{
  "experimentMode": {
    "name": "DeepScan",
    "title": "DEEP SCAN",
    "description": "Combines a single exclusion and inclusion list with multiple ID injections to comprehensively fragment relevant precursor ions",
    "details": "Generates up to 1 exclusion list per sequence\n Generates up to 1 inclusion list per sequence\n Injects ID samples until all inclusion list ions are fragmented or user-defined number of ID samples are reached",
    "imgSrc": "Deep_Scan.png"
  },
  "experimentTemplate": {
    "settings": [
      {
        "name": "experimentHeaderImage"
      },
      {
        "name": "selectPycoTemplate"
      },
      {
        "name": "experimentDetails"
      },
      {
        "name": "instrumentMethods"
      },
      {
        "name": "experimentParameters"
      }
    ],
    "injections": [
      {
        "name": "customInjectionsGridDeepScan"
      },
      {
        "name": "standardInjectionsGrid"
      }
    ]
  },
  "experimentConcepts": [
    {
      "experimentParameters": [
        {
          "header": "Experiment Parameters"
        },
        {
          "name": "overrideFactorParameters"
        },
        {
          "name": "exclusionPeakWindowExtension"
        },
        {
          "name": "inclusionPeakWindowExtension"
        },
        {
          "name": "inclusionIntensityFactor"
        },
        {
          "name": "preferredIonsParameters"
        },
        {
          "name": "exclusionTimeParameter"
        },
        {
          "name": "isotopesExclusionList"
        },
        {
          "name": "exclusionListIntensityThreshold"
        },
        {
          "name": "inclusionListIntensityThreshold"
        }
      ]
    },

    {
      "customInjectionsGridDeepScan": [
        {
          "name": "deepScanInjectionHeaders"
        },
        {
          "name": "deepScanInjectionColumnHeaders"
        }
      ]
    },
    {
      "deepScanInjectionHeaders": [
        {
          "header": "AcquireX Template Injections"
        },
        {
          "name": "numberOfBlanks",
          "displayName": "# Header Blanks",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 20,
          "model": 0,
          "errorStatus": false,
          "id": "blankInjections",
          "details": [
            {
              "description": [
                "Step 1: Sample injection",
                "Step 2: Background ion detection",
                "Step 3: Exclusion list creation"
              ]
            }
          ]
        },
        {
          "name": "numberOfInjections",
          "displayName": "Incl. Ref",
          "type": "boolean",
          "model": 0,
          "errorStatus": false,
          "id": "sampleInjections",
          "details": [
            {
              "description": [
                "Step 1: Sample injection",
                "Step 2: Component ion detection",
                "Step 3: Inclusion list creation"
              ]
            }
          ]
        },
        {
          "name": "numberOfDeepScanInjections",
          "displayName": "# Deep Scan Injections",
          "type": "number",
          "minimumValue": 0,
          "maximumValue": 30,
          "model": 0,
          "errorStatus": false,
          "id": "deepScanInjections",
          "details": [
            {
              "description": [
                "Step 1: New method creation from template method using exclusion and/or inclusion lists",
                "Step 2: Sample injection",
                "Step 3: Exclusion and Inclusion list modification from fragmented precursor ions"
              ]
            }
          ]
        },
        {
          "name": "washBlock",
          "type": "block",
          "id": "insertOrDeleteWashInj"
        }
      ]
    },
    {
      "deepScanInjectionColumnHeaders": [
        {
          "name": "name",
          "displayName": "Name",
          "type": "String"
        },
        {
          "name": "sampleType",
          "displayName": "Type",
          "type": "String"
        },
        {
          "name": "matrix",
          "displayName": "Exclusion Ref",
          "type": "Boolean"
        },
        {
          "name": "instMethod",
          "displayName": "Instrument Method",
          "type": "String"
        },
        {
          "name": "vialPosition",
          "displayName": "Vial",
          "type": "String"
        },
        {
          "name": "injVol",
          "displayName": "Inj Vol(ul)",
          "type": "Number"
        }
      ]
    },
    {
      "experimentHeaderImage": [
        {
          "src": "Design_Experiment_Deep-Scan.png",
          "type": "image"
        }
      ]
    },
    {
      "instrumentMethods": [
        {
          "header": "Instrument Methods"
        },
        {
          "name": "fullScanMethod",
          "id": "blankMethod",
          "displayName": "Full Scan Method",
          "type": "string",
          "isFullScan": true,
          "needInclusion": false,
          "needExclusion": false,
          "isFragmentType": false,
          "instrumentMethodError": false,
          "model": "",
          "associatedSampleTypeList": [ 1, 2, 4 ],
          "tooltip": {
            "header": "Full Scan Method",
            "message": "The instrument method that the Xcalibur data system uses to generate data for detecting peaks, component-like features, and constant background ions; and to assemble precursor ion exclusion and inclusion lists. Make sure to use an AcquireX template method or that your MS instrument method meets the following criteria:",
            "list": [ "Uses the MS1 Full Scan with a single continuous scan range.", "Turns polarity switching off." ]
          },
          "errorMessage": "The Full Scan Method is not present in the specified path."
        },
        {
          "name": "msnTemplateMethod",
          "id": "mS2Method",
          "displayName": "MSn Template Method",
          "type": "string",
          "isFullScan": false,
          "needInclusion": true,
          "needExclusion": true,
          "isFragmentType": false,
          "instrumentMethodError": false,
          "model": "",
          "associatedSampleTypeList": [ 3 ],
          "tooltip": {
            "header": "MSn Template Method",
            "message": "The instrument method to be combined with precursor exclusion or inclusion lists that an Xcalibur analysis generated using the Full Scan Method. Make sure to use an AcquireX template method or that your MS instrument method meets the following criteria:",
            "list": [
              "(If applicable) Adds the Targeted Mass filter between the MS and ddMS2 scan nodes.",
              "(If applicable) Adds the Targeted Mass Exclusion filter between the MS and ddMS2 scan nodes.",
              "Selects the AcquireX check boxes for the appropriate filters."
            ]
          },
          "errorMessage": "The MSn Template Method is not present in the specified path."
        }
      ]
    }
  ],


  "modeInfo": {
    "method": [
      {
        "name": "0",
        "format": "{blankMethod}"
      },
      {
        "name": "3",
        "format": "{msnMethod}_Excl_Incl_{idString}"
      }
    ],
    "append": [
      {
        "name": "0",
        "boolValue": true
      },
      {
        "name": "3",
        "idNumber": "min:2",
        "boolValue": false
      }
    ],
    "block": [
      {
        "name": "0",
        "idValue": "1"
      },
      {
        "name": "3",
        "idValue": "{idNumber}+1"
      }
    ],
    "sampleId": [
      {
        "name": "0",
        "idValue": "1"
      },
      {
        "name": "3",
        "idValue": "ID {idNumber}"
      }
    ],
    "actions": [
      {
        "name": "0",
        "preValue": "",
        "postValue": ""
      },
      {
        "name": "1",
        "isMatrix": true,
        "preValue": "",
        "postValue": "PostAcquisitionLpeExcAction"
      },
      {
        "name": "2",
        "preValue": "",
        "postValue": "PostAcquisitionLpeIncAction"
      },
      {
        "name": "3",
        "preValue": "DefaultPreAcquisitionAction",
        "postValue": "PostAcquisitionReduceAction"
      }
    ],
    "massListName": [
      {
        "name": "0",
        "ApiValue": ""
      },
      {
        "name": "1",
        "isMatrix": true,
        "ApiValue": "GetName"
      },
      {
        "name": "2",
        "ApiValue": "GetName"
      },
      {
        "name": "3",
        "ApiValue": "GetName,SampleId"
      }
    ],
    "massListNextName": [
      {
        "name": "0",
        "ApiValue": ""
      },
      {
        "name": "3",
        "ApiValue": "GetNextName,SampleId"
      }
    ],
    "name": "DeepScan"
  },
  "version": "1.0"
}