values for a limited duration, or control special features, such a detecting the next peak as "negative". The additional functions are intended to assist in editing the list. The initial events are at the start of the list The timed events are in order

Gets the List of time events

Count the number of timed (as opposed to initial) events

The number of timed events

Step past any initial events, and find the first time event

The node for the first timed event

Find the first event matching a specific event code

The code to search for (returned) the number of the event in the list The node containing the first event matching the supplied event code

Find the first event matching a specific event code and kind

Initial or timed version The code to search for (returned) the number of the event in the list The node containing the first event matching the supplied event code

Creates the initial default events for the collection

Make a copy of the current event collection

A copy of the event collection

Extends the "Scan" object to provide charge envolope information, which is available from certain instrumnets.

Creates a new ExtendedScan from a Scan. All extended data is empty

Default constructor for Extended Scan

Create an extended scan object from a file and a scan number.

File to read from Scan number to read The scan read, or null of the scan number if not valid

read extended scan data from file.

The raw file. The scan number. The stats.

Return a slice of a scan which only contains data within the supplied mass Range or ranges. For example: For a scan with data from m/z 200 to 700, and a single mass range of 300 to 400: This returns a new scan containing all data with the range 300 to 400. All annotaion and charge envolope data is discarded, as peaks whcih make up envelopes are not guranteed to be in any slice.

The mass ranges, where data should be retained. When multiple ranges are supplied, all data which is in at least one range is included in the returned scan If this is true, then the scan will reset the scan's mass range to the bounds of the supplied mass ranges This setting only applies when the scan has both profile and centroid data. If true: When there isa centroid near the start or end of a range, and the first or final "above zero" section of the profile includes that peak, then the profile is extended, to include the points which contribute to that peak. A maximum of 10 points may be added A copy of the scan, with only the data in the supplied ranges

Gets centroids with additional charge envelope information (when available)

Gets a value indicating whether charge envelope data was recorded for this scan

Gets additional annotations per peak, related to change envelopes

Gets the change envelopes. This include overall information about the envelope, plus the set of included peaks,

The file header.

Gets or sets the creator Id. The creator Id is the full text user name of the user when the file is created.

Gets or sets the creator Login name. The creator login name is the user name of the user when the file is created, as entered at the "user name, password" screen in windows.

Gets or sets the creator Id. The creator Id is the full text user name of the user when the file is created.

Gets or sets the creator Login name. The creator login name is the user name of the user when the file is created, as entered at the "user name, password" screen in windows.

Gets or sets the type of the file. If the file is not recognized, the value of the FileType will be set to "Not Supported"

Gets or sets the file format revision Note: this does not refer to revisions of the content. It defines revisions of the binary files structure.

Gets or sets the file creation date in local time.

Gets or sets the modified date in local time. File changed audit information (most recent change)

The modified date.

Gets or sets the number of times modified.

The number of times the file has been modified.

Gets or sets the number of times calibrated.

The number of times calibrated.

Gets or sets the file description. User's narrative description of the file, 512 unicode characters (1024 bytes)

The file description.

Provides a means of reading headers from Xcalibur files.

Creates the reader.

File header reader factory object

Read a file header. The file header contents are returned. The file is not kept open.

Name of file to read Access to the contents of the file header.

This class is designed to allow iteration through MS data in a file, based on a filter. To use this, first open a raw file then create this object based on the open file. To process all the matching scans:


            FilteredScans scans=new FilteredScans(myFile,"MS2");
            int next=scans.NextSpectrumNumber;
            while(next > 0)
            {
               scans.MoveSpectrumPosition (next);
               var scan=myFile.GetSegmentedScanFromScanNumber(next,null);
               //process the scan, then move to the next
               next=scans.NextSpectrumNumber;
            }

Test if the file is open

True if it is open.

Set the filter used for iterating over spectra. This can be used with the method to iterate over scans with a certain filter

an object containing the Filter to be used for iterating over spectra

Initializes a new instance of the class. Creates an iterator to step through the selected file

The file. The scan filter.

Move the iterator to the start of the list. Permitting this loop to process all matching scans int next = iterate.MoveFirst(); int count = 0; while (next > 0) { // add your application code to // fetch and process scan "next" // end of application code block iterate.SpectrumPosition = next; count++; next = iterate.NextSpectrumNumber; }

The first valid spectrum number, or -1 if not scans match the given filter

Move the iterator to the end of the list

The last valid spectrum number, or -1 if not scans match the given filter

Gets the filter used for iterating over spectra, in string form. This can be used with the method to iterate over scans with a certain filter

Gets the Previous Spectrum, matching the filter returns the previous spectrum number in file. 0 if there is no file open

Gets the Next Spectrum, matching the filter returns the next spectrum number in file. 0 if there is no file open

Sets the CurrentSpectrumNumber to the new Spectrum Number The Set property has no return value

Gets a value indicating whether there may be spectra before the current scan. Note that this does not check if this scan matches the filter. returns true if there is an Previous spectrum in file. Otherwise false

Gets a value indicating whether there are more scans after the current scan Note that this does not check if this scan matches the filter. returns true if there is an Next spectrum in file. Otherwise false

The filter extensions. These are internal, as they are only supported for use by the ScanEventHelper class.

Calculate the filter mass resolution.

The filter. The .

Calculates the number of masses, corrected for multiple activations.

The filter. The .

Test if the compensation voltage value is valid.

The filter. The i. The .

Defines a combination of plain text and interface defintions of filters.

Gets a Standard (parsable) text form of the filter. This does not include any compound names.

Gets the scan filer (as accessable fields)

Gets a string which combines the compound name and the filter text.

Gets the compound name

Creates a new instance of FilterWithString, parsing the filter based on a supplied raw file.

The raw data, used to parse this filter The text form of the filter

Creates a new instance of FilterWithString.

Gets a value indicating whether this object only has a compound name, and does not have any filter text or filter interface defined. When this is set: Only the Name property should be used.

Results of the find algorithm

Gets or sets the scan number for this result

Gets or sets the scan number predicted for this peak

Gets or sets the retention time of the peak which has been found

Gets or sets a score based on both forward and reverse matching factors

Gets or sets the score from forward search

Gets or sets the score from reverse search

Gets or sets the intensity of the supplied chromatogram at this result

Gets or sets the score from Match algorithm.

Gets or sets the peak found for this result

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current collection.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Copy constructor

object to copy

Settings for the spectrum find algorithm. This algorithm validates a detected peak, by proving that the masses in the supplied spectrum for the peak maximize near the peak.

Gets or sets the forward threshold for find algorithm.

Gets or sets the match threshold for find algorithm

Gets or sets the reverse threshold for find algorithm

Gets or sets the spec points.

The spec points.

Gets the spec points.

The spec points.

Get a copy of the find spectrum

A copy of the find spectrum.

Update the spectrum (for the find algorithm)

The spectrum to find

The forward threshold.

The match threshold.

The reverse threshold.

The find spectrum.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Make a copy of this object

a copy of this object

User parameters for the Genesis peak integration algorithm. These settings determine how the chromatogram is integrated.

Gets or sets a value indicating whether to constrain the peak width of a detected peak (remove tailing) width is then restricted by specifying a peak height threshold and a tailing factor.

Gets or sets the expected peak width (seconds). This controls the minimum width that a peak is expected to have (seconds) if valley detection is enabled. The property is expressed as a window. With valley detection enabled, any valley points nearer than [expected width]/2 to the top of the peak are ignored. If a valley point is found outside the expected peak width, Genesis terminates the peak at that point. Genesis always terminates a peak when the signal reaches the baseline, independent of the value set for the ExpectedPeakWidth.

Gets or sets the percent of the total peak height (100%) that a signal needs to be above the baseline before integration is turned on or off. This applies only when the ConstrainPeak is true. The valid range is 0.0 to 100.0%.

Gets or sets the edge detection Signal to Noise threshold. This displayed as "S/N Threshold" in product UI. Larger values cause peaks to become narrower. A peak is considered ended if the following condition is met: height <= (BaseNoise * SignalToNoiseThreshold)) Where BaseNoise is the calculated noise on the fitted baseline, and height is the height above baseline.

Gets or sets the Tailing Factor, which controls how Genesis integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This applies only when the is true. The valid range is 0.5 through 9.0.

Gets or sets a value indicating whether to perform base to base integration

Gets or sets a value determining how far down from the peak apex a valley must be. The peak edge is set to values below this defined ratio. This test assumes an edge of a peak is found when the baseline adjusted height of the edge is less than the ratio of the baseline adjusted apex height and the peak S/N cutoff ratio. If the S/N at the apex is 500 and the peak S/N cutoff value is 200, Genesis defines the right and left edges of the peak when the S/N reaches a value less than 200. Range: 50.0 to 10000.0. Technical equation:if height < (1/PeakSignalToNoiseRatioCutoff)*height(apex) => valley here

Gets or sets the percentage of the valley bottom that the peak trace can rise above a baseline (before or after the peak). If the trace exceeds RisePercent, Genesis applies valley detection peak integration criteria. This method drops a vertical line from the apex of the valley between unresolved peaks to the baseline. The intersection of the vertical line and the baseline defines the end of the first peak and the beginning of the second peak. This test is applied to both the left and right edges of the peak. The RisePercent criteria is useful for integrating peaks with long tails. Useful range: 0.1 to 50

Gets or sets a value determining how deep a valley must be. The range is 1.0 to 100.0. for valley detection. Technical equation:height(here +/- VALLEY_WIDTH) > ValleyDepth*SNR+height(here) => valley here

Gets or sets a value indicating whether to enable RMS noise calculation. If not set, noise is calculated peak to peak. It is set by default.

Gets or sets the Baseline noise tolerance. controls how the baseline is drawn in the noise data. The higher the baseline noise tolerance value, the higher the baseline is drawn through the noise data. The valid range is 0.0 to 100.0

Gets or sets the minimum number of scans that Genesis uses to calculate a baseline. A larger number includes more data in determining an averaged baseline. The valid range is 2 to 100.0.

Gets or sets a factor which controls the width of the RMS noise band above and below the peak detection baseline and is applied to the raw RMS noise values to raise the effective RMS noise during peak detection. The left and right peak boundaries are assigned above the noise and, therefore, closer to the peak apex value in minutes. This action effectively raises the peak integration baseline above the RMS noise level. Range: 0.1 to 10.0. Default: 2.0.

Gets or sets the minutes between background scan recalculations. Baseline is refitted each time this interval elapses.

Gets or sets the smallest permitted signal to noise ratio. Peaks are rejected if they have a lower signal to noise ratio than this.

Gets or sets the lowest permitted percentage of the largest peak. Do not return peaks which are less than this % of the highest peak above baseline.

Gets or sets a value indicating whether peaks are filtered by relative signal height

Constrain the width of the peak. Default false

Expected peak width (seconds). default 0.0

Percent of the total peak height (100%) that a signal needs to be above the baseline. Default 5%.

edge detection Signal to Noise threshold. default 0.5

which controls how Genesis integrates the tail of a peak. default 1.0

perform base to base integration? default false

how far down from the peak apex a valley must be. default 200

percentage of the valley bottom that the peak trace can rise above a baseline (before or after the peak). default 10%

How deep a valley must be. default 1.0

Should noise be calculated as RMS? default true

The higher the baseline noise tolerance value, the higher the baseline is drawn through the noise data. default 10.0

minimum number of scans that Genesis uses to calculate a baseline. default 16.

controls the width of the RMS noise band above and below the peak detection baseline. default 2.0

minutes between background scan recalculations. default 5.0

The smallest permitted signal to noise ratio. Default 0.5. range in UI 0.0 to 999.

lowest permitted percentage of the largest peak. Default 10.0.

peaks are filtered by relative signal height? default false.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class. Maps settings from an Xcalibur processing method.

The access.

make a copy of this object

A copy of this object

Defines the format of a log entry, including label (name of the field), data type, and numeric formatting.

Gets or sets the display label for the field. For example: If this a temperature, this label may be "Temperature" and the DataType may be "GenericDataTypes.FLOAT"

Gets or sets the data type for the field

Gets or sets the precision, if the data type is float or double, or string length of string fields.

Gets or sets a value indicating whether a number should be displayed in scientific notation

Initializes a new instance of the class.

The label. Type of the data. The string length or precision. This indicates whether a number should be displayed in scientific notation. Optional parameter has a default value = false.

Gets a value indicating whether this is considered numeric data. This is the same test as performed for StatusLogPlottableData". Integer types: short and long (signed and unsigned) and floating types: float and double are defined as numeric.

Tests whether this is a variable header. A "variable header", if present as the first field in a table of headers, defines that each record has a variable number of valid fields. The first field in each data record will then be converted to "validity flags" which determine which of the fields in a data record have valid values.

The number of fields in the header. True if this specifies that "variable length" records are used.

Re-formats the specified value per the current header's settings.

The value, as a string. The formatted value.

Format a bool string based on the header.

The value to format. The true string value. The false string value. The formatted bool value.

Format a numeric value.

The value to format. The formatted numeric value.

The centroid peak interface.

Gets or sets mass.

Gets or sets intensity.

Gets or sets resolution.

Gets or sets base Line.

Gets or sets noise.

Gets or sets charge.

Gets or sets Peak Options Flag.

Gets or sets the signal to noise.

Methods for creating a value for one scan in a chromatogram.

Sum all masses within the ranges

List of ranges to sum If the ranges have equal mass values, then are used to determine a band subtracted from low and added to high to search for matching masses Sum of intensities in all ranges

Return the largest intensity (base value) in the ranges supplied

Ranges of positions (masses, wavelengths) If the ranges have equal mass values, then are used to determine a band subtracted from low and added to high to search for matching masses Largest intensity in all ranges

User parameters for the ICIS peak integration algorithm. These settings determine how the chromatogram is integrated.

Gets or sets the number of scans. Each scan is checked to see if it should be considered a baseline scan. This is determined by looking at a number of scans (BaselineWindow) before and after the a data point. If it is the lowest point in the group it will be marked as a "baseline" point. Range: 1 - 500 Default: 40

Gets or sets the Noise level multiplier. This determines the peak edge after the location of the possible peak, allowing the peak to narrow or broaden without affecting the baseline. Range: 1 - 500 Default multiplier: 5

Gets or sets the noise level multiplier (a minimum S/N ratio). This determines the potential peak signal threshold. Range: 1 - 1000 Default multiplier: 10

Gets or sets a value indicating whether to constrain the peak width of a detected peak (remove tailing) width is then restricted by specifying a peak height threshold and a tailing factor.

Gets or sets the tailing factor. This controls how Genesis integrates the tail of a peak. This factor is the maximum ratio of the trailing edge to the leading side of a constrained peak. This applies only when the ConstrainPeak is true. The valid range is 0.5 through 9.0.

Gets or sets the minimum number of scans required in a peak. Range: 0 to 100. Default: 3.

Gets or sets the minimum separation in scans between the apexes of two potential peaks. This is a criterion to determine if two peaks are resolved. Enter a larger number in a noisy environment when the signal is bouncing around. Range: 1 to 500. Default: 10 scans.

Gets or sets the number of scans on each side of the peak apex to be allowed. Range: 0 to 100. Default: 0 scans. 0 specifies that all scans from peak-start to peak-end are to be included in the area integration.

Gets or sets the number of scans past the peak endpoint to use in averaging the intensity. Range: 0 to 100. Default: 5 scans.

Gets or sets a value indicating whether noise is calculated using an RMS method

Gets or sets a value which determines how the ICIS peak detector determines which signals are noise. The selected points can determine a noise level, or be fed into an RMS calculator, depending on the RMS setting.

The _baseline window.

The _area noise factor.

The _peak noise factor.

The _constrain peak width.

The _peak height percentage.

The _tailing factor.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

make a copy of this object

a copy of this object

Contains common instrument information.

Initializes a new instance of the class.

Gets or sets the type of the device.

Gets or sets the base URI.

Gets or sets the name of the instrument

Gets or sets the Model of instrument

Gets or sets the Serial number of instrument

Gets or sets the Software version of instrument

Gets or sets the Hardware version of instrument

Gets or sets Units of UV or analog data (not used for MS instruments)

Gets or sets the run header of the instrument.

Gets or sets the list of auto filters.

Gets or sets the list of instrument methods.

Gets or sets the tune data for the instrument

Gets or sets the Status log data for the instrument

Gets or sets the segment event table for the current instrument

Gets or sets names for channels (for UV or analog data)

Data about an instrument, for example, instrument name

Gets or sets the name of the instrument

Gets or sets the model of instrument

Gets or sets the serial number of instrument

Gets or sets the software version of instrument

Gets or sets the hardware version of instrument

Gets or sets the Names for the channels, for UV or analog data:

Gets or sets the units of the Signal, for UV or analog

Gets or sets additional information about this instrument.

Gets or sets Device suggested label of X axis

Gets or sets Device suggested label of Y axis (name for units of data, such as "°C")

Gets or sets a value indicating whether the instrument is valid.

Gets a value indicating whether this file has accurate mass precursors

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct by copying fields from interface

Interface to copy from

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Test if this is a TSQ quantum series file. Such files may have more accurate precursor mass selection.

True if this is a raw file from a TSQ Quantum

This static factory class provides methods for exporting instrument method from a raw file

Creates the instrument method exporter with an input raw file name. It returns an interface which can be used to export an instrument method from a raw file. Example: using (var exporter = InstrumentMethodExporterFactory.ReadFile(rawFile)) { if (!exporter.HasError && exporter.HasInstrumentMethod) { exporter.ExportInstrumentMethod("Export instrument method file name", false); } }

Name of the raw file. Interface object for exporting the instrument method.

create a reader for instrument methods

A factory to read instrument methods.

Provides a means of opening instrument methods.

create a reader for instrument methods

A factory to read instrument methods.

Read an instrument method. The file contents are returned. The file is not kept open. Because this reads a file, try catch is suggested around this activity. Caller must test IsError after opening to obtain any detected error conditions in the file.

Name of file to read Access to the contents of the file.

Instrument Method Writer Extension Methods

Creates a device section with the given device name and writes the binary data and text data to it. If the same device name is already exist, it will get overwritten.

The instrument method writer object. The instrument method in binary format. The instrument method in text string. The device name True if

This static factory class provides methods to create an instrument method writer for creating/updating an instrument method file.

Creates the instrument method writer with an input file name. The method should open a file if it exists and loads the data into internal structure and then close the file; otherwise, a new in-memory method file should be created (since it's in-memory, the data isn't persisted to a file yet). After editing the device method, caller should use either the "Save" or "SaveAs" method to persist the data to a file.

Name of the instrument method file. Instrument method writer object. Null or empty file name argument.

Because there is no input file name, this method will create an "Unnamed" in-memory instrument method file (since it's in-memory, the data isn't persisted to a file yet). After editing the device method, caller should use the "SaveAs" method with a valid file name to save the data to a file.

Instrument method writer object.

Creates the instrument method writer factory.

Instrument method writer factory object.

Defines which instrument is selected in a file.

Initializes a new instance of the class.

Index of the instrument. Type of the device.

Gets the Stream number (instance of this instrument type). Stream numbers start from 1

Gets the Category of instrument

A Metadata class represents key/value pair of Index and InstrumentType of an instrument in the raw file.

Gets or sets the index of the Instrument.

Gets or sets the type of the instrument.

Holds the results of integrating a single chromatogram. The results are a peak list and the chromatogram data.

Gets or sets the data read from the raw file

Gets or sets the peaks found in the chromatogram

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Setting for all peak integrators, plus selection of integrator to use

Gets or sets settings for Avalon integrator

Gets or sets settings for genesis integrator

Gets or sets settings for ICIS integrator

Gets or sets choice of integrator to use

Gets Avalon.

Gets Genesis.

Gets ICIS settings.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Constructor, which should be used when not serializing, with the parameter set "true"

When true: default events are added to the Avalon integrator. This is not needed when the object is about to be used by a serializer, as in that case the initial settings will already be in the serialized object

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class.

The access.

Make a deep copy of this object

deep copy of peak detection settings

Events are either at the start of peak detection (Initial) or part way through the data (Timed)

Event value before any peak detection begins.

An event which occurs at a specific time in the chromatogram.

Class for initial and timed events. Includes the event, any attributes and the event time.

Initializes a new instance of the class. Create an empty event

Gets or sets the event which is occurring (for example "start cluster")

Gets or sets a value which determines if this is an initial value, or a timed event.

Gets or sets the event time. If this is a timed event, this is the time the event occurs, in minutes.

Gets or sets the first data value associated with the event

Gets or sets the second data value associated with the event

Set the initial value of a timed event. This sets an event at time=0.

The event being programmed initial value of the event

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current collection.

Exception filter string with invalid format

Initializes a new instance of the class. Basic analysis exception, no specified reason.

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception Trapped inner exception

Initializes a new instance of the class. Construct an exception, with serialization.

Data to serialize this object Stream for serializing

Parameters to the Ion Ratio confirmation algorithm, for a single mass.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Constructor, which should be used when not serializing, with the parameter set "true"

The construct.

The initialize.

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class.

The access to mass test. Peak integration settings Smoothing settings

Gets or sets the smoothing data for the ion ratio peak calculation. This is the only interaction with m_smoothingPoints. This class is only a place holder. Other users of this class will fill this data item and use the settings.

The smoothing points.

Gets the integration choice item. This is the only interaction with m_integrationChoice. This class is only a place holder. Other users of this class will fill this data item and use the settings.

The integration choice item.

Gets or sets the integration choice item. This is the only interaction with m_integrationChoice. This class is only a place holder. Other users of this class will fill this data item and use the settings.

The integration choice item.

Gets the smoothing data for the ion ratio peak calculation. This is the only interaction with m_smoothingPoints. This class is only a place holder. Other users of this class will fill this data item and use the settings.

The smoothing points.

Gets or sets mass to be tested

Gets or sets the Expected ratio The ratio of the qualifier ion response to the component ion response. Range: 0 - 200%

Gets or sets a Window determine how accurate the match must be The ratio must be +/- this percentage.

Copy all settings from this object to another

Destination of copy

Copy all settings to this object from another

Source of copy

Copies the base values. Creates a deep copy.

Cloned object

Ion Ratio Confirmation settings

Gets or sets Qualifier Ion Coelution The time the retention time can vary from the expected retention time for the ion to still be considered confirmed. Units: minutes Bounds: 0.000 - 0.100

Gets or sets a value indicating whether this Ion Ratio Confirmation is enabled.

true if enable; otherwise, false.

Gets or sets the type of the windows.

The type of the windows.

Gets or sets the qualifier ions.

The qualifier ions.

Gets the qualifier ions.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Initializes a new instance of the class.

The component.

This class encapsulates the results of an ion ratio test for one ion.

Gets or sets a value indicating whether the coelution test has passed for this ion

Gets or sets the results of the coelution test targetCompoundPeak.Apex.RetentionTime - ion.Apex.RetentionTime;

Gets or sets the measured ion ratio, as a percentage (qualifierIonResponse * 100) / targetCoumpoundResponce

Gets or sets the Window in absolute % used to bound this test

Gets or sets a value indicating whether the ratio test passed for this ion

Gets or sets the Mass which was tested

Gets or sets The peak which was found in the IRC chromatogram

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Result.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Copy constructor

Object to copy

The Reaction interface. Defines a reaction for fragmenting an ion (an MS/MS stage).

Gets the precursor mass (mass acted on)

Gets the collision energy of this reaction

Gets the isolation width of the precursor mass

Gets a value indicating whether precursor range is valid. If this is true, then is still the center of the range, but the values and define the limits of the precursor mass range

Gets the start of the precursor mass range (only if )

Gets the end of the precursor mass range (only if )

Gets a value indicating whether collision energy is valid.

Gets the activation type.

Gets a value indicating whether this is a multiple activation. In a table of reactions, a multiple activation is a second, or further, activation (fragmentation method) applied to the same precursor mass. Precursor mass values should be obtained from the original activation, and may not be returned by subsequent multiple activations.

Gets the isolation width offset.

Methods to read a scan from a file

Create a scan object from a file and a scan number.

File to read from Scan number to read The scan read, or null of the scan number if not valid

Create a scan object from a file and a retention time.

File to read from time of Scan number to read The scan read, or null if no scan was read

Will be used with Channel labels. Currently not implemented.

Initializes a new instance of the class.

The source to copy the values from.

Gets or sets the index.

Gets or sets the label text.

Label Peak Information.

Initializes a new instance of the class. Default Constructor.

Gets or sets mass.

Gets or sets intensity.

Gets or sets resolution.

Gets or sets base Line.

Gets or sets noise.

Gets or sets charge.

Gets or sets Peak Options Flag.

Gets or sets the signal to noise.

This class defines table of replicates for a calibration level

Initializes a new instance of the class. Default construction of replicates

Initializes a new instance of the class. Create a new replicate table for a calibration level.

Level to base this replicate table on

Initializes a new instance of the class. Create a new replicate table for a calibration level.

Level to base this replicate table on

Gets or sets the Replicate Collection.

Gets the number of replicates for this level

Gets the replicates of this calibration level

array access operator to return Replicate array element.

Index into the array The requested replicate

array access operator to return Replicate array element.

Index into the array The requested replicate

Add a replicate to the list of replicates. If the supplied replicate has keys which match a keyed item in the current collection, then the matching record is replaced.

An additional replicate of this calibration level

Add a replicate collection to the list of replicates. If any of the supplied replicates has keys which match a keyed item in the current collection, then the matching record is replaced.

The collection to add

Add all replicates from this collection to the list of replicates. This addition only succeeds if the collections have the same calibration level If any of the supplied replicates has keys which match a keyed item in the current collection, then the matching record is replaced.

The replicates to add true if the collection was added, false if the calibration levels do not match.

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current sample.

Count all included/excluded replicates. The included and excluded counts are incremented by the number of included and excluded points. These counters are not set to zero, allowing this method to be called repeatedly, for example to count replicates for all levels.

(updated) included counter (updated) excluded counter

delete all replicates from the list of replicates.

Finds the replicate with amount and response.

Amount to match Response to match the matching replicate

Find the first replicate which matches the given key, and has no second key

Key to find Found replicate, or null

Find the replicate which matches a given key and

First key (for example file or sample name) Key for this peak (for example component name) The replicate which matches a given key and peak key, or null if not found.

Find the replicate which matches a the keys in a given replicate

replicate to match The matching replicate, or null if not found.

Return the highest included response. Any excluded points are ignored.

The highest response included in the calibration curve

Return the lowest included response. Any excluded points are ignored.

The lowest response included in the calibration curve

Update the count of included and excluded replicates. The included counter is incremented if this is an included point, otherwise the excluded counter is incremented. These counters are not set to zero, allowing this method to be called repeatedly, for example to count replicates for all calibration levels.

Replicate to count (updated) included counter (updated) excluded counter

The results of finding a single peak from a list. This includes the peak that is found, how it was found, and in the case of spectral searching, the spectral search results.

Gets or sets the peak which best matches the location rules.

Gets the peak which best matches the location rules.

Gets or sets a record of how this peak was found. The find results are only valid when this is set to "Spectrum".

Gets or sets a value indicating whether RT adjustments could be made to the RT reference. This flag is only meaningful when RT reference adjustments are made based on a reference peak (see the locate class). If a valid reference peak is supplied, then the expected RT can be adjusted based on the reference. If no reference peak is found (a null peak) then the expected RT cannot be adjusted, and this flag will be false.

Gets or sets the Find Results. When using spectrum LocateMethod this will contain the best matching peaks and find scores.

Gets the peak which best matches the location rules.

The results for this peak, or empty list

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Copy constructor

The object to copy

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current collection.

Holds the results of locating a single peak from chromatogram. The results are a and the chromatogram data.

Gets or sets the data read from the raw file

Gets or sets the peaks found in the chromatogram

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Copy these results

Object to fill with the results

Represents a single log.

Gets or sets the labels in this log.

Gets or sets the values in this log.

Gets or sets the length of the log.

Information returned when a peak baseline is manually adjusted on a chromatogram

Gets or sets x (time) of new baseline start point (left of peak)

Gets or sets x (time) of new baseline end point (right of peak)

Gets or sets y (intensity) of new baseline start point (left of peak)

Gets or sets y (intensity) of new baseline end point (right of peak)

Copy this object

copy of object

Contains the options for displaying and calculating the masses.

The initial tolerance.

The initial precision.

The initial tolerance units.

Initializes a new instance of the class. Default Constructor

Initializes a new instance of the class. Parameter Constructor

tolerance value units of tolerance value precision (decimal places)

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Gets or sets the tolerance value.

The tolerance.

Gets or sets the precision (decimal places).

Gets or sets the tolerance units.

Gets the tolerance string of the current toleranceUnits setting.

Gets the tolerance string from the enumeration strings resource.

The tolerance units. The tolerance units as a string.

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current object.

Get the tolerance window around a specific mass

Mass about which window is needed The distance (in amu) from the mass which is within tolerance. For example: myWindow=GetToleranceAtMass(myMass); accept data between "myMass-myWindow" and "myMass+myWindow"

Contains the generic header definitions of the Status log header, Trailer extra header and Tune header. If caller is not intended to use any one of these headers, caller should either pass a null argument or zero length array. i.e. TrailerExtraHeaders = null or TrailerExtraHeaders = new IHeaderItem[0]

Initializes a new instance of the class.

Gets or sets the status log headers. Optional property, it has a default value of no header items (zero length array)

The status log headers.

Gets or sets the trailer extra headers. Optional property, it has a default value of no header items (zero length array)

The trailer extra headers.

Gets or sets the tune headers. Optional property, it has a default value of no header items (zero length array)

The tune headers.

Information about the mass spec device data stream

Initializes a new instance of the class. Default field values: Comment1 = ""; Comment2 = ""; ExpectedRunTime = 0; MassResolution = 0.5; Precision = 2;

Gets or sets the expected run time. The value should be greater than zero. The expected run time. All devices MUST do this so that the real-time update can display a sensible Axis.

The expected run time.

Gets or sets the mass resolution (width of the half peak). Optional property, it has a default value of 0.5.

The mass resolution.

Gets or sets the first comment about this data stream. Optional property, it has a default value of empty string. The comment is for "Sample Name" in Chromatogram view title (max 39 chars).

The comment1.

Gets or sets the second comment about this data stream. Optional property, it has a default value of empty string. This comment is for "Comment" in Chromatogram view title (max 63 chars).

The comment2.

Gets or sets the number of digits of precision suggested for formatting masses. Optional property, it has a default value of 2.

The precision.

Class which includes the coefficients for mass calibration from a particular scan, and means to convert between mass and frequency

Gets or sets the coefficient 1.

Gets or sets the coefficient 2.

Gets or sets the coefficient 3.

Gets or sets the base frequency.

Gets or sets the delta frequency.

Converts the given frequency to it's corresponding mass.

sample number to convert converted mass.

Converts the given mass to frequency.

The mass to convert converted frequency

Gets or sets the highest mass.

Gets or sets the (largest) segment range of the scans processed.

General math routines

Calculates the discrete Fourier transform of a set of real-valued data points. Calculates the FFT of a set of dataPointsCount real-valued data points. The routine replaces the input data stored in data[0..dataPointsCount-1] by the positive frequency half of its complex Fourier transform. The real-valued first and last components of the complex transform are returned as elements data[0] and data[1], respectively. dataPointsCount MUST be a power of 2. This routine also calculates the inverse transform of a complex data array if it is the transform of real data (the result in this case must be multiplied with 2/n).

The input array of real-valued data points. The number of data points in the array (must be a power of 2). Flag indicating to calculate the FFT (sign=1) or the inverse FFT (sign=-1).

Calculates the discrete Fourier transform of a set of data points. Calculates the discrete Fourier transform of a set of data points. The routine replaces data[0..2*dataPointsCount-1] by its discrete Fourier transform, if sign is input as 1; or replaces data[0..2*dataPointsCount-1] by dataPointsCount times its inverse discrete Fourier transform, if sign is input as -1. data is a complex array of length dataPointsCount or (i.e. dataPointsCount real/imaginary pairs, which make up dataPointsCount array elements), equivalently, a real array of length 2*dataPointsCount. dataPointsCount MUST be an integer power of 2.

Data to transform, as real and imaginary pairs (index 0= real, 1=imaginary etc.) Number of valid points in the data. Sign of the data

Swap array elements

The array to swap. The source The destination.

Encapsulates information about MSAnalogInstrument.

Initializes a new instance of the class.

Represents the MassSpec instrument.

Initializes a new instance of the class.

The MS instrument data. This class provides a default implementation of IMsInstrumentData

Gets or sets the centroid data. It's a second stream with profile scan.

Gets or sets the event data.

Gets or sets the frequencies (for LT/FT).

Gets or sets the noise data.

Gets or sets or sets the scan data.

Gets or sets the statistics data.

Initialize MS Instrument data from a scan and a scan event.

The scan. The scan event. The .

Class to manage the MS order information in a filter. Simplifies the reaction tables into one entry per MS/MS stage.

Initializes a new instance of the class. Construct an MS Order table from a filter or event

filter or event to analyze

Gets the reaction data for all MS/MS stages

create reactions table

Data from raw file Table of reactions

Create a list of MS/MS stages (one per parent)

Reactions, which may have multiple per stage

format the MS order.

The scan filter.

The MS reaction. This is reaction to fragment a precursor mass. Reactions are used for MS/MS, Parent and Neutral scan types.

Gets or sets the precursor mass (mass acted on). For a product ion scan, this would be a parent mass. For a parent ion scan, this would be the fragment mass. If this is a multiple reaction, this value is not used.

Gets or sets the collision energy of this reaction

Gets or sets the isolation width of the precursor mass

Gets or sets a value indicating whether precursor range is valid. If this is true, then is still the center of the range, but the values and define the limits of the precursor mass range

Gets or sets the start of the precursor mass range (only if )

Gets or sets the end of the precursor mass range (only if )

Gets or sets a value indicating whether collision energy is valid. When not valid "CollisionEnergy" should not be tested or displayed.

Gets or sets the activation type. This defines how an ion is fragmented.

Gets or sets a value indicating whether this is a multiple activation. In a table of reactions, a multiple activation is a second, or further, activation (fragmentation method) applied to the same precursor mass. Precursor mass values should be obtained from the original activation, and may not be returned by subsequent multiple activations.

Gets or sets the isolation width offset.

Defines one stage of MS/MS, which may have multiple reactions. For a parent or neutral scan, one stage is required. For an MS/MS scan, one stage per MS/MS level is needed. For example: define 2 stages for an MS3 experiment. Each stage must have one or more reactions.

Gets or sets the set of reactions done at an MS stage. There must be at least one reaction for a valid stage. The first reaction of a stage must not have the MultipleActivation property set. Subsequent reactions of a stage must have the MultipleActivation property set.

Gets the precursor mass for this MS/MS stage. This is the precursor mass of the first reaction, and is defined as "0" if no reactions have been added yet.

Initializes a new instance of the class. Construct an MS stage from a list of reactions

Reactions for this stage

Contains objects containing data, related to "MS data systems". Used as an interchange between various common core DLLs. Several types are just "default get/set" implementations of interfaces Some types have business logic in them.

A request for a Neutral loss chromatogram

Gets or sets tolerance applied to precursor mass

Find the data for one scan.

The scan, including header and scan event. The chromatogram point value for this scan.

Exception for data reading. Thrown when a newer file format is detected. This is usually because an appliction has been compiled against an older generation file reader DLL. The application must be upgraded to use newer tools, which can decode this file.

Initializes a new instance of the class. Basic analysis exception, no specified reason.

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception Trapped inner exception

Initializes a new instance of the class. Construct an exception, with serialization.

Data to serialize this object Stream for serializing

Defines noise and baseline at a given mass (Part of support for reading orbitrap data)

Gets or sets the mass.

Gets or sets the noise.

Gets or sets the baseline.

Exception for raw data reading. Called when a Device specific method is made without first selecting a Device. For example: requesting a chromatogram

Initializes a new instance of the class. Basic analysis exception, no specified reason.

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception Trapped inner exception

Initializes a new instance of the class. Construct an exception, with serialization.

Data to serialize this object Stream for serializing

Exception for raw data reading. Called when a MS specific method is made without first selecting the MS data. For example: Requesting "scan filters" from UV data. These should all be handled in the code (never intentionally thrown to caller)

Initializes a new instance of the class. Basic analysis exception, no specified reason.

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception Trapped inner exception

Initializes a new instance of the class. Construct an exception, with serialization.

Data to serialize this object Stream for serializing

Factory to create objects which make MS chromatograms in parallel. Chromatograms are delivered on threads, such that action methods to perform peak integration etc. can be performed in parallel, and while other chromatograms, if they end at a later time, are still being generated from the raw file Chromatograms are generated from scans read from the raw file. Each scan is read only once. Data from the scans is reduced to mass and intensity information only, to reduce memory consumed. If the data is "FT format" with a set of supplied centroids, then the data is generated from the centroids only (no profiles are read from the raw file). If the data is not FT format then the regular "segmented scan" data is used. Scans are read in increasing scan number order. Scans which are outside of the required ranges to build the chromatograms are not read. Methods to "get chromatograms" are not called directly on supplied raw data interfaces. This also supports async reading from multiple raw files, as the returned information is a thread array, which the caller must sync (with "WaitAll") to complete operations on a given file.

Attach data sources to a Chromatogram batch generator (for MS chromatograms), based in data available via IRawDataPlus. This method has an IO overhead, as it configures a ChromatogramBatchGenerator, with a table of "scan number and RT", which is read from the raw data. It requires that the "rawData" interface supplied has an efficient implementation of RetentionTimeFromScanNumber.

Tool to generate chromatograms The raw data. Thrown if there is no available MS data.

Create the list of all MS scans.

The data. The list of scan headers.

Defines an implementation of "IScanWithSimpleData",

Gets or sets the scan event.

Gets or sets the data.

The fast scan from raw data class, which supplies code needed for the chromatogram batch generator to get from the IRawDataPlus interface. Enhanced version uses methods which only return mass and intensity data.

Initializes a new instance of the class.

The raw data.

The scan reader.

The scan index, to the available scans. The .

Encapsulates information about PDA Instrument.

Initializes a new instance of the class.

Defines the PDA scan header and wavelength settings

Gets or sets the start time.

Gets or sets the TIC.

Gets or sets the long wavelength.

Gets or sets the short wavelength.

Gets or sets the wave length step.

Gets or sets the Absorbance Unit's scale.

This class encapsulates a peak. (the result of peak detection)

Initializes a new instance of the class. default constructor

Initializes a new instance of the class. copy constructor

The peak to copy from.

Create by copying a peak.

The peak to copy.

Gets or sets the list of peaks that have been merged

Gets the list of peaks that have been merged

Gets a value which determines how signal to noise has been calculated. When this returns .Value, a numeric value can be obtained from .

Gets the signal to noise ratio. If is .Value, then this property returns the signal to noise ratio. Otherwise this should not be used. Use .ToString() instead.

Gets or sets the position, height, baseline at left limit

Gets or sets the position, height, baseline at peak apex

Gets or sets the position, height, baseline at right limit

Gets or sets the Integrated peak area

Gets or sets the Mass of the base peak from the apex scan.

Gets or sets the Mass to charge ratio of peak.

Gets or sets the expected RT after making any RT adjustments.

Gets or sets the Noise measured in detected peak (for signal to noise calculation)

Gets or sets a value indicating whether the "Noise" value was calculated by an RMS algorithm.

Gets or sets the scan number at peak apex. The apex of the peak corresponds to a particular signal. This gives the scan number of that signal. If no scan numbers are sent with the peak detection signal, then the scan number = "signal index at apex +1". Note that there is no guarantee that left and right edges will always be exactly on a scan, even though most peak detectors behave that way, so this is not added as a property of

Gets or sets a Name for this peak (for example, compound name)

Gets or sets the number of scans integrated

Gets or sets a value which describes why the peak started. It is only set by the Genesis Detector.

Gets or sets a value which describes why the peak ended. It is only set by the Genesis Detector.

Gets or sets a value indicating whether this is a valid peak. Peaks are assumed to have valid data, but may be marked invalid by an integrator, if failing certain tests. Invalid peaks should never be returned to a calling application by an integrator algorithm. Invalid peaks must never be: Drawn in a plot, listed in a report etc. An application should indicate "Peak not found" when a peak is flagged as "Invalid".

Gets or sets a value indicating whether this is saturated.

true when integration/mass range has saturation.

Gets or sets a value indicating whether valley detection was used when detecting this peak.

Gets or sets the Direction of peak (Positive or Negative)

Gets or sets the chi-squared error in fitting the peak.

Gets or sets the calculated width, or 'gamma_r'.

Gets or sets the calculated intensity, or 'gamma_A'.

Gets or sets the calculated position, or 'gamma_t0'.

Gets or sets the calculated fourth parameter for gamma (gamma_M) or EMG functions.

Gets or sets the peak shape used in the fitting procedure.

Gets or sets the number of data points used in the fit.

Find baseline height for a peak at specified time

Retention time to use for interpolation Interpolated baseline height at

Gets or sets a value indicating whether calculated values (such as height) may return negative numbers. If false: negative calculated numbers are returned as 0

Gets or sets peak Purity.

Gets Low time from peak purity calculation

Gets High time from peak purity calculation

Gets or sets the Low value of the retention time range, after a peak purity calculation.

Gets or sets the High value of the retention time range, after a peak purity calculation..

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Peak.

Class to hold chromatogram settings of a peak

Initializes a new instance of the class. Constructor for PeakChromatogramSettings

Initializes a new instance of the class. Construct this object from read only interface

The settings to copy from

Gets or sets the scan filter. This determines which scans are included in the chromatogram.

Gets the chromatogram settings. This defines how data for a chromatogram point is constructed from a scan.

Gets the chromatogram settings When there is a trace operator set, This defines how data for a chromatogram point is constructed from a scan for the chromatogram to be added or subtracted.

Gets or sets the chromatogram settings. This defines how data for a chromatogram point is constructed from a scan.

Gets or sets the chromatogram settings When there is a trace operator set, This defines how data for a chromatogram point is constructed from a scan for the chromatogram to be added or subtracted.

Gets or sets the device type. This defines which data stream within the raw file is used.

Gets the instrument index (starting from 1). For example: "3" for the third UV detector.

Gets or sets the trace operator. If the operator is not "None" then a second chromatogram can be added to or subtracted from the first.

Create a deep copy of this object

Copy of object

These settings detail how a peak is to be identified from the list of possible peaks found by integrating a chromatogram. The peak is expected at a certain time, which may be adjusted using a retention time reference. The peak is then selected from possible peaks within a window around the selected time.

Gets or sets a value indicating whether retention time should be adjusted based on a reference peak.

Gets or sets the expected time, as in the method (before any adjustments)

Gets or sets a value which determine how a single peak is found from the list of returned peaks from integrating the chromatogram. For example: Highest peak in time window.

Gets or sets the window, centered around the peak, in minutes. The located peak must be within a window of expected +/- width.

Gets or sets a setting which is used to restrict the chromatogram. Only scans within the range "adjusted expected RT" +/- Window are processed. For example: a 1 minute window setting implies 2 minutes of data.

Gets or sets settings for finding a peak based on spectral fit

Gets settings for finding a peak based on spectral fit

Gets or sets a rejection parameter for peaks

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

make a copy of this object

a copy of this object

A record of the signal at a certain point in a detected peak. For example, the Apex.

Initializes a new instance of the struct. Create A new point on a detected peak

Retention time at this point The signal height at this point above the baseline (signal.intensity - baseline) baseline height at retentionTime

Gets or sets the retention time at this point, in minutes.

Gets or sets the intensity minus baseline at RT

Gets or sets the baseline height at RT

Test that two peak points are equal

first point to compare second point to compare true if they have the same contents

Test that two peak points are not equal

first point to compare second point to compare true if they do not have the same contents

Test two peaks for equality

peak to compare true if they are equal

Object.GetHashCode

The hash code

Settings PDA peak purity calculations

Gets or sets the % of the detected baseline.

Gets or sets a value indicating whether to compute Peak Purity.

Gets or sets a value indicating whether to use the enclosed wavelength range, not the total scan

Gets or sets the high limit of the scan over which to compute

Gets or sets the low limit of the scan over which to compute

Gets or sets the max of a scan must be greater than this to be included

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Make a copy of this object

a copy of this object

Defines a peak which has included system suitability results.

Initializes a new instance of the class. Initializes from a peak and system suitability results. This clones data from the passed in interfaces.

The peak. The suitability results.

Gets or sets the suitability results.

Gets the resolution of the peak (from other peaks)

Gets a value indicating whether the resolution test passed

Gets a value indicating whether the symmetry test passed

Gets a value indicating whether the peak width test passed

Gets a value indicating whether the peak tailing test passed

Gets a value indicating whether the column overload test passed

Gets a value indicating whether the signal to noise test passed

Gets a value indicating whether the saturation test passed

Gets a value indicating whether the concave peak test passed

Gets a value indicating whether the baseline clipping test passed

Gets a value indicating whether the following values have been calculated: PassedResolutionChecks, MeasuredResolution

Gets a value indicating whether the following values have been calculated: PassedSymmetryChecks

Gets a value indicating whether the following values have been calculated: PassedPeakWidth, PassedTailing, PassedColumnOverload, PassedNoise, PassedSaturated, PassedConcave, PassedBaselineClipped

Gets a value indicating whether the ResolutionCheck was performed, and the results of the test, when run.

Gets a value indicating whether the SymmetryCheck was performed, and the results of the test, when run.

Gets a value indicating whether the PeakWidth test was performed, and the results of the test, when run.

Gets a value indicating whether the Tailing test was performed, and the results of the test, when run.

Gets a value indicating whether the ColumnOverload test was performed, and the results of the test, when run.

Gets a value indicating whether the Noise test was performed, and the results of the test, when run.

Gets a value indicating whether the Saturated test was performed, and the results of the test, when run.

Gets a value indicating whether the Concave test was performed, and the results of the test, when run.

Gets a value indicating whether the BaselineClipped test was performed, and the results of the test, when run.

Defines a precursor mass, and means of fragmenting it

Gets or sets the mass of the precursor

Gets or sets the method used to fragment the precursor

Gets or sets the level of activation to fragment the precursor

Gets or sets the precision of this value (number of decimal places found when parsing)

Compares the current object with another object of the same type.

A 32-bit signed integer that indicates the relative order of the objects being compared. The return value has the following meanings: Value Meaning Less than zero This object is less than the parameter. Zero This object is equal to . Greater than zero This object is greater than . An object to compare with this object.

Provides a means of opening processing methods.

create reader.

The reader

Read a processing method. The file contents are returned. The file is not kept open.

Name of file to read Access to the contents of the file.

This class defines a QC level. This is based on a calibration level, with a name and expected amount (base amount) The QC level add a TestPercent and a means of testing

Gets or sets the QC test standard: 100 * (yobserved-ypredicted)/ypreditced

Initializes a new instance of the class. Create a copy of a QC level

Level to copy

Test if an amount passes the QC test for this level

The calculated amount for the QC true if the QC test passes, within tolerance

Initializes a new instance of the class. Default construction of QC level

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current level.

Initializes a new instance of the class. Create a quality control level

A name associated with the level The amount of calibration compound (usually a concentration) for this level QC test standard: 100 * (yobserved-ypredicted)/ypreditced

A range of double Low, High.

Implements the operator ==.

The first. The second. The result of the operator.

Implements the operator !=.

The first. The second. The result of the operator.

Create an immutable (constant) range from center and delta, such that the range is center +/- delta.

The center. The delta. The .

Create an immutable (constant) range from low and high.

The low. The high. The range.

Initializes a new instance of the class.

Initializes a new instance of the class. Construct a range from limits

low limit of range High limit of range

Initializes a new instance of the class. Construct a range from another range, adding a tolerance if ends are the same

range to copy If limits are same (with 1e-10) this is subtracted from low and added to high of the new range

Initializes a new instance of the class. Construct a range from another range, adding a tolerance if ends are the same (within 1.0E-10).

range to copy If limits are same (within 1e-10) the tolerance is subtracted from low and added to high of the new range

Initializes a new instance of the class. Construct a range from another range.

range to copy

Gets or sets the low end of range

Gets or sets the high end of range

Test for inclusion.

The value. True if in range

Compares the current object with another object of the same type.

Indicates whether this instance and a specified object are equal.

Another object to compare to. true if and this instance are the same type and represent the same value; otherwise, false.

Returns the hash code for this instance.

A 32-bit signed integer that is the hash code for this instance.

Factory to produce immutable ranges of double

Create an immutable (constant) range from low and high.

The low. The high. The range.

Create an immutable (constant) range from center and delta, such that the range is center +/- delta.

The center. The delta. The .

Construct a range from another range, adding a tolerance if ends are the same (within 1.0E-10).

range to copy If limits are same (within 1e-10) the tolerance is subtracted from low and added to high of the new range

Construct a range from another range, adding a tolerance if ends are the same

range to copy If limits are same (with 1e-10) this is subtracted from low and added to high of the new range

Encapsulates raw file data.

Initializes a new instance of the class.

Gets or sets the date when this data was created

Gets or sets the name of acquired file (excluding path)

Gets or sets the name of person creating data

Gets or sets the xml schema version for this file.

Gets or sets all instrument names.

Gets or sets the information about the sample.

Gets or sets the MS instruments.

Gets or sets the UV instruments.

Gets or sets the PDA instruments.

Gets or sets the instrument types map. This metadata is used to support GetInstrumentTypes method.

Gets or sets the list of instrument methods.

Gets The number of instruments (data streams) in this file.

get the number of instruments (data streams) of a certain classification. For example: the number of UV devices which logged data into this file

The device type to count The number of devices of this type

Class to read raw files New code should not use this class directly. Use only the static class: "RawFileReaderFactory" Catch exceptions from the construction, which will be thrown if the DLLs are missing. Call the "OpenFile" method to open a raw file. The returned interface from OpenFile is "IRawDataPlus". The IRawDataPlus interface implements the IRawData interface, so the returned object can also be passed to code expecting IRawData.

Initializes a new instance of the class.

Initialize: Load the required DLLs.

Open the requested raw file

Name of file to open Interface to read the raw data

Class to read raw files, using 64 bit technology. Call the "ReadFile" method to open a raw file. The returned interface from ReadFile is "IRawDataPlus". The IRawDataPlus interface implements the IRawData interface, so the returned object can also be passed to code expecting IRawData. To access data for the same file from multiple threads, see

create a thread manager.

The thread manager

create reader.

The factory

Open a raw file for reading.

Name of file to read Access to the contents of the file.

Open a raw file for reading, creating a manager tool, such that multiple threads can access the same open file.

Name of file to read Access to the contents of the file.

A replicate is a measurement of a single calibration peak in 1 file.

Gets or sets the amount of target compound in calibration or QC standard.

Gets or sets the response of this sample, for example: Ratio of target peak area to ISTD peak area

Gets or sets the retention time of this replicate, for drift calculations

Gets or sets a value indicating whether to exclude this data point from the calibration curve.

Gets or sets the first key name associated with this replicate (for example a file name)

Gets or sets the second key name associated with this replicate (for example a peak or compound name)

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Replicate.

Exception for raw data reading. Called when a Chromatogram reading method is made without first selecting a devices with chromatographic data. For example: requesting a chromatogram from a device of type "Other" (such a an auto sampler).

Initializes a new instance of the class. Basic analysis exception, no specified reason.

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception

Initializes a new instance of the class. Exception, with reason as text, which application can display or log

Reason for exception Trapped inner exception

Initializes a new instance of the class. Construct an exception, with serialization.

Data to serialize this object Stream for serializing

The run header.

Gets or sets the number for the first scan in this stream (usually 1)

Gets or sets the number for the last scan in this stream

Gets or sets the time of first scan in file

Gets or sets the time of last scan in file

Gets or sets the lowest recorded mass in file

Gets or sets the highest recorded mass in file

Gets or sets the mass resolution value recorded for the current instrument. The value is returned as one half of the mass resolution. For example, a unit resolution controller would return a value of 0.5.

Gets or sets the expected acquisition run time for the current instrument.

double ExpectedRunTime { get; }

Gets or sets the max integrated intensity.

Gets or sets the max intensity.

Gets or sets the tolerance unit.

Encapsulates various information about sample.

Max number of user text column count (20)

Initializes a new instance of the class.

Gets or sets the comment about sample (from user).

Gets or sets the Code to identify sample.

Gets or sets the description of sample.

Gets or sets the vial or well form auto sampler.

Gets or sets the amount of sample injected.

Gets or sets bar code from scanner (if attached).

Gets or sets the bar code status.

Gets or sets a name to identify the Calibration or QC level associated with this sample. Empty if this sample does not contain any calibration compound.

Gets or sets the bulk dilution factor (volume correction) of this sequence row.

Gets or sets the instrument method filename of this sequence row.

Gets or sets the name of acquired file (excluding path).

Gets or sets the name of calibration file.

Gets or sets the ISTD amount of this sequence row.

Gets or sets the row number.

Gets or sets the path to original data.

Gets or sets the processing method filename of this sequence row.

Gets or sets the type of the sample.

Gets or sets the sample volume of this sequence row.

Gets or sets the sample weight of this sequence row.

Gets or sets the collection of user text.

Create a deep copy of the current object.

A deep copy of the current object.

Class to represent a scan

Initializes a new instance of the class. Default construction.

Initializes a new instance of the class. Overload for processed data (such as averaged or subtracted)

The converter from mass to frequency (used by FT data averaging and exporting). Optional: Noise and baseline table

Copy scan data. This protected method is inteded for derived object use only. It is not a "deep clone" of a scan.

Scan to copy

Gets or sets A second data stream for the scan

Gets A second data stream for the scan

Gets a value indicating whether this scan has a centroid stream.

Gets a value indicating whether this scan has a noise table. This will be true only if the scan was constructed with the overload containing this table. Note that this is not related to having "noise and baseline" values with centroid stream data. This is a separate table, used for spectrum averaging and subtraction of orbitrap data

Gets or sets a value indicating whether the User Tolerance value is being used.

Gets or sets the mass resolution for all scan arithmetic operations

Gets or sets a value indicating whether, when requesting "Preferred data", the centroid stream will be returned. For example "", "". If this property is false, or there is no centroid stream, then these methods will return the data from . For greater efficiency, callers should cache the return of "". Typically data processing, such as elemental compositions, should use these methods.

Gets peak flags (such as saturated) for default data stream (usually centroid stream, if present). Falls back to data if centroid stream is not preferred or not present

Gets Mass of base peak default data stream (usually centroid stream, if present). Falls back to data if centroid stream is not preferred or not present

Gets Noise of base peak for default data stream (usually centroid stream, if present). Falls back to zero if centroid stream is not preferred or not present

Gets Resolution of base peak for default data stream (usually centroid stream, if present). Falls back to zero if centroid stream is not preferred or not present

Gets peak flags (such as saturated) for default data stream (usually centroid stream, if present). Falls back to data if centroid stream is not preferred or not present

Gets Intensity for default data stream (usually centroid stream, if present). Falls back to data if centroid stream is not preferred or not present

Gets the Mass for default data stream (usually centroid stream, if present). Falls back to data if centroid stream is not preferred or not present

Gets Noises for default data stream (usually centroid stream, if present). Returns an empty array if centroid stream is not preferred or not present

Gets Resolutions for default data stream (usually centroid stream, if present). Returns an empty array if centroid stream is not preferred or not present

Gets or sets the number of scans which were combined to create this scan. For example: By the scan averager. This can be zero if this is a "scan read from a file"

Gets or sets Header information for the scan

Gets Header information for the scan

Gets or sets Type of scan (for filtering)

Gets or sets The data for the scan

Gets The data for the scan

Gets or sets IScanSubtract interface pointer.

Interface to perform subtraction

Gets or sets IScanAdd interface. This delegates addition of FT profile scans.

Interface to perform addition

Gets or sets the Tolerance value.

Get or sets a value indicating whether scan + and - operators will merge data from scans which were not scanned over a similar range. Only applicable when scans only have a single segment. By default: Scans are considered incompatible if: The span of the scanned mass range differs by 10% The start or end of the scanned mass range differs by 10% If this is set as "true" then any mass ranges will be merged.

Create a scan object from a file and a retention time.

File to read from time of Scan number to read The scan read, or null of the scan number if not valid

test if 2 scans can be averaged or subtracted.

Returned as "true" if all segments are the same Current scan object The scan to possibly add true if scans can be merged

Create an object which can be used to read scans from a file, with optional caching. This is valuable if repeated operations (such as averaging) are expected over the same region of data. Scans returned from each call are unique objects, even if called repeatedly with the same scan number.

Number of scans cached. When set to 1 or more, this creates a FIFO, keeping track of the most recently read scans. If a scan in the FIFO is requested again, it is pulled from the cache. If a scan is not in the cache, then a new scan is read from the file. If the cache is full, the oldest scan is dropped. The newly read scan is that added to the FIFO cache. If size is set to 0, this makes a trivial object with no overheads, that directly gets scans from the file. Object to read scans from a file

Create a scan object from a file and a scan number.

File to read from Scan number to read The scan read, or null of the scan number if not valid

Merge the two scans.

current scan object(this). scan object to merge. returns the sum of two scans.

Averages the two scans.

scan object to average. divider (or) common factor. returns the average scan.

Subtract method for MS data.

current scan object. scan object to subtract. returns the subtracted scan object.

Converts the segmented scan to centroid scan. Used to centroid profile data.

The scan to centroid The centroided version of the scan

Make a deep clone of this scan.

An object containing all data in the input, and no shared references

Order mass ranges by lowest mass.

generate frequency table for this scan. This method only applied to "FT" format scans which have mass to frequency calibration data. When a scan in constructed from processing algorithms, such as averaging, a frequency to mass converter is used to create this scan. This same converter can be used to create a frequency table, which would be needed when writing averaged (or subtracted) data to a raw file.

The frequency table.

Generates a "noise and baseline table". This table is only relevant to FT format data. For other data, an empty list is returned. This table is intended for use when exporting processed (averaged, subtracted) scans to a raw file. If this scan is the result of a calculation such as "average of subtract" it may be constructed using an overload which includes a noise and baseline table. If so: that tale is returned. Otherwise, a table is generated by extracting data from the scan.

The nose and baseline data

The add centroids.

The current scan. The input scan.

Addition of FTMS centroid scans (called by operator +=)

current scan object(this). scan to right of + operator (that) The sum of the two scans

The add scan stats.

The left scan. The right scan. The scan stats. The base height. The base mass.

The add segment.

The left scan. The left segment. The right segment. The segment number. The result scan segments. The base height. The base mass. The process segments.

Add segments.

The _identical flag. The left scan. The right scan. The process segments. The sum of the two scans, which is also in "leftScan".

The append peak.

The results. The new peak. The mass fuzz (tolerance).

Determine if this is a basic profile type.

The packet type. True if it is basic profile type.

Attempt to find the tolerance factor, from the base peak of a scan return "true" on fail.

The centroid count. The centroid stream. The base mass. The tolerance factor. The is orbitrap data. The calculated tolerance factor.

Returns the default tolerance factor.

flag to Check if we have LTQ-FT or Orbitrap data The calculate default tolerance factor.

The calculate mass fuzz.

The current scan. The left centroid. The right centroid. The tolerance factor. The is orbitrap data. The left iterator. The right iterator. The process segments. The calculated mass fuzz.

Calculates the Mass tolerance for centroid peak.

current mass tolerance value. tolerance factor previous mass tolerance value flag to check if we have LTQ-FT or Orbitrap data. tolerance unit The calculate mass fuzz for centroid peak.

Calculates the Mass tolerance for profile peak.

current mass tolerance value. tolerance factor previous mass tolerance value flag to check if we have LTQ-FT or Orbitrap data. tolerance unit The calculated mass fuzz for profile peak.

Calculates the tolerance factor

CentroidStream object calculates the tolerance factor at specified index. flag to Check if we have LTQ-FT or Orbitrap data The calculate tolerance factor for labels.

Calculate total scan size.

The segments. The total scan size.

Check for identical.

The identical flag. The current scan object. The input scan object. The number of segments found

The combine peaks.

The left. The right.

The convert centroid stream tolerance.

The current scan. The centroid stream. The counter. The use peak width as mass fuzz. The resolution factor. The converted centroid stream tolerance.

Create an empty centroid stream.

The size. The scan number. A centroid stream which has "size" data packets.

Create a segmented scan.

The number of peaks in the scan. The created scan

Assuming that the methods ReplaceScanDataArrays and UpdateSegmentSizes have already been called, the result scan is formatted ready to accept new data Merge the data from the results of adding each segment

The scan. The segments.

The fill segment range.

The left segment. The right segment. The output segmented scan.

find segment start packet index number.

The left segment. The right segment. The iterator. The count of peaks before this segment in the left scan. The count of peaks before this segment in the right scan.

Fix the length of segment tables after a merge

scan which will contain a merge segments which are result of addition

The get subtracted index.

The current scan. The right scan. The output peak count. The base height. The base mass. Index of the subtracted scan

get the sum index.

The current scan. The right scan. The output peak count. The base height. The base mass. The scan index data for the summed scans

get the tolerance factor.

The current scan. The right scan. The left centroid. The right centroid. The right centroid count. Get the tolerance factor. The is orbitrap data. The left centroid count. The tolerance factor.

Test if is known profile type.

The packet type. true if this is known to be profile

The merge segments.

The scan. The all results.

Order the segment ranges of the scan, and order the "allResults" table to match This is part of the process to centroid a scan when this is done, it is more efficient to combine "allResults" into a single segment

The scan ranges. The all results. The segment range table

Addition of SegmentedScan's. this case for profile data,which matches with identical or similar segments.

set if the flags have the same segments left scan of addition "left + right" right scan of addition "left + right"

Added for supporting addition of FTMS profile points

Index into input data Mass Tolerance

Adds the two CentroidSteam's

Current position in the output buffer previous output CentroidStream. current CentroidStream. index. mass value.

The put peak.

The result count. The out put. The in put. The position. The mass fuzz. The process segments.

Adds the two segmented scan.

index into output array previous output peak. current peak object. index. mass value.

The remove zeros.

The stream. The new size.

The remove zeros.

The scan. The new size.

create the arrays for the scan, with a new length

The scan. The total.

Create a new scan out of the data in resultScanSegments in the private method, the scan is assumed to have valid segment ranges and the correct size of the segment tables only the data for the segments needs to be replaced

The scan. The segments.

Scale the label intensities by a common factor.

common factor CentroidStream object to scale. returns the scaled Centroid Stream object.

Search for the base peak resolution.

base mass value CentroidStream object to search. peak value. The search base peak index.

Select only non zero values from an array.

The values. The array of non zero values

The sub centroids.

The current scan. The input scan.

The sub ft centroid data.

The current scan. The right scan. The subtracted scan

Subtract FT Profile Data

The object subtract from this The result of the subtraction of the two scans

Add FT Profile Data

The object subtract from this The result of the subtraction of the two scans

The sub label.

The output index. The out put. The input. The position. The mass fuzz.

Subtract a background peak.

The output (foreground scan) counter. The output (foreground scan). The input (background scan). The input (background scan) counter. The mass fuzz (tolerance).

The subtract profile segments.

The identical flag. The current scan. The input scan.

The subtract segment.

The left scan. The left segment. The right segment. The segment number. The result scan segments. The base height. The base mass.

The subtract segments.

The identical flag. The left scan. The right scan. The subtraction result

Try to merge similar scans.

The current scan object. The input scan object. The both centroids. The counter. The can merge. True if can merge similar scans.

The update segment sizes.

The scan. The segments.

The validate centroid scan.

The stream.

The validate segmented scan.

The scan.

Convert tolerance into mass.

The prof. The positions. The converted tolerance.

Find peaks in the current segment (part of centroiding)

The scan segment (SIM/SRM range)

The read from file.

The raw file. The scan number. The stats.

The fragment result.

Gets or sets Intensity.

Gets or sets Mass.

Gets or sets Options.

Helper class for parallel chromatogram generation. This object pulls data from constructor data into the required properties to meet the interface. This object can be used over 1 billion times when generating chromatograms from a sequence of raw files (especially the scan event helper), so all data is pulled into properties. This object can then be used as a "class" rather than "interface" permitting the compiler to inline.

Initializes a new instance of the class.

The scan. The scan index.

Gets the header, wrapper from supplied interface.

Gets the index.

Gets the scan event helper.

Gets the data.

Gets the scan event

Provides a means of averaging scans

Create a factory, which can be used to average scans.

The tool to average

Create a scan averaging tool, for use with a specific raw file. This can then be use to average selected scans from the file. Processing of scan filters, and default values for tolerance also use the supplied raw data interface.

Access to data to be averaged Interface to perform averaging

Defines an extended centroid scan (FTMS data), which includes analysis of charge envelopes.

Gets a value indicating whether charge envelope data was recorded for this scan

Gets additional annotations per peak, related to change envelopes

Gets the change envelopes. This include overall information about the envelope, plus the set of included peaks,

All isotopes just having a different charge will be grouped together in a charge envelope. Due to calculation restrictions it is quite likely that there are further peaks which theoretically be part of the same charge envelope, but where noise level, neighborhood, hardware limitations keep those peaks unassigned. This interfaces has statistics about a charge envelope, but not the contributing peaks.

This is the monoisotopic mass that a particular peak belongs to. The value is a calculated one, it is very likely that this cannot be seen at all in the spectrum. But it is the reference point of all members of one charge envelope. Note that the value becomes 0 if the value is not isotopically resolved. See also and Keep in mind that depending on instrument calibration this value may not exactly match a calculated mass.

This cross-correlation factor is the maximum of all cross-correlation values over all averagines. An averagine is a statistical model of the isotope distribution of the same molecule at a given charge. The observed peaks within the spectrum are fitted to the model, the overlap is calculated by a cross-correlation that only takes the intensities into account. The averagine model is strongly linked to peptide analysis. As an example, averagine mass distribution for pesticides are totally different. Cross-correlation factors vary in the range 0 to 1. 0 will be set if is also 0. In this case, the fit was unsuccessful. The value is also 0 if is set.

This is the index to the top peak centroid in the centroid list coming with the same scan. One can use this to get access to the mass of the so called top peak.

The top peak is that peak in a charge envelope that fulfills two requirements in this order: 1) never being considered to be part of another charge envelope, and 2) having the highest abundance.

Return whether this charge envelope was created using isotopically resolved species. For isotopically resolved peaks the is set. If not resolved, only an average mass is returned.

When peaks are non-isotopically resolved (see ), this value contains the average mass of all species in the envelope, otherwise it contains 0.

Defines a set of peaks which are part of a charge envelope

Gets or sets the collection of peaks in this charge envelopes

Gets or sets the index into the centroids for the top peak

Data about a single peak within a charge envelope. This grouping has a separate structure explained in . While presentation to CC consumers may be different, the (at least Orbitrap-)generated data structure allocates one 16-bit value for each centroid.

Returns true if the peak is a monoisotopic peak, false otherwise.

Returns true if the conditions below met, false otherwise. The top peak is that peak in a charge envelope that fulfills two requirements in this order: 1) never being considered to be part of another charge envelope, and 2) having the highest abundance.

Returns true if the peak and its charge envelope have further isotope sibling (according to averagine model, etc). Note that a charge envelope must be considered non-isotopically resolved if at least one of its peaks has this flag "false", and it can be considered an error if some peaks of an envelope have this flag set and other peaks not.

Advanced Peak Detection on (FT) scans allow to better calculate charges of peaks. This is done by finding correlations of peaks. If found, the assumption is considered valid that these peaks belong to the same species of a molecule, but with different charges. This grouping has a separate structure explained in . While presentation to CC consumers may be different, the (at least Orbitrap-)generated data structure allocates one 16-bit value for each centroid. The 16-bit value contains three bits and an index number into an array of s which also come with the same scan. TODO This is an interface. Implementation details ( such as "structure is 16 bit") are not meaningful here. Describe instead "What information is presented to the consumer". Using IPeakAnnotation you can ???

Returns null if information is not available (as with non-APD annotated Orbitrap spectra or unresolved peaks), the index to the corresponding otherwise. Values out of range must not exist and should be checked in advance.

Defines data which explains how charges are calculated. ChargeEnvelopes contains summary information about each detected envelope. CentroidAnnotations can be used to determine which charge envelope (if any) a peak belongs to.

Gets or sets a flag indicating whether there are charge envelopes.

Gets a value indicating whether this is valid "charge envelope" data, when decoded from a raw file. Raw files have diagnostic sections of potentially unknown formats, so it is possible that, even though some data exists, it cannot be decoded as charge envelopes.

Gets summary informtion the "charge envelopes". Purpose needs to be detailed?

Gets the "Centroid Annotations". Purpose needs to be detailed?

This class can be ued to decode instrument specific additional data saved with a scan.

Obtain the annotations for a specific scan

The raw file scan number Annotations for this scan

Read centroid data for a scan, with annotations (where available). These annotaions are set by the charge calculator in some instruments.

The raw file scan number set if reference and exception peaks should be returned The extended scan

Read centroid data for a scan, with annotations (where available). These annotaions are set by the charge calculator in some instruments. This version returns an internal type

The raw file scan number set if reference and exception peaks should be returned The extended scan

An extension of centroids which includes: Peak charge envelopes. Annotations for each centroid

Created an extended centroid stream by making a copy of the base data

Gets or sets the annotation about charge envelopes for each peak

Gets or sets a value indicating whether charge envelope data was recorded for this scan

This class converts the byte array within the debug section of an Orbitrap scan to a list of centroid annotations. Those annotations may point to charge envelopes, they also become available.

Gets or sets a flag indicating whether there are charge envelopes.

Gets or sets a value indicating whether this is valid data. It is valid, even if there is no data available. It is invalid if data has been found, but cannot be decoded.

Get access to the charge envelopes. It is an empty array if no APD data has been calculated or if unfolding the binary data shows errors.

Returns the charge envelopes of the scan

Get access to the centroid peak annotations. It is an empty array if no APD data has been calculated or if unfolding the binary data shows errors.

Returns the peak annotations of the scan

This class defines the characteristics of an Orbitrap debug subsegment. The debug section according to unified_data_format.html has the format: Type Meaning Uint32 Or'd combination of all debug sub-section flags + some extra bits SubSection defined below SubSection further sub-sections, end defined by overall length of debug section The debug sub-section according to unified_data_format.html has the format: Type Meaning Uint32 Content flags (0x100 = transients, 0x80000 for extensions, see below) UInt32 Count of 32-bit word of this sub-section UInt32[] Content depending on sub-section The APD extensions and all other extensions have an UInt32 specifier as first 32-bit word what data follows. The specifiers are: Value Meaning 1 transients (effectively not in use) 2 Annotations (array of 16-bit values for each centroid) 3 ChargeEnvelopes (array of those) The APD annotations section is an array or annotation elements, each consisting of 16-bit values, one for each centroid. For an odd number of centroids, there exists a further 16-bit value of unknown content. Each annotation has a format described in class description of . The APD charge envelopes section is an array or charge envelopes. Each charge envelopes has a format described in class description of .

What type of sub-segment do we have?

According to unified_data_format.html, DBUGCON definition, the 9th LSB bit is a send_transient section.

This value is reserved for extensions of the debug section. Sub-segments have a further indicator describing the packet type.

This debug segment extension is an array of s.

This is the offset into the byte array to which this structure belongs.

Access to the size of data in section without headers in 32-bit words.

What kind of debug sub-segment is contained in this sub-segment?

This structure is one element of the annotations . The format is: Bit Meaning 0-12 (LSB) Index into array of charge envelopes (0x1FFF=no envelope) 13 Flag IsNonIsotopicallyResolved 14 Flag IsClusterTop 15 Flag IsMonoisotopic

Implementation of

Not resolved

Implementation of

This structure is one element of the charge envelopes . The format is: Type Meaning double Usually monoisotopic mass (with respect to instrument accuracy), can be average mass float Cross-correlation of applied model (like averagine), can be 0 for various reasons (U)Int32 Index into centroid list of peak being most abundant in this envelope

Access to the stored mass, which is either the monoisotopic mass or rge average mass, depending on flags of the annotation section.

Cross-correlation in the range [0 - 1] of the fitting of the envelope.

Index into the array of centroids. The indexed centroid is the most abundant of all centroids belonging to this envelope. Orbitrap format never uses addresses more than 2**30 peaks, so no need for uint.

This class implements . It bases on a stored Orbitrap data block.

Initialize a and assign the structure on which it bases.

Data structure containing its core values

Returns the monoisotopic mass for a model-fitted envelope and all species belonging to this envelope with respect to the mass accuracy or 0 if resolved non-isotopically. See .

Cross-correlation value of the model fitting in the range 0-1. Value remains 0 for non-isotopically resolved peaks or unsuccessful fittings.

Index into centroid list to the most abundant centroid within this envelope. The value can be used for grouping.

Returns true if at least one peak belonging to the charge envelope was non-isotopically resolved. Call the setter for each in order to detect non-isotopically resolved peaks.

Returns 0 for a model-fitted envelope or the average mass if resolved non-isotopically. See .

category of tokens with a scan filter

A mass range token.

A generic token (a string, such as "Full").

A data format ("p" or "c").

A polarity token ("+" or "-").

An MS order token.

A parent mass.

A data dependent token "d".

Describes a scan, based on interpreting filter strings. This class need not be serialized or cloned, as it is intended to be "read only" All information can be kept as a string. Call FromString to initialize this. This class is designed for use where filter information is only available as a string (such as with implementations of IRawData) Newer code (with IRawDataPlus) should use IScanFilter for details about filters.

Gets or sets the Polarity, Positive or Negative ions

Gets or sets a value indicating whether this scan depends on data in previous scans

Gets or sets a value indicating whether the scan is centroid format (else profile)

Gets the precursor masses and their means of activation

Gets or sets the MS or MS/MS order (for example 2 for MS/MS)

Gets or sets the Mass Ranges scanned

Gets or sets a value indicating whether this is an MSX scan type

Gets or sets the tolerance used when matching mass ranges. It is initialized to 0.0005. On parsing a string (using the FromString method), this is set based on the precision of the "low mass value" from the string. For example, for a mass range of "34.256 - 41.365" the precision is determined to be 3 decimal places and the tolerance is initialized to "0.0005" which will match items which have the same "3 decimals places". It is assumed that all values in a parsed string have the same mass precision.

Create a scan definition from a filter strings. The string is formatted as a list of text tokens, separated by spaces. Most tokens can be any text, apart from some specifically parsed items: + Positive - Negative d data dependant c Centroid p Profile [Ranges] scanned ranges, for example [100.1-300.2,556.8-901.4]

String to parse Scan definition which matches the string

Sort the filters in alphabetic and numeric order of appropriate fields. It is assumed that the supplied list has been automatically generated, and therefore filters with the same parameters will have those in the same order in the string.

Items to sort A sorted list of the filters

Sort the filters in alphabetic and numeric order of appropriate fields. Compact the filters, so that filters which match within tolerance are eliminated. This is designed to take input from "Auto filter" or similar methods. It is not designed to take a "user generated list". It is assumed that the supplied list has been automatically generated, and therefore filters with the same parameters will have those in the same order in the string.

Items to sort Tolerance for matching precursor masses. If this is zero, then the tolerance is based on the number of precision digits entered in the text A sorted list of the filters

Initializes a new instance of the class. Default constructor

The list of sub strings (tokens) in the supplied filter text

The tokens.

Convert to a text string

String form of the filter

Strip a number. Removes a number from the start of the supplied string.

The string, which should start with a number. The number of decimal places found in the string. The stripped number.

Parse definitions.

The filters. The parsed scan definitions

Convert definitions to strings.

The definitions. The strings for each scan definition

Create a unique list of definitions, from a list which may have duplicates.

The definitions. The precursor mass tolerance. The list of unique definitions

Match a generic token

Token to look for List of all tokens in the scan filter True if the token is found

Read the activation code string.

The string being parsed. The precursor to update.

Find ranges from token.

The item. The parsed. The mass ranges

Create from a string.

The string to create from.

Add the MS order.

The number of parent masses expected before this call. The item. The number of parent masses expected after parsing the MS order.

Add initial mass range.

The item to parse. The mass ranges found so far. True if more mass ranges are expected.

Add a single char item.

The item to add.

Add a mass range.

The item containing a range. The mass ranges found so far. True if more mass ranges are expected.

Add a parent mass.

The number of parent masses expected. The item. The next token. True if more parent masses are expected.

Add a token.

The token. The token class.

Test if a scan type "passes the filter", that is the scan type is the same as, or is a superset of the scan definition.

The type of the scan which needs to be checked true if the supplied scan has passed a filter against this scan definition is out of range.

Test if a scan type "passes the filter", that is the scan type is the same as, or is a superset of this scan definition. The exact test is: All tokens in "this" must be present in "scanTypeFilter".

The type of the scan which needs to be checked Mass tolerance used to match MS/MS precursors true if the supplied scan has passed a filter against this scan definition

Test for a matching token. Test that the token from "the tokens in this" is contained within "scan type to check"

The scan type to check (for being a superset of "this"). The token to look for, in "scan type to check" The tokens of the scan being tested. The precursor mass tolerance. True if there is a match thrown if the token is not valid

Match precursors.

The scan type filter. The precursor mass tolerance. True if precursors match.

Get comparison tolerance.

The precursor mass tolerance. The precursor. The other precursor. The comparison tolerance.

match the ranges.

The filter. The tolerance. True if ranges match.

Compares the current object with another object of the same type.

Compares the current Ranges with another object's Ranges.

Compares the current object's Precursors with another object's Precursors.

The scan event builder. This class permits a scan event to be built, by adding MS/MS reactions, mass ranges etc. It can be used as a helper to log MS data into a raw file. This builder does not support parsing from a filter string, or conversion to filter string format. The "ToString" method provides basic .Net object formatting only. The builder may be constructed as default or from IScanEvent or IScanFilter.

Initializes a new instance of the class.

Copies data from the supplied event.

Initializes a new instance of the class. Note that this constructor makes a best case mapping between filter and event Some items specific to filter (such as "MassPrecision") cannot be preserved. Event only features (such as "IsCustom") are initialized to defaults. applications using this feature should test use cases.

Copies data from the supplied filter.

copy base interface items.

The other.

Initializes a new instance of the class. Most properties are initialized to "Any" (feature not used). Numeric values have defaults (0), apart from ScanTypeIndex which is set to "-1" for undefined.

Gets or sets the accurate mass setting.

Gets or sets Compensation Voltage Option setting. Composition voltage is exclusive with source fragmentation, so only one may be active.

Gets or sets Compensation Voltage type setting. Composition voltage is exclusive with source fragmentation, so only one may be active. When set to SingleValue a value must be added using AddSourceFragmentationInfo. When set to Ramp two values must be added using AddSourceFragmentationInfo. When set to SIM, there must be one value added per (scanned) mass range.

See for possible values

Gets or sets the corona scan setting.

Gets or sets the dependent scan setting. A scan is "dependent" if the scanning method is based on analysis of data from a previous scan.

Gets or sets the detector scan setting.

See for possible values

Gets or sets the detector value.

Floating point detector value

Gets or sets the electron capture dissociation setting.

Gets or sets the electron capture dissociation value.

Floating point electron capture dissociation value

Gets or sets the electron transfer dissociation setting.

Gets or sets the electron transfer dissociation value.

Floating point electron transfer dissociation value

Gets or sets the enhanced scan setting.

Gets or sets the field free region setting.

See for possible values

Gets or sets the higher energy CID setting.

Gets or sets the higher energy CID value.

Floating point higher energy CID value

Gets or sets the ionization mode scan setting.

See for possible values

Gets or sets a value indicating whether this is a custom event. A custom event implies that any scan derived from this event could be different. The scan type must be inspected to determine the scanning mode, and not the event.

Gets a value indicating whether this event is valid.

Gets the number expected SID values.

The number of values

Gets the number expected CV values.

The number of values

Gets or sets the lock scan setting.

Gets or sets the mass analyzer scan setting.

See for possible values

Gets the mass calibrator count.

Gets the number of (precursor) masses

The size of mass array

Gets the number of mass ranges for final scan

The size of mass range array

Gets or sets the scan MS/MS power setting.

See for possible values

Gets or sets the Multi notch (Synchronous Precursor Selection) type

Gets or sets the multi-photon dissociation setting.

Gets or sets the multi-photon dissociation value.

Floating point multi-photon dissociation value

Gets or sets the Multiplex type

Gets or sets MultiStateActivation type setting.

Gets or sets the event Name.

Gets or sets the parameter a.

Gets or sets the parameter b.

Gets or sets the parameter f.

Gets or sets the parameter r.

Gets or sets the parameter v.

Gets or sets the photo ionization setting.

Gets or sets the polarity of the scan.

See for possible values

Gets or sets the pulsed dissociation setting.

Gets or sets the pulsed dissociation value.

Floating point pulsed dissociation value

Gets or sets the scan data format (profile or centroid).

Gets or sets the scan type setting.

See for possible values

Gets or sets encoded form of segment and scan event number.

HIWORD == segment, LOWORD == scan type

Gets or sets the sector scan setting. Applies to 2 sector (Magnetic, electrostatic) Mass spectrometers, or hybrids.

See for possible values

Gets or sets source fragmentation scan setting.

Gets the total amount of source fragmentation information. This is all data for SID and CV, and is internally needed to support IScanEvent. To separately count the number of SID vales and CV values, use SourceFragmentationValueCount and CompensationVoltageValueCount

The size of source fragmentation info array

Gets the number of Source Fragmentation values.

The size of source fragmentation values array

Gets the number of Compensation Voltage Fragmentation values.

The size of Compensation Voltage values array

Gets the source fragmentation mass range count.

Gets or sets the source fragmentation type. source fragmentation is exclusive with Composition voltage, so only one may be active. When set to SingleValue a value must be added using AddSourceFragmentationInfo. When set to Ramp two values must be added using AddSourceFragmentationInfo. When set to SIM, there must be one value added per (scanned) mass range.

See for possible values

Gets or sets supplemental activation type setting.

Gets or sets the turbo scan setting.

Gets or sets the ultra scan setting.

Gets or sets the wide band scan setting.

add a mass calibrator.

The calibrator to add.

Adds a set of mass calibrators.

The calibrators to add.

Adds a mass range.

The mass range.

Adds a set of mass ranges.

The mass ranges to add.

Adds an MS stage. For example: for an MS3 scan, 2 MS stages should be added, with the 2 required precursor masses. Each stage may have one or more reactions. Neutral Loss, Neutral Gain and Parent have 1 stage. For multiplex mode, each multiplexed precursor should be added as a separate stage.

The stage.

Gets an MS stage. For example: for an MS3 scan, there will be 2 MS stages with the 2 required precursor masses. Each stage may have one or more reactions. Neutral Loss, Neutral Gain and Parent have 1 stage.

The index. The stage at the given index

Gets the MS stage count.

Add a source fragmentation value. This is for "source fragmentation (sid) and is only used when "SourceFragmentation" has been enabled. Add one value for "Single value" mode or two values for "Ramp" mode of the enabled feature. For SIM mode, add one value per target mass range.

The value.

Add a compensation voltage value. This is for "compensation voltage (cv)" and used only when "CompensationVoltage" has been enabled. Add one value for "Single value" mode or two values for "Ramp" mode of the enabled feature. For SIM mode, add one value per target mass range.

The value.

Adds a source fragmentation mass range.

The mass range to add.

Clears the mass calibrators list.

clear the list of mass ranges.

Resets the list of MS/MS stages. This may be needed if an event is cloned from another event, but the new object needs different MS/MS stages.

Clears the source fragmentation values.

Clears the Compensation Voltage values.

Clears the source fragmentation mass ranges list.

Retrieves activation type at 0-based index.

Use to get the count of activations. Index of activation to be retrieved activation of MS step; See for possible values

Retrieves precursor(collision) energy value for MS step at 0-based index.

Use to get the count of energies. Index of precursor(collision) energy to be retrieved precursor(collision) energy of MS step

Retrieves precursor(collision) energy validation flag at 0-based index.

Use to get the count of precursor(collision) energy validations. Index of precursor(collision) energy validation to be retrieved precursor(collision) energy validation of MS step; See for possible values

Gets the first precursor mass. This is only valid data where "GetPrecursorRangeValidity" returns true for the same index.

The index. The first mass

Retrieves multiple activations flag at 0-based index of masses.

Use to get the count of masses. Index of flag to be retrieved true if mass at given index has multiple activations; false otherwise

Gets the isolation width.

The index. The isolation width

Gets the isolation width offset.

The index. The isolation width offset

Gets the last precursor mass. This is only valid data where "GetPrecursorRangeValidity" returns true for the same index.

The index. The last mass

Retrieves mass value for MS step at 0-based index.

Use to get the count of mass values. Index of mass value to be retrieved Mass value of MS step Will be thrown when index >= MassCount

Gets the mass calibrator, at a given index.

The index, which should be from 0 to MassCalibratorCount -1 The mass calibrator. Thrown when requesting calibrator above count

Retrieves mass range for final scan at 0-based index.

Use to get the count of mass ranges. Index of mass range to be retrieved Mass range for final scan at 0-based index Will be thrown when index >= MassRangeCount

Determine if a precursor range is valid.

The index. true if valid

Gets the reaction data for the mass at 0 based index. Descries how a particular MS/MS precursor mass is fragmented. Equivalent to calling GetMass, GetEnergy, GetPrecursorRangeValidity, GetFirstPrecursorMass GetLastPrecursorMass, GetIsolationWidth, GetIsolationWidthOffset, GetEnergyValid GetActivation, GetIsMultipleActivation. Depending on the implementation of the interface, this call may be more efficient than calling several of the methods listed.

index of reaction reaction details

Retrieves a source fragmentation value at 0-based index.

Index of source fragmentation value to be retrieved Source Fragmentation value at 0-based index Will be thrown when index >= SourceFragmentationValueCount

Retrieves a compensation voltage value at 0-based index.

Index of compensation voltage value to be retrieved Compensation Voltage value at 0-based index Will be thrown when index >= CompensationVoltageValueCount

Retrieves a source fragmentation info value at 0-based index.

Use to get the count of source fragmentation info values. Index of source fragmentation info to be retrieved Source Fragmentation info value at 0-based index Will be thrown when index >= SourceFragmentationInfoCount

Get the source fragmentation mass range, at a given index.

The index. The mass range.

copy mass calibrators from another event.

The other event.

copy MS/MS stages from another event.

The event from which data is copied from.

Adds a set of MS stages.

The stages.

copy scanned mass ranges from another event.

The other event.

copy source fragmentation info from another event.

The other event.

copy source fragmentation mass ranges from another event.

The other event.

copy various tables from another event.

The other event.

copy various tables from another event base.

The other event.

This class adds extended features to the Scan Event interface. It acts as a "helper class" rather than "extension methods" so that it can hold certain state information. A common use case is: Scan event information is read from a raw file. Multiple uses are made of this (for example, testing if this scan should participate in 1000s chromatograms). This class can organize information from the scan event, such that "filter comparisons" or other work with events and filters are more efficient. There is a very small overhead in constructing this object, which still keeps the original interface reference in its construction factory. The class is designed for thread safe testing. TestScanAgainstFilter or TestScanAgainstNames may be called on multiple threads.

The match tolerance for comparing two energy values

The instrument mass resolution (used in determining if mass ranges match up or not)

Gets the scan event which was used to construct this object. If the object was created from IScanFilter, this will be null

Test if two tri-states are different.

The state 1. The state 2. True if "filter failed to match"

Initializes a new instance of the class.

The scan event. Event code from scan index, -1 (default) if not known

Thread safe initialize

Gets or sets the reactions.

create reactions table

The scan event helper factory creates a ScanEventHelper from a scanEvent interface.

The scan event. event code (form scan index). -1 for "not known" The .

This scan event helper factory creates a ScanEventHelper from an IScanFilter interface. This constructor permits an application to test if a scan filter contains another filter. The contructed object from this method is considered a "scan" and another scan filter can be tested against it, using "TestScan". Example: Crreate this from "+ d". You can test that "+" or "d" filters match this (return true from TestScanAgainstFilter).

The scan filter. The .

Test if activation is set for any reaction.

The activation type. The .

Test scan against component or compound names.

The names. True if the scan should be included

Test that this scan (event) passes the supplied scan filter.

The filter Helper. The .

test a scan against a filter.

The filter helper. true, if the scan passes the filter Thrown on invalid filter rule

Test electron capture dissociation.

The filter. The .

Test multi photon dissociation.

The filter. The .

Test against compensation voltage.

The filter. The .

Test against source fragmentation.

The filter. The .

Test scan against meta filter.

The filter. The .

Check the parent masses.

The filter. The filter helper. The .

Get the compensation voltage value.

The index. The number of source fragmentation values, (which are before CV values in the table) The .

Test of the multiplex precursor conditions match.

The scan filter. The filter helper. True if matched

Get the number of compensation voltage values.

The .

Test if the precursor conditions match.

The scan filter. The filter helper (optimized filter data) The precursor mass. The .

This class constructs a table of "segments and events". Because this implements IScanEvents this class can then be used to record the "method scan events" into a raw file. The information can be organized as a set of segments, with a set of events per segment. The segments were designed to represent "time slices of a chromatogram" though no time bounds are required by this object. Many instruments just create a flat table (1 segment with all the events).

Initializes a new instance of the class.

Initializes a new instance of the class. Copy from another sets of events

The other events (to copy).

Add a segment.

The events for this segment.

Gets the number segments.

Gets the number of events in a specific segment (0 based)

The segment number The number of events in this segment

Get an event, indexed by the segment and event numbers (zero based).

The segment. The event number. The event.

Get an event, using indexed event number (zero based). This gets events from all segments in order, use "ScanEvents" to get the total count of events.

The event Number. The event.

Gets the total number of scan events, in all segments

The scan filter helper. Analyses a filter to save time on filter to scan comparisons. This is done by making a list of rules to apply. Uses properties, which can be inlined for high performance. Does not implement any interfaces, to avoid slowdown of virtual calls. (properties may be use billions of times for filter against scan comparisons). Used for high performance (parallel) chromatogram generation.

The no meta filter.

The instrument mass resolution (used in determining if mass ranges match up or not)

Gets the filter.

Gets the rules, which have been found in the supplied filter. For example, a filter text of "ms !d" includes 2 rules 1: The MS order must be one. 2: The scan must not be dependent

Gets the MS order.

Gets a value indicating whether "multiplex" is in the "On" state

Gets a value indicating whether the MS order is any value other than "MS".

Gets the mass resolution.

Gets the multi activation corrected mass count.

Gets a value indicating whether the filter has multiple reactions.

Gets a value indicating whether the filter's "dependent" flag is in the "on" tristate.

Gets a value indicating whether the filter has any masses.

Gets a value indicating whether this object can keep track of "already tested" scan events. To enable it: Call InitializeAvailableEvents, with the result of "IRawDataPlus.ScanEvents"

Determines if an event was tested, and the test results.

This has never been tested

This event has been tested, but failed

Event tested, and passed the filter

Sets the table of "known scan events" This can be used to optimize filtering

Planned scan events. This interface may be obtained from IRawDataPlus (ScanEvents property)

Initializes a new instance of the class.

The filter. In this mode a tolerance matching for precursors is "accurate" (based on the precision value), except for data dependent scans. For all "non accurate" precursor selections, and for all data dependent scans a default (wide) tolerance is used. number of decimal places for masses in filter

Gets a value indicating whether the filter resolution was set to "Accurate precursor value". Else it will be "DefaultFilterMassResolution"

Gets the precursor tolerance (half of MassResolution)

Record the match result for a scan type segment/event)

Result for this segment and event number Segment number for this scan event Event number for this scan event

Determine if this scan type has already been tested, and find the result

Segment number for this scan event Event number for this scan event state of the scan type test

This class holds information needed to select a scan, using either a filer or a compound name. Static methods are available to construct common versions.

Gets or sets a value indicating whether the "scan filter" will be used as a selection mechanism. ScanFilter must never be null when this returns true.

Gets or sets the scan filter. If UseFilter is false, or this is null, it is not used as a selection mechanism.

Gets or sets the name. This is the component or compound name list to filter against. If this is null or empty, it is not used as a selection mechanism.

Create a selector which selects by filter string, based on a specific data source

The filter. The .

Create a selector which selects by filter string, based on a specific compound name

The compound name. The .

Create a selector which selects all scans (no filtering)

The .

Summary information about a scan.

Initializes a new instance of the class.

The source to copy the values from. If set, make a "deep copy" which will evaluate any lazy items and ensure no internal source references source is null.

Initializes a new instance of the class.

Gets or sets the indication of data format used by this scan. See also SpectrumPacketType for decoding to an enum.

Gets the packet format used in this scan. (read only). Value can be set using the "PacketType" property.

Gets or sets the highest mass in scan

Gets or sets the lowest mass in scan

Gets or sets the longest wavelength in PDA scan

Gets or sets the shortest wavelength in PDA scan

Gets or sets the intensity of highest peak in scan

Gets or sets the mass of largest peak in scan

Gets or sets the total Ion Current for scan

Gets or sets the time at start of scan (minutes)

Gets or sets the Number of point in scan

Gets or sets the number of channels acquired in this scan, if this is UV or analog data,

Gets or sets the number of the scan

Gets or sets the event (scan type) number within segment

Gets or sets the time segment number for this event

Gets or sets a value indicating whether this scan contains centroid data (else profile)

Gets or sets the frequency.

Gets or sets a value indicating whether is uniform time.

Gets or sets the absorbance unit scale.

Gets or sets the wave length step.

Gets or sets a lazy mechanism returning a string defining the scan type.

Gets or sets a String defining the scan type, for filtering

Gets or sets the cycle number. Cycle number used to associate events within a scan event cycle. For example, on the first cycle of scan events, all the events would set this to '1'. On the second cycle, all the events would set this to '2'. This field must be set by devices if supporting compound names for filtering. However, it may be set in all acquisitions to help processing algorithms.

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Copy all fields

Copy into this object If set, make a "deep copy" which will evaluate any lazy items and ensure no internal source references

Produce a deep copy of an object. Must not contain any references into the original.

A deep clone of all objects in this

Defines a scan with mass range segments.

Initializes a new instance of the class. Default constructor; sets the size of data arrays to 0.

Create a scan from simple X,Y data. This method creates a scan with one segment. For efficiency, the references to the mass and intensity data are maintained within the constructed object. If this is not desired, clone the mass and intensity arrays on calling this constructor. Masses are assumed to be in ascending order.

Mass data for the scan Intensity data for the scan A scan with one segment masses is null. intensities is null. Intensities must have same length as masses

Sum all masses within the ranges

List of ranges to sum If the ranges have equal mass values, then tolerance is subtracted from low and added to high to search for matching masses Sum of intensities in all ranges

Sum all masses within the ranges

List of ranges to sum If the ranges have equal mass values, then are used to determine a band subtracted from low and added to high to search for matching masses Sum of intensities in all ranges

Return the largest intensity (base value) in the ranges supplies

Ranges of positions The largest intensity in all ranges If the ranges have equal mass values, then tolerance is subtracted from low and added to high to search for matching masses Sum of intensities in all ranges

Return the largest intensity (base value) in the ranges supplied

Get the largest value in a range

The fixed range. The base value so far. The largest of, the passed in base value and the base value in the range.

Test if this is a valid object (all streams are not null. All data has same length)

True if valid.

Test if this is a valid object (all streams are not null. All data has same length)

is thrown if this instance does not contain valid data.

Gets the Mass ranges for each scan segment

Gets or sets the Mass ranges for each scan segment

Gets or sets The number of segments

Gets or sets the number of data points in each segment

Gets SegmentLengths.

Gets or sets the positions (mass or wavelength) for each point in the scan

Gets or sets the Intensity (or absorbance) values for each point in the scan

Gets or sets flags, such as "saturated" for each peak.

Gets or sets the The size of the position and intensity arrays. The number of peaks in the scan (total for all segments)

Gets or sets the he number of this scan.

Sum all intensities of peaks within the ranges

The sum so far. The fixed Range. Sum of intensities in all ranges

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

Make a deep clone of this object.

An object containing all data in this, and no shared references

Find the index of the first packet in a segment

segment number (starting from 0) the index of the first packet in a segment

Change the defined length of the scan (for internal use only)

new scan size

Convert to simple scan. This permits calling code to free up references to unused parts of the scan data.

The .

Return only data within the supplied ranges. This internal method can assume that the ranges are in mass order, and do not overlap.

ranges of data to include if set, then this scan is profile data. Zeros are added to terminate sliced profiles If this is set: There must be a valid centroid stream. Profile points near a centroid must be included, even if outside of the range. Centroid data, which may be used to extend profiles so that points which contribute to the centroid are shown A new scan, with data in the desired ranges only

Sequence File Writer Extension Methods

Retrieves the user label at given 0-based label index.

The sequence file access interface object. Index of user label to be retrieved String containing the user label at given index

Provides a means of opening sequences.

Creates the sequence file reader.

Sequence file reader factory object

Read a sequence. The file contents are returned. The file is not kept open.

Name of file to read Access to the contents of the file.

This static factory class provides methods to create and open existing sequence file.

Creates the sequence file writer.

Name of the file. True open an existing sequence file with read/write privilege; false to create a new unique sequence file Sequence file writer object

Creates the UV type of device factory.

UV type of device factory object

Checks the file exists.

Name of the in-acquisition raw file. Device writer can't attach the raw file that doesn't exist.

A simple mass and intensity scan. Represents a scan as two simple array objects This format only creates two objects, and uses much less memory that "array of class with mass and intensity".

Gets or sets the masses.

Gets or sets the intensities.

Basic implementation of a simple scan header, with scan number and time.

Gets or sets the retention time.

Gets or sets the scan number.

A collection of scans, designed to slide forwards through a raw file.

Initializes a new instance of the class.

The spectrum reader. Optional: Reader for batch of scans. If not supplied, spectrumReader is used. Table of scan number and RT of scans in raw file

return data within scan range.

The start scan. The end scan. A ref copy of the scans in range.

Load all the scans in a range.

The start scan index. The end scan index.

A simple scan with header.

Gets or sets the scan.

Gets or sets the header.

Settings for smoothing algorithm, useful for chromatograms etc.

Initializes a new instance of the class. default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Gets or sets the number of points for smoothing the chromatogram

Gets or sets the number of times to repeat smoothing

Gets or sets the envelope shape used by smoothing algorithm

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance.

class to represent spectrum data

Gets or sets Intensity of spectral peak

Gets or sets Mass of spectral peak

Test that two spec points are equal

first point to compare second point to compare true if they have the same contents

Test that two spec points are not equal

first point to compare second point to compare true if they do not have the same contents

Test two points for equality

point to compare true if they are equal

Object.GetHashCode

Stores the Status log for an instrument

Gets or sets the header information for the status log

Gets or sets the array of values for the status logs for the current instrument

Stores one record of status log values

Gets or sets the RetentionTime for this log entry

Gets or sets the array of status log values

Results of running system suitability tests

Gets or sets the resolution of the peak (from other peaks)

Gets or sets a value indicating whether the resolution test passed

Gets or sets a value indicating whether the symmetry test passed

Gets or sets a value indicating whether the peak width test passed

Gets or sets a value indicating whether the peak tailing test passed

Gets or sets a value indicating whether the column overload test passed

Gets or sets a value indicating whether the signal to noise test passed

Gets or sets a value indicating whether the saturation test passed

Gets or sets a value indicating whether the concave peak test passed

Gets or sets a value indicating whether the baseline clipping test passed

Gets or sets a value indicating whether the following values have been calculated: PassedResolutionChecks, MeasuredResolution

Gets or sets a value indicating whether the following values have been calculated: PassedSymmetryChecks

Gets or sets a value indicating whether the following values have been calculated: PassedPeakWidth, PassedTailing, PassedColumnOverload, PassedNoise, PassedSaturated, PassedConcave, PassedBaselineClipped

Gets a value which determines if the ResolutionCheck was performed, and the results of the test, when run.

Gets a value which determines if the SymmetryCheck was performed, and the results of the test, when run.

Gets a value which determines if the PeakWidth test was performed, and the results of the test, when run.

Gets a value which determines if the Tailing test was performed, and the results of the test, when run.

Gets a value which determines if the ColumnOverload test was performed, and the results of the test, when run.

Gets a value which determines if the Noise test was performed, and the results of the test, when run.

Gets a value which determines if the Saturated test was performed, and the results of the test, when run.

Gets a value which determines if the Concave test was performed, and the results of the test, when run.

Gets a value which determines if the BaselineClipped test was performed, and the results of the test, when run.

Initializes a new instance of the class. Default constructor

Initializes a new instance of the class. Copy constructor

The access.

Return tri-state test status, based on if a test has been run, and the test results

true if a test has been run The results of the test (if run) ignored otherwise A status of not tested, when the test is not run, or the pass/fail result when the test has been run

Make a copy of the system suitability results

The .

Parameters for the system suitability algorithm

Gets or sets a value indicating whether resolution checks will be performed

Gets or sets a threshold value which determines if a peak's resolution or ok or not. The default value is 90%. Resolution is defined as the ratio: 100 × V/P where: V = depth of the Valley: the difference in intensity from the chromatogram at the apex of the target peak to the lowest point in the valley between the target peak and a neighboring peak P = Peak height: the height of the target peak, above the peak's baseline

Gets or sets a value indicating whether peak symmetry checks are to be performed. Symmetry is determined at a specified peak height and is a measure of how even-sided a peak is about a perpendicular dropped from its apex.

Gets or sets the Peak Height at which symmetry is measured. The default value is 50%. You can enter any value within the range 0% to 100%.

Gets or sets the Symmetry Threshold The SOP defined Symmetry Threshold is > 70% at 50% peak height. This represents a realistic practical tolerance for capillary GC data. You can enter any value within the range 0% to 100%. The default value is 80% at 50% peak height. The algorithm determines symmetry at the SymmetryPeakHeight For the purposes of the test, a peak is considered symmetrical if: (Lesser of L and R) × 100 / (Greater of L and R) > Symmetry Threshold % where: L = the distance from the left side of the peak to the perpendicular dropped from the peak apex R = the distance from the right side of the peak to the perpendicular dropped from the peak apex Measurements of L and R are taken from the raw file without smoothing.

Gets or sets a value indicating whether peak classification checks are to be run

Gets or sets the Peak Height at which suitability tests the width of target peaks. You can enter any value within the range 0% to 100%. The default value is 50%.

Gets or sets the minimum peak width, at the specified peak height, for the peak width suitability test. The default value is 1.8. You can set any value in the range 0 to 30 seconds.

Gets or sets the maximum peak width, at the specified peak height, for the peak width suitability test. The default value is 3.6. You can set any value in the range 0 to 30 seconds.

Gets or sets the Peak Height at which the algorithm measures the tailing of target peaks. The default SOP value is 10%. You can enter any value within the range 0% to 100%.

Gets or sets the failure threshold for the tailing suitability test. The default SOP defined failure threshold is %lt 2 at 10% peak height. The valid range is 1 to 50. Tailing is calculated at the value defined in . For the purposes of the test, a peak is considered to be excessively tailed if:


             R / L > Failure Threshold %
             where:
             L = the distance from the left side of the peak to the perpendicular dropped from the peak apex
             R = the distance from the right side of the peak to the perpendicular dropped from the peak apex
             Measurements of L and R are taken from the raw file without smoothing.

Gets or sets the Peak Height at which the algorithm measures column overloading. The default SOP value is 50%. You can enter any value within the range 0% to 100%.

Gets or sets the failure threshold value for the column overload suitability test. The default SOP defined threshold is 1.5 at 50% peak height. The valid range is 1 to 20. A peak is considered to be overloaded if:


            L / R > Failure Threshold %
            where:
            L = the distance from the left side of the peak to the perpendicular dropped from the peak apex
            R = the distance from the right side of the peak to the perpendicular dropped from the peak apex
            Measurements of L and R are taken from the raw file without smoothing.

Gets or sets the Number of Peak Widths for Noise Detection testing parameter for the baseline clipping system suitability test. The default value is 1.0 and the permitted range is 0.1 to 10. A peak is considered to be baseline clipped if there is no signal (zero intensity) on either side of the peak within the specified number of peak widths. The range is truncated to the quantitation window if the specified number of peak widths extends beyond the window’s edge.

Gets or sets the threshold for system suitability testing of the signal-to-noise ratio. The default value is 20 and the permitted range is 1 to 500. The algorithm calculates the signal-to-noise ratio within the quantitation window using only baseline signal. Any extraneous, minor, detected peaks are excluded from the calculation.

Initializes a new instance of the class. default constructor

Initializes a new instance of the class. Construct instance from interface, by cloning all settings

Interface to clone

Creates a new object that is a copy of the current instance.

A new object that is a copy of this instance. 2

Class to create accessors for raw a raw file, for multiple threads.

Initializes a new instance of the class. To use this: Construct an interface "IRawDataPlus". Construct this object from the IRawDataPlus. Call to make a separate object for each thread to use. After all threads are completed, and the raw file is no longer needed, dispose of the original IRawDataPlus.

The file.

Create an accessor for one thread to use. Call this method once for each thread you plan to create.

An interface to read data, which should be used by a single thread.

Select instrument. This private method keeps track of the selected instrument within the raw data. When a thread is using a different instrument than the last thread's call, then the IO library selected instrument is changed. If all threads use one instrument (such as MS), then this will not result in multiple calls to the IO library.

The instrument type. The instrument index.

Include reference and exception data. Remembers the state of this from previous calls, and only sets this to the IO library when changed from the last call.

The include reference and exception data.

Request the object to keep a cache of the listed item. Setting the caching to "zero" disables further caching.

Item to cache Limit of number of items to cache (optional, default false) if set True, all values returned from the cache are unique (cloned) references. By default, the cache just keeps references to the objects

Clear items in the cache

item type to clear

Count the number currently in the cache

Item type to count The number of items in this cache

The raw file thread accessor. This class is a private thread safe wrapper. It works by using the "parent" object as a lock object for all threads. In addition, the parent manages all state of the underlying wrapped interface. This object also wraps enumerators and iterators fully, to protect against detector changes from other threads.

Initializes a new instance of the class.

The thread safe raw file access.

Capture that the parent object's selected device

Ensure that the parent object has the expected device selected

Performs application-defined tasks associated with freeing, releasing, or resetting unmanaged resources.

Get a scan number from a retention time

Retention time (minutes) Scan number in the data stream for this time

Gets the current instrument's run header

Gets the number of instrument methods in this file.

Gets the name of the computer, used to create this file.

Gets additional (binary) data from a scan. The format of this data is custom (per instrument) and can be decoded into objects by a specific decoder for the detector type.

Scan whose data is needed

Get the scan statistics for a scan.

scan number Statistics for scan

Gets the segmented scan from scan number. It will also fill object, if any supplied.

The scan number. statistics for the scan The segmented scan

Test if a scan is centroid format

Number of the scan True if the scan is centroid format

Gets the filter strings for this file.

A string for each auto filter from the raw file

Gets an instrument method.

The index. A text version of the method

Gets the definition of the selected instrument.

data about the selected instrument, for example the instrument name

Get a string representing the scan type (for filtering). For more complete tests on filters, the returned string can be converted to a ScanDefinition, by using the static constructor ScanDefinition.FromString(string scanType). If the RT is known, and not the scan number, use ScanNumberFromRetentionTime to convert the time to a scan number. Example: ScanDefinition definition=ScanDefinition.FromString(GetScanType(ScanNumberFromRetentionTime(time));

Scan number whose type is needed Type of scan, in string format. To compare individual filter fields, the ScanDefinition class can be used. ScanDefinition

Get the retention time (minutes) from a scan number

Scan number Retention time (start time) of scan

Get the centroids saved with a profile scan

Scan number determines if peaks flagged as ref should be returned centroid stream for specified .

Gets the status log for retention time.

The retention time. object containing status log information.

returns the number of entries n the current instrument's status log

The .

Returns the header information for the current instrument's status log

The headers (list of prefixes for the strings).

Returns the Status log values for the current instrument

Index into table of status logs true if they should be formatted (recommended) The status log values.

Gets the tune data.

tune data index object containing tune data for specified .

return the number of tune data entries

The .

Return the header information for the current instrument's tune data

The headers/>.

return tune data values for the specified index

index into tune tables true if formatting should be done The tune data>.

Gets the path to original data.

Gets the name of acquired file (excluding path).

Choose the data stream from the data source.

Type of instrument Stream number

Gets the instrument as last set by a call to . If this has never been set, returns null.

Gets the date when this data was created.

Gets the name of person creating data.

Gets various details about the sample (such as comments).

Gets the number of instruments (data streams) in this file.

Gets a value indicating whether the last file operation caused an error.

Gets a value indicating whether the file is being acquired (not complete).

get the number of instruments (data streams) of a certain classification. For example: the number of UV devices which logged data into this file.

The device type to count The number of devices of this type

Create a chromatogram from the data stream

Definition of how the chromatogram is read First scan to read from. -1 for "all data" Last scan to read from. -1 for "all data" Chromatogram points

Create a chromatogram from the data stream

The the device type for an instrument data stream

The data stream The device at type the index

Gets names of all instruments stored in the raw file's copy of the instrument method file.

The instrument names.

Gets a value indicating whether the data file was successfully opened

Gets or sets a value indicating whether reference and exception peaks should be returned (by default they are not)

Re-read the current file, to get the latest data. Only meaningful if the object has an implied backing file (such as IO.DLL and .raw files) No-op otherwise

The .

Gets the trailer extra header information. This is common across all scan numbers

The headers.

Gets the Trailer Extra values for the specified scan number. If = true, then the values will be formatted as per the header settings

scan whose trailer data is needed true if the data should be formatted The strings representing trailer data>.

returns the (unformatted) Trailer Extra value for a specific field in the specified scan number. The object type depends on the field type, as returned by Numeric values (where the header for this filed returns "True" for IsNumeric can always be cast up to double. The integer numeric types SHORT and USHORT are returned as short and ushort. The integer numeric types LONG and ULONG are returned as int and uint. All logical values (Yes/No, True/false, On/Off) are returned as "bool", where "true" implies "yes", "true" or "on". CHAR and UCHAR types are returned as "byte". String types WCHAR_STRING and CHAR_STRING types are returned as "string".

scan who's data is needed zero based filed number in the record, as per header Value of requested field

Returns the (unformatted) Trailer Extra values for all field in the specified scan number. The object types depend on the field types, as returned by GetTrailerExtraHeaderInformation. This offers higher performance, where numeric values are needed, as it avoids translation to and from strings. It is also designed for efficient copy of data from one file to another. Numeric values (where the header for this field returns "True" for IsNumeric) can always be cast up to double. The integer numeric types SHORT and USHORT are returned as short and ushort. The integer numeric types LONG and ULONG are returned as int and uint. All logical values (Yes/No, True/false, On/Off) are returned as "bool", where "true" implies "yes", "true" or "on". Char type is returned as "sbyte". Uchar type is returned as "byte". String types WCHAR_STRING and CHAR_STRING types are returned as "string".

scan who's data is needed Values of all fields Thrown if the selected device is not of type MS

Returns the (unformatted) Tune Data values for all fields in the specified record number. The object types depend on the field types, as returned by GetTuneDataHeaderInformation. This is designed for efficient copy of data from one file to another. Numeric values (where the header for this field returns "True" for IsNumeric) can always be cast up to double. The integer numeric types SHORT and USHORT are returned as short and ushort. The integer numeric types LONG and ULONG are returned as int and uint. All logical values (Yes/No, True/false, On/Off) are returned as "bool", where "true" implies "yes", "true" or "on". Char type is returned as "sbyte". Uchar type is returned as "byte". String types WCHAR_STRING and CHAR_STRING types are returned as "string".

zero bases index into tune records who's data is needed Values of all fields Thrown if the selected device is not of type MS

Gets the (raw) status log data at a given index in the log. Deigned for efficiency, this method does not convert logs to display string format.

Index (from 0 to "GetStatusLogEntriesCount() -1") Log data at the given index

Gets the (raw) status log data at a given retention time in the log. Designed for efficiency, this method does not convert logs to display string format.

Retention time/ Log data at the given time

Get the advanced LT/FT formats data, such as the noise data, baseline data and frequencies

The scan number. Returns an IAdvancedPacketData object which contains noise data, baseline data and frequencies for specified . It might return empty arrays for scans which do not have these data. Thrown if the selected device is not of type MS

Gets the array of headers and values for this scan number. The values are formatted as per the header settings.

The scan for which this information is needed Extra information about the scan

Gets the segment event table for the current instrument

A two dimensional array of events. The first index is segment index (segment number-1). The second is event index (event number -1) within the segment.

Request the object to keep a cache of the listed item. Setting the caching to "zero" disables further caching.

Clear items in the cache

item type to clear

Count the number currently in the cache

Item type to count The number of items in this cache

Gets the raw file header.

Gets the file error state.

Gets extended the run header details.

Gets the auto sampler information.

Calculate the filters for this raw file, and return as an array

Auto generated list of unique filters

Calculate the filters for this raw file within the range of scans supplied, and return as an array.

First scan to analyze Last scan to analyze Auto generated list of unique filters

Get the filter for a scan number.

The scan number. The .

Get a filter interface from a string.

The filter string. An interface representing the filter fields, converted from the supplied string.

Get a filter interface from a scan event interface. Permits filtering to be done based on programmed events, such as an item from the "ScanEvents" table, or from constructed data using . This method initializes the filter based on the current raw file (for example: mass precision)

The event data. An interface representing the filter fields, converted from the supplied event. Thrown if the selected device is not of type MS

Get a filter interface from a string, with a given mass precisions

The filter string. Precisions of masses (number of decimal places) An interface representing the filter fields, converted from the supplied string.

Obtain an interface to iterate over a scans which match a specified filter. The iterator is initialized at "scan 0" such that "GetNext" will return the first matching scan in the file. This is a low level version of

Filter, which all returned scans match. This filter may be created from a string using An iterator which can step back and forth over scans matching a given filter.

Get filtered scan enumerator.

The filter, which all enumerated scans match. This filter may be created from a string using An enumerator which can be used to "foreach" over all scans in a file, which match a given filter. Note that each "step" through the enumerator will access further data from the file. To get a complete list of matching scans in one call, the "ToArray" extension can be called, but this will result in a delay as all scans in the file are analyzed to return this array. For fine grained iterator control, including "back stepping" use

Get filtered scan enumerator.

The filter, which all enumerated scans match. This filter may be created from a string using The start Time. The End Time. An enumerator which can be used to "foreach" over all scans in a time range, which match a given filter. Note that each "step" through the enumerator will access further data from the file. To get a complete list of matching scans in one call, the "ToArray" extension can be called, but this will result in a delay as all scans in the time range are analyzed to return this array. For fine grained iterator control, including "back stepping" use

Gets a value indicating whether this file has an instrument method.

Export the instrument method to a file.

The method file path. Force over write. If true, and file already exists, attempt to delete existing file first. If false: UnauthorizedAccessException will occur if there is an existing read only file. True if the file was saved. False, if no file was saved, for example, because there is no instrument method saved in this raw file.

Gets a value indicating whether this file has MS data.

Gets the scan events.

Gets the set of user labels

Gets the scan event details for a scan

The scan number. The interface, to get detailed information about a scan.

Gets the scan event as a string for a scam

The scan number. The event as a string.

Gets an entry from the instrument error log.

Zero based index. The number of records available is RunHeaderEx.ErrorLogCount An interface to read a specific log entry

Gets the labels and index positions of the status log items which may be plotted. That is, the numeric items. Labels names are returned by "Key" and the index into the log is "Value".

Gets the status log data, from all log entries, based on a specific position in the log. For example: "position" may be selected from one of the key value pairs returned from in order to create a trend plot of a particular value. The interface returned has an array of retention times and strings. If the position was selected by using , then the strings may be converted "ToDouble" to get the set of numeric values to plot.

The position within the list of available status log values. An interface containing the times and logged values for the selected status log field.

Get all instrument friendly names from the instrument method.

The instrument friendly names"/>.

Get scan dependents. Returns a list of scans, for which this scan was the parent.

The scan number. The filter precision decimals. Information about how data dependant scanning was performed.

Gets the unique compound names as arrays of strings.

The Compound Names.

Gets the unique compound names as arrays of strings by given filter.

The scan Filter. The compound names"/>.

Get the scan filters which match a compound name. When implemented against raw files, this may have a performance impact on applications. For files which have a programmed event table, this will be fast, as the information can be taken directly from the events. If there is no event table, then event data is checked for every scan in the file (slower).

The compound name. The array of matching scan filters (in string format).

Create a chromatogram from the data stream. Extended version: Parameters include option for component names. Includes base peak data for each scan.

Definition of how the chromatogram is read First scan to read from. -1 for "all data" Last scan to read from. -1 for "all data" For mass range or base peak chromatograms, if the ranges have equal mass values, then are used to determine a band subtracted from low and added to high to search for matching masses. For example: with 5 ppm tolerance, the caller can pass a single mass value (same low and high) for each mass range, and get chromatograms of those masses +/- 5 ppm. Chromatogram points

Create a chromatogram from the data stream. Extended version: Parameters include option for component names. Includes base peak data for each scan.

Definition of how the chromatogram is read First scan to read from. -1 for "all data" Last scan to read from. -1 for "all data" Chromatogram points

Test if a scan passes a filter. If all matching scans in a file are required, consider using or

the scan number the filter to test True if this scan passes the filter

The filtered scan iterator wrapper. must wrap this, to set device correctly each call

Initializes a new instance of the class.

The raw file thread accessor. The filter.

Gets the filter which was used to construct this

Gets the previous scan number, which matches the filter. Returns 0 if there is no open file.

Gets the next scan number, which matches the filter. Returns 0 if there is no open file.

Sets the iterator's position. This scan number does not have to match the given filter. This can be used to find next or previous matching scan, from a given scan.

Gets a value indicating whether there are possible previous scans before the current scan. This does not guarantee that another matching scan exists. It simply tests that the current iterator position is not the first scan in the file.

Gets a value indicating whether there are possible next scans after the current scan. This does not guarantee that another matching scan exists. It simply tests that the current iterator position is not the last scan in the file.

This method is similar to GetSegmentedScanFromScanNumber in the IRawData interface. The method returns only the mass and intensity values from the scan data for a scan. Values for flags etc. are not returned, saving data space and improving efficiency. This method never returns "reference and exception peak" data. The method is designed for improved performance in custom XIC generators.

The scan whose mass intensity data are needed Mass and intensity values from the scan.

This method is similar to GetCentroidStream in the IRawData interface. The method returns only the mass and intensity values from the "centroid stream" data for a scan. This is also known as "Label Stream" Values for flags etc. are not returned, saving data space and improving efficiency. This method never returns "reference and exception peak" data. The method is designed for improved performance in custom XIC generators.

The scan who's mass intensity data are needed Mass and intensity values from the scan "centroid data".

When deciding what data should be read from a scan, centroids or regular scan (or if the data is needed at all) scan event data is needed. This method permits events to be read as a block for a range of scans, which may reduce overheads involved in requesting one by one. Potentially, in some data models, the same "event" may apply to several scans so it is permissible for the same reference to appear multiple times.

The first scan whose event is needed The last scan An array of scan events

Gets the (raw) status log data at a given index in the sorted log. The form of the log removes duplicate and out of order times Designed for efficiency, this method does not convert logs to display string format.

Index (from 0 to "GetStatusLogEntriesCount() -1") Log data at the given index

Data structure used internally by scan definition

Gets or sets the token.

Gets or sets the token class.

Compares the current token with another token

The compare generic.

The other. A 32-bit signed integer that indicates the relative order of the objects being compared. The return value has the following meanings: Value Meaning -1 This object is less than the parameter. Zero This object is equal to . 1 This object is greater than .

Stores the trailer extra values for a scan within an instrument

Gets or sets the scan Number

Gets or sets the array of trailer extra values for a scan within an instrument

Stores the header and tune data record values for an instrument

Gets or sets the array of headers for Tune data

Gets or sets the tune data values for an instrument

Stores one set of tune data values for an instrument

Gets or sets the index number of the tune record

Gets or sets the array of tune data values for an instrument

Encapsulates information about UVInstrument.

Initializes a new instance of the class.

Defines the UV instrument data header for UV type devices

Gets or sets the frequency. The Frequency will be ignored by Analog devices

Gets or sets a value indicating whether is uniform time. If the Uniform flag is TRUE (time is uniform by frequency ) then there is NO time value. ex. "intensity, time" The IsUniformTime will be ignored by Analog devices

Gets or sets the number of channels.

Gets or sets the start time.

Gets or sets the tic.

Copies the specified source. Copy all the non static fields of the current object to the new object. Since all the fields are value type, a bit-by-bit copy of the field is performed.

Create a copy of the same object type

The ScanWithSimpleData interface. Defines very basic MS data and intensity, plus the event for the scan.

Gets the scan event.

Gets the data.

ICommonCoreDataObject is an interface that for CommonCoreData objects. It allows for clearing the dirty flags during a save operation. For example, before saving your data object that implements CommonCoreDataObject, cast it to a ICommonCoreDataObject and set IsDirty to false. All data objects that implement the abstract class CommonCoreDataObject implement the ICommonCoreDataObject interface as well.

Provides a custom deep equality operation when checking for equality.

The value to compare. True if objects are equal

Performs the default settings for the data object. This can be overridden in each data object that implements the interface to perform initialization settings.

CommonCoreData object is an abstract class. It includes a deep equals feature/>

Serves as a hash function for a particular type.

A hash code for the current .

Compares this object with another. Traverse the set of member variables to compare against the object that was passed in. Determines whether the specified is equal to the current .

The to compare with the current . true if the specified is equal to the current ; otherwise, false. The parameter is null.

Provides a custom deep equality operation when checking for equality.

The value to compare. True if the items are equal, false if they are not.

Compares this object with another. Traverse the set of member variables to compare against the object that was passed in.

object to compare with if true, compare sub-objects true if equal

Performs the default settings for the data object. This can overridden in each data object that implements the interface to perform initialization settings.

CoreDataElementAttribute is used in the custom deep equals operation. This attribute allows a user to specify whether or not to include a property in the equals operation.

Gets or sets a value indicating whether this is ignore.

true if ignore; otherwise, false.

Initializes a new instance of the class and sets the Ignore property to false.

The comparer.

Type of objects compared

Initializes a new instance of the class.

The comparison.

Compare x and y.

The x. The y. The standard comparison result (from IComparer).

Make a thread safe cache of the "n" most recently used copies of an object. For example: If different parts of an application are likely to read the same data from a file multiple times, this can be used to reduce the file operations.

Type of item to cache

Obtain a record from a data source, based on an index Example: Scan from raw file, based on scan number.

Index of object Object read from data source

Initializes a new instance of the class.

Maximum number of items in the cache. Oldest items are discarded when the cache is full Delegate to read a new item, when not in the cache.

The queue item.

Gets or sets Index.

Gets or sets Value.

Get an item from the cache, or from the data reader (if not cached). Automatically caches new items, discarding oldest items.

Record number item from the cache. May be "null" if this item is not in the cache, and the reader has no value for this index

Gets the number of cached items

Gets the maximum number of cached items

Gets or sets a value indicating whether all items returned from the cache are Deep Cloned. If true: Items found in the cache are deep cloned. New items read are saved in the cache as a deep clone, such that the item returned to the caller is never the same as any reference in the cache. If false: references are saved in and returned from the cache without any clone.

Empty the cache

Determine how the calibration curve is weighted

This allows you to weight all calibration data points equally during the least-squares regression calculation of the calibration curve.

This allows you to specify a weighting of 1/X for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of their quantity.

This allows you to specify a weighting of 1/X^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their quantity.

This allows you to specify a weighting of 1/Y for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of their response (or response ratio).

This allows you to specify a weighting of 1/Y^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants are weighted by the inverse of the square of their response (or response ratio).

This allows you to specify a weighting of 1/s^2 for all calibration data points during the least-squares regression calculation of the calibration curve. Calibrants at a given level are weighted by the inverse of the standard deviation of their responses (or response ratios). For this weighting factor to be used, there must be two or more replicates at each level. If only one calibrant is available for any level, 1/s^2 weighting cannot be used.

Treatment of calibration curve origin

The origin is included (as an extra point) on the calibration curve.

The origin is not added to the curve

The curve is forced through the origin

The Regression algorithm used

A linear (first order) polynomial least-squares fit of the experimental data using slope and intercept coefficients: Y = mX + B where m is the slope of the curve and B is the intercept point on the Y-axis.

A linear polynomial least-squares fit of the experimental data of the following mathematical form: log10[Y] = m log10[X] + B where m is the slope of the curve and B is the intercept point on the Y-axis.

A calibration curve which calculates a quadratic (second order) polynomial least-squares fit of the experimental data using the following mathematical form: Y = AX2 + BX + C, where A, B, and C are the polynomial coefficients. At least three calibration levels are required for this curve fit type.

A calibration curve which calculates a quadratic (second order) polynomial least-squares fit of the experimental data using the following mathematical form: log [Y] = A log [X2] + B log [X] + C where A, B, and C are the polynomial coefficients. Note: ignore/force/include origin options are not used with this Regression algorithm type.

Locally Weighted regression always kicks out replicates at either the lowest or highest level. With points at only three levels, a loess regression is discontinuous at the mid-point between the lowest and highest level.

A calibration type in which the response factor is calculated for replicates at all calibration levels and then averaged. The amount in a sample can then be calculated by dividing the response by the average response factor.

A calibration curve in which data at each calibration level are averaged. This averaging results in a single averaged data point at each calibration level. Averaged calibration points are plotted by connecting adjacent points with straight lines. This calibration curve can be used with one or more calibration levels. Calibration supports ignore/force origin options for this calibration curve type.

A calibration curve in which a cubic polynomial curve is fit between each pair of calibration levels such that the slopes of the separate cubic polynomial curves match at common calibration curve points. Calibration supports ignore/force origin options for this calibration curve type. Note: At least four calibration levels are required for this type of curve fit. If the origin is forced, only three calibration levels are required.

Defines why the peak detector has determined that a peak has started or ended

edge intensity intercepted baseline + 05.*noise value.

edge fits at least one of the three valley criteria.

reserved for manually entered integration limits.

edge reached the peak constraint percentage height.

edge reached the tailing factor RT limit before the STRIPE height.

Tilt is as in a pinball machine, something bad happened, such as hitting the edge of the survey window.

Determines how signal to noise is reported

No noise value has been calculated

No detected noise

Use SignalToNoise property to get the value

Determines how a component peak has been selected from a set of possible peaks

search was by spectral fit.

search was by largest peak in the search window.

search was by nearest retention time.

search was by spectral purity.

peak was detected by the generic chromatogram peak detector.

Peak was reworked from the original (for example manual)

Determines is the peak is rising, or inverted

Peak rises, like a mountain

Peak is inverted (like a valley)

An algorithm for peak detection.

The genesis peak detection algorithm.

The ICIS peak detection algorithm

The avalon peak detection algorithm

The parameterless peak detection algorithm

Represents the results of an optional test.

Failed Test

Passed Test

Not Tested

This specifies a smoothing envelope shape.

Smooth with equal weights.

Smooth with a gaussian weighting envelope.

The units that you can associate with mass tolerance

millimass units: a unit of mass equal to 0.001 atomic mass unit, used in physics and chemistry. This unit is also called the millidalton (mDa). The millimass unit is an SI unit, but its proper SI symbol is mu, not the older symbol mmu

parts-per-million: a concentration, a unit of proportion equal to 10^-6.

atomic mass units: the unit of mass used by chemists and physicists for measuring the masses of atoms and molecules. Early in the nineteenth century, scientists discovered that each chemical element is composed of atoms, and that each chemical compound is composed of molecules in which atoms are combined in a fixed way. The definition of the unified atomic mass unit as 1/12 the mass of the most common atoms of carbon, known as carbon-12 atoms. (Most elements are mixtures of atoms which have different masses because they contain different numbers of neutrons; these varieties are called isotopes.) Careful experiments have measured the size of this unit; the currently accepted value (1998) is 1.660 538 73 x 10-24 grams. (This number equals 1 divided by Avogadro's number; see mole.) In addition, 1 amu equals approximately 931.494 MeV (see electron volt). In biochemistry, the atomic mass unit is called the dalton (Da).

Mode of handling multiple chromatogram traces (from the same filtered scans)

There is only one chromatogram

The two chromatograms are summed

The second chromatogram is subtracted from the first

Determines how void time is calculated

A value is specified

The time of the first peak in the void chromatogram is used.

Determines how the ICIS peak detector determines which signals are noise.

A single pass algorithm to determine the noise level.

A multiple pass algorithm to determine the noise level. In general, this algorithm is more accurate in analyzing the noise than the INCOS Noise algorithm, but it takes longer.

Features which can be set per peak, such as "reference compound"

No peak flags

Saturation flag (signal over ADC limit)

Fragmentation flag (peak split by centroider)

Merged flag (peaks combined by centroider)

Exception peak flag (part of reference, but not used by calibration)

Reference peak flag (hi-res internal reference compound)

Mathematically modified packet

High resolution SIM lock mass

Determines how much of the the chromatogram is used. Data outside of the calculated window is ignored

Do not restrict the chromatogram

The chromatogram processed is restricted by the baseline and noise window

Static class used to convert enumeration values to custom strings. This class is necessary because there is no mechanism to override the ToString() method for enumerations.

To get the customized string for an enumeration value, a program must call the static method EnumFormat.ToString(value) and not value.ToString().

Gets the display text for an enumeration value.

A string is searched for in three places, in this order: A custom string specified by SetCustomString(). A string resource in the resource file (enum namespace).Enumerations named (type name).(enum name). From the DisplayTextAttribute for the enumeration value. If no value is found, the standard string representation of the enumeration is returned. The enumeration value for which to obtain the text string. The string for the enumeration value.

Sets a custom string for an enumeration value. This will override any string set with a DisplayTextAttribute.

The enumeration value for which to set the custom text string. The custom text string for this enumeration value.

Extension methods. Includes extensions to several types and interfaces defined in this DLL, plus some extensions to common .Net types.

Determines whether [the specified source] [is null or empty] .

Type parameter The source. if [the specified source] [is null or empty]; otherwise, .

Test if a value is within range

The range. The value. True if the value is within or equal to the range limits (closed range).

find the first data value which is equal to or after start (for example, first value within a tolerance range). Similar to Array.Binary search, but faster as does not need to call comparer functions

Array of increasing data (for example masses in a scan) Position to look for (for example start of X axis range) The first value after start, or -1 if there are no points after start

Create the ion chromatogram value from a scan data which is the sum of the intensities of all masses between given limits. These limits are typically calculated (elsewhere) based on a known mass +/- tolerance.

The scan data. The low mass limit. The high mass limit. The summed intensities.

Create the ion chromatogram value from a centroid stream, which is the largest of the positive intensities of all masses between given limits. These limits are typically calculated (elsewhere) based on a known mass +/- tolerance. If there are no peaks in range, or all data in range has negative intensities, zero is returned.

The centroids. The low mass limit. The high mass limit. The largest positive peak intensity within limits, or zero if there are no positive values within limits.

Create the ion chromatogram value from a scan, which is mass of the largest of the positive intensities of all masses between given limits. These limits are typically calculated (elsewhere) based on a known mass +/- tolerance. If there are no peaks in range, or all data in range has negative intensities, zero is returned.

The centroids. The low mass limit. The high mass limit. The mass of the peak with the largest positive peak intensity within limits, or zero if there are no positive values within limits.

The centroids. The mass of the peak with the largest positive peak intensity within limits, or zero if there are no positive values within limits.

Perform binary search on IList

The list. The value. The comparer. Type of items in list The index of the found item, or compliment of the next item after the supplied value. Thrown if arguments are null

Test if a raw file has MS data.

The raw data. True if the file has MS data

Test if a raw file has MS data, and select the MS detector, if available.

The raw data. True if the MS data has been selected. False if the file does not have MS data.

Get a filtered scan enumerator, to obtain the collection of scans matching given filter rules. Gets scans within the given time range.

The raw data. The filter. The start Time. The end Time. The collection of scans

Calculate the filters for this raw file for scans within the time range supplied.

the raw data start of time window end of time window Auto generated list of unique filters

Calculate the compound names for this raw file for scans within the time range supplied.

the raw data start of time window end of time window Array of compound names within the supplied time range

Get the scans included in the time range

raw file start time of range end time of range first scan in range last scan in range True if scans numbers are returned

Get a filtered scan enumerator, to obtain the collection of scans matching given filter rules.

The raw data. The filter. The collection of scans

Get a scan enumerator, to obtain the collection of scans matching a given compound.

The raw data. The filter. The collection of scans

Test is a scan is of a given compound

raw file scan number compound name true if this is a scan of the compound

Get a scan enumerator, to obtain the collection of scans matching a given compound, within a given time range

The raw data. The compound name. The start Time. The end Time. /// The collection of scans within the supplied time range, which have this compound name

Test if a scan passes a filter. This extension is provided for improved efficiency where the same filter string needs to be used to test multiple scans, without repeating the parsing. Parsing can be done using: GetFilterFromString(string filter), with the IRawDataPlus interface. Also consider using when processing all scans in a file.

The raw data. the scan number the filter to test True if this scan passes the filter

Test if a scan passes a filter. This extension is provided for improved efficiency where the same filter string needs to be used to test multiple scans, without repeating the parsing. Consider using one of the overloads of BuildFilterHelper() Parsing can be done using: GetFilterFromString(string filter), with the IRawDataPlus interface. Also consider using when processing all scans in a file.

The raw data. the scan number the filter to test True if this scan passes the filter

Constructs an object which has an analysis of the selections being made by a scan filter. Improves efficiency when validating many scans against a filter. Filter precision is automatically set, based on the file.

The raw data. the filter to analyze Helper, to efficiently validate scans.

Constructs an object which has an analysis of the selections being made by a scan filter. Improves efficiency when validating many scans against a filter.

The raw data. the filter to analyze Precision of filter Helper, to efficiently validate scans.

The raw data. the filter to analyze Helper, to efficiently validate scans.

Constructs an object which has an analysis of the selections being made by a scan filter. Improves efficiency when validating many scans against a filter.

The raw data. the filter to analyze Filter Precision Helper, to efficiently validate scans.

Format ionization mode, based on the scan filter string format.

The raw data. The mode to format. The .

Format activation type, based on the scan filter string format.

The raw data. The mode to format. The .

Format mass analyzer, based on the scan filter string format.

The raw data. The analyzer to format. The .

Get the mass tolerance and precision values from a raw file

Raw file The default tolerance and filter precision

Enumerate over a range of scans

File to read from start of scan range final scan in scan range An enumerator for a collection of scans

Enumerate over a set of scans

File to read from Numbers for the scans An enumerator for a collection of scans

Gets the average of scans between the given times, which match a filter string.

File to read from start time end time filter string mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.

Gets the average of scans between the given times, which match a compound name.

File to read from start time end time compound name mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.

Gets the average of scans between the given scan numbers, which match a compound name.

File to read from start scan number end scan number compound name mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.

Gets the average of scans between the given scan numbers, which match a filter string.

File to read from start scan end scan filter string mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.

Create a scan averager.

The data. The average options. The .

Gets the average of scans between the given times, which match the supplied filter rules.

File to read from start time end time filter rules mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.

Gets the average of scans between the given scan numbers, which match the supplied filter rules.

File to read from start scan end scan filter rules mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). the averaged scan. Use Scan.ScansCombined to find how many scans were averaged.

Calculates the average spectra based upon the list supplied. The application should filter the data before making this code, to ensure that the scans are of equivalent format. The result, when the list contains scans of different formats (such as linear trap MS centroid data added to orbitrap MS/MS profile data) is undefined. If the first scan in the list contains "FT Profile", then the FT data profile is averaged for each scan in the list. The combined profile is then centroided. If the first scan is profile data, but not orbitrap data: All scans are summed, starting from the final scan in this list, moving back to the first scan in the list, and the average is then computed. For simple centroid data formats: The scan stats "TIC" value is used to find the "most abundant scan". This scan is then used as the "first scan of the average". Scans are then added to this average, taking scans alternatively before and after the apex, merging data within tolerance.

File to read from list of scans to average mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). Merge segments, even if mass ranges are not similar. Only applies to data with 1 mass segment The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.

Calculates the averaged and subtracted spectra based upon the lists supplied. The application should filter the data before making this code, to ensure that the scans in both lists are of equivalent format. The result, when the lists contains scans of different formats (such as linear trap MS centroid data added to orbitrap MS/MS profile data) is undefined. If the first scan in the list contains "FT Profile", then the FT data profile is averaged for each scan in the list. The combined profile is then centroided. If the first scan is profile data, but not orbitrap data: All scans are summed, starting from the final scan in this list, moving back to the first scan in the list, and the average is then computed. For simple centroid data formats: The scan stats "TIC" value is used to find the "most abundant scan". This scan is then used as the "first scan of the average". Scans are then added to this average, taking scans alternatively before and after the apex, merging data within tolerance.

File to read from foreground scans: list of scans to average background scans: list of scans which are averaged, and then subtracted from the averaged foreground scans mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.

Calculates the averaged and subtracted spectra based upon the lists supplied. If the first scan in the list contains "FT Profile", then the FT data profile is averaged for each scan in the list. The combined profile is then centroided. If the first scan is profile data, but not orbitrap data: All scans are summed, starting from the final scan in this list, moving back to the first scan in the list, and the average is then computed. For simple centroid data formats: The scan stats "TIC" value is used to find the "most abundant scan". This scan is then used as the "first scan of the average". Scans are then added to this average, taking scans alternatively before and after the apex, merging data within tolerance.

File to read from time range to average. time ranges to subtract. The sets of scans matching the filter in each of these time ranges are joined to define the background. Filter to apply for averaging mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.

Calculates the averaged and subtracted spectra based upon the lists supplied, which include the named compound. If the first scan in the list contains "FT Profile", then the FT data profile is averaged for each scan in the list. The combined profile is then centroided. If the first scan is profile data, but not orbitrap data: All scans are summed, starting from the final scan in this list, moving back to the first scan in the list, and the average is then computed. For simple centroid data formats: The scan stats "TIC" value is used to find the "most abundant scan". This scan is then used as the "first scan of the average". Scans are then added to this average, taking scans alternatively before and after the apex, merging data within tolerance.

File to read from time range to average. time ranges to subtract. The sets of scans matching the filter in each of these time ranges are joined to define the background. Compound to select scans for averaging mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.

Get the list of scans which conatin a given copound, in the range "nearest scan time to range.Low" to "nearest scan time to range.High"

Raw file Compound name to match against scan event Retention Time range

Creates a list of all scans in the given range, which pass a filter string

The raw file. The filter. The start scan number. The end scan number. List of filtered scan numbers

Creates a list of all scans in the given range, which have a component name

The raw file. The compound. The start scan number. The end scan number. List of filtered scan numbers

Creates a list of all scans in the given range, which pass the supplied filter rules.

The raw file. The filter. The start scan number. The end scan number. List of filtered scan numbers

Creates a list of all scans in the given time range, which pass the supplied filter rules.

The raw file. The filter. The start time. The end time. List of filtered scan numbers

Creates a list of all scans in the given time range, which pass the supplied filter rules. This version returds scans from the "nearest scan to start time" to "nearest scan to end time".

The raw file. The filter. The time range. List of filtered scan numbers

Creates a list of all scans in the given time range, which pass the supplied filter rules. This version returds scans from the "first scan >= start time" to "last scan Less or equal to end time".

The raw file. The filter. The time range. List of filtered scan numbers

Creates a list of all scans in the given time range, which pass a filter

The raw file. The filter. The start time. The end time. List of filtered scan numbers

Convert a time range to a the nearest scan range

The raw File. The time range. The scan range of the nearest scans to the start and end times

Convert a time range to am inlcuded scan range, include scans which are within or equal to the time limits supplied.

The raw File. The time range. The scan range of the lowest and highest scans in the time range supplied, including scans at the boundary times.

Creates a list of all scans in the given scan range, which pass a filter

The sample raw file. The start scan number. The end scan number. The (analyzed) filter. The list of matching scans.

Creates a list of all scans in the given scan range, which pass a filter

The sample raw file. The start scan number. The end scan number. The (analyzed) filter. The list of matching scans.

File to read from list of ScanStatistics mass tolerance settings. If not supplied, these are default from the raw file The average Options (for FT format data). The average of the listed scans. Use Scan.ScansCombined to find how many scans were averaged.

Subtracts the background scan from the foreground scan

File to read from Foreground data (Left of "scan-scan" operation Background data (right of"scan-scan" operation) The result of foreground-background

Test if this file has variable trailers. Calling code must select and MS data stream first. If this is true, then the number of items returned in each scan for "trailer extra" can vary.

The raw data. True, if the trailer extra records are variable sized.

Test if a set of headers defines "variable sized records".

The headers. True, if the records controlled by these headers are variable sized.

Get trailer extra data for scan with validation. Gets the "trailer extra" custom scan data in object form. The application should select MS data before calling this. For example, If the string "Ion Time" is found at index 3 in the headers with format "double", and an application needs to read this double value from scan 19, then the application can first test if item[3] is valid in scan 19, by inspecting the returned boolean array (result.Item1[3]). If this array element is "true" then the "Ion Time" (double) value in the returned object array at index 3 may be used. If result.Item1[3] is false, then this value is not available. So: If producing a chart of this value, the retention time of this scan should be omitted from the data series. (Do not record "0" for a missing value). Argument exceptions may be returned by the underlying file, if (for example) the scan number is out of range.

The raw file. The scan number. The headers as read by IRawDataPlus.GetTrailerExtraHeaderInformation. When processing multiple scans, it is more efficient for an application to request this data once, and supply it to each call. Instruments may have fixed record sizes. Having read the headers, an application may call this bool hasVariableRecords = headers.HasVariableRecords(); and if this returns "false" then there is no need to call this extension, as all values will be valid in all scans. A tuple, whose first element is an array of valid flags, and second is the exact data returned from GetTrailerExtraValues, for the supplied scan.

Contains enumerations used for scan filters and scan events.

Specifies polarity of scan.

Scan is negative ion

Scan is positive ion

Accept any type of scan polarity.

Specifies data type of scan.

Centroid format data

Profile format data

When filtering: accept any state of this feature

Specifies how source fragmentation values are interpreted.

No numeric value: e.g. SID

A single value: e.g. SID=40

A ramp: e.g. SID=40-50

SIM: e.g. SIM [100@40, 200@50]

Accept any value

Specifies scan mode in scans.

A full scan.

A zoom scan.

A SIM (selected Ion Monitoring) scan.

A SRM (Selected Reaction Monitoring) scan.

A CRM (Continuous Reaction Monitoring) scan.

any scan.

A Q1 MS scan (first quad of triple).

A Q3 MS scan (third quad of triple).

The feature state. By default: On. This tri-state enum is designed for filtering

The on state. The feature is used

The off state. The feature is not used.

The any state. When filtering, match any state of this feature.

Specifies scan power in scans.

Constant Neutral Gain scan(ICIS Data Only)

Constant Neutral Loss scan(ICIS Data Only)

Parent scan(ICIS Data Only)

Any scan power

basic MS

MS^2 (MS/MS)

order MS^3

order MS^4

order MS^5

order MS^6

order MS^7

order MS^8

order MS^9

order MS^10

Specifies ionization mode in scans.

Mode is electron impact.

Mode is chemical ionization.

Mode is fast atom bombardment.

Mode is electro spray.

Mode is atmospheric pressure chemical ionization.

Mode is nano spray.

Mode is thermo spray.

Mode is field desorption.

Mode is matrix assisted laser desorption ionization.

Mode is glow discharge.

Mode is any (For filtering only). If reported by an instrument: Mode was not recorded by instrument.

Paper spray ionization.

Card nanospray ionization.

The extension ionization mode 1.

The extension ionization mode 2.

The extension ionization mode 3.

The extension ionization mode 4.

The extension ionization mode 5.

The extension ionization mode 6.

The extension ionization mode 7.

The extension ionization mode 8.

The extension ionization mode 9.

The ion mode is beyond known types.

Specifies inclusion or exclusion of the detector value.

The detector value valid.

Any detector value (for filtering).

The detector value is not valid.

Specifies precursor(collision) energy validation type.

Energy value is valid

Not valid (accept any when filtering)

Specifies type of mass analyzer in scans.

Ion trap

Triple quad

Single quad

Time of flight

Fourier Transform

Magnetic sector

Match any type

Specifies type of sector scan.

Magnetic sector scan

Electrostatic sector scan

Match any sector scan

Specifies type of field free region in scans.

First Field Free Region

Second Field Free Region

Accept any Field Free Region

Specifies compensation voltage type.

No numeric value: e.g. SID

A single value: e.g. SID=40

A ramp: e.g. SID=40-50

SIM: e.g. SIM [100@40, 200@50]

Accept any value

The activation types are used to link a specific precursor mass with an activation type. There are 26 possible mode values, including some reserved values.

Collision induced dissociation

Multi-photon dissociation.

Electron-capture dissociation (ECD) is a method of fragmenting gas phase ions for tandem mass spectrometric analysis (structural elucidation).

Pulsed-Q Dissociation (PQD) is a proprietary fragmentation technique that eliminates the low mass cut-off for Thermo Scientific™ linear ion trap mass spectrometers, facilitating the use of isobaric mass tags for quantitation of proteins.

Electron transfer dissociation (ETD). ETD induces fragmentation of cations (e.g. peptides or proteins) by transferring electrons to them.

Higher-energy collisional dissociation.

Match any activation type

SA activation

Proton transfer reaction

Negative electron transfer dissociation

Negative Proton-transfer-reaction

Ultra Violet Photo Dissociation

Mode a (reserved) .

Mode b (reserved) .

Mode c (reserved) .

Mode d (reserved) .

Mode e (reserved) .

Mode a (reserved) .

Mode g (reserved) .

Mode h (reserved) .

Mode i (reserved) .

Mode J (reserved) .

Mode K (defined as NegativeProtonTransferReaction).

Mode L (reserved).

Mode M (reserved).

Mode N (reserved).

Mode O (reserved).

Mode P (reserved).

Mode Q (reserved).

Mode R (reserved).

Mode S (reserved).

Mode T (reserved).

Mode U (reserved).

Mode V (reserved).

Mode W (reserved).

Mode X (reserved).

Mode Y (reserved).

Mode Z (reserved).

end of list

Determines how accurate mass calibration was done.

Calibration is internal (calibration compound mixed with injected data).

Calibration is external (calibration compound used on a previous injection).

No recorded accurate mass calibration.

Access to basic data about a replicate As defined in Xcalibur PMD

Gets the amount of target compound in calibration or QC standard.

Gets the Ratio of target peak height to ISTD peak height in result file.

Gets the Ratio of target peak area to ISTD peak area in result file.

Gets a value indicating whether to exclude this data point from calibration curve.

Gets the raw file name for the replicate

A replicate is a measurement of a single calibration peak in 1 file. This interfaces defines required features of a replicate for the regression code. A calibration system needs to implement at least this information (typically from a calibration table and peak integration results). The real class "Replicate" implements this.

Gets the amount of target compound in calibration or QC standard.

Gets the response of this sample, for example: Ratio of target peak area to ISTD peak area

Gets or sets a value indicating whether this data point should be excluded from the calibration curve.

Gets the key name associated with this replicate (for example a file name)

Gets the second key name associated with this replicate (for example a compound name)

Implementation of ICloneable.Clone method. Creates deep copy of this instance.

An exact copy of the current Replicate.

Interface to pass replicate information to curve fitting methods

Gets the replicates of this calibration level

Gets the number of replicates for this level

Gets or sets the amount of calibration compound (usually a concentration) for this level

array access operator to return Replicate array element.

Index into the array The requested replicate

(updated) included counter (updated) excluded counter

Read only access to a calibration level.

Gets the name for this calibration level

Gets the amount of calibration compound (usually a concentration) for this level

interface to read QC level settings

Gets the QC test standard: 100 * (yobserved-ypredicted)/ypreditced

Import format for Xcalibur PMD

Gets replicate data, as saved in a PMD file

Interface to read replicate information

Gets the replicates of this calibration level

Gets the number of replicates for this level

Gets an array access operator to return Replicate array element.

Index into the array The requested replicate

This interface represents replicate information after preforming calibration calculations and determining statistics. These statistics are may be used to annotate calibration curves.

Gets or sets the calculated % RSD for a replicate table

Gets the average value of the response factor

Statistics calculated from a replicate table

Gets the calculated % RSD for a replicate table

Gets the calculated % CV for a replicate table

Gets the average retention time of all peaks added to the replicate table

Gets the average response factor (or average response for ISTD)

Gets a value indicating whether the calibration or QC level was "found"

This interface represents replicate information after preforming calibration calculations and determining statistics. These statistics are may be used to annotate calibration curves.

Read only access to Results of running system suitability tests