﻿<?xml version="1.0" encoding="utf-8"?>
<srm_settings format_version="19.1" software_version="Skyline (64-bit) 19.1.0.193">
  <settings_summary name="Default">
    <peptide_settings>
      <enzyme name="Trypsin" cut="KR" no_cut="P" sense="C" />
      <digest_settings max_missed_cleavages="2" />
      <peptide_prediction use_measured_rts="false" measured_rt_window="5" use_spectral_library_drift_times="false" spectral_library_drift_times_peak_width_calc_type="resolving_power" spectral_library_drift_times_resolving_power="0" spectral_library_drift_times_width_at_dt_zero="0" spectral_library_drift_times_width_at_dt_max="0">
        <predict_retention_time name="iRT" time_window="10">
          <irt_calculator name="iRT" database_path="D:\MS_DATA_HFX\iRT2to30.irtdb" />
        </predict_retention_time>
      </peptide_prediction>
      <peptide_filter start="25" min_length="8" max_length="25" auto_select="true">
        <peptide_exclusions />
      </peptide_filter>
      <peptide_libraries pick="library" />
      <peptide_modifications max_variable_mods="3" max_neutral_losses="1" internal_standard="none">
        <static_modifications>
          <static_modification name="Carbamidomethyl (C)" aminoacid="C" formula="H3C2NO" unimod_id="4" short_name="CAM" />
          <static_modification name="Deamidated (NQ)" aminoacid="N, Q" variable="true" formula="O - HN" unimod_id="7" short_name="Dea" />
          <static_modification name="Oxidation (M)" aminoacid="M" variable="true" formula="O" unimod_id="35" short_name="Oxi">
            <potential_loss formula="H4COS" massdiff_monoisotopic="63.998285" massdiff_average="64.10701" />
          </static_modification>
        </static_modifications>
        <heavy_modifications />
      </peptide_modifications>
      <quantification weighting="none" fit="none" normalization="none" ms_level="2" units="pmol" />
    </peptide_settings>
    <transition_settings>
      <transition_prediction precursor_mass_type="Monoisotopic" fragment_mass_type="Monoisotopic" optimize_by="None">
        <predict_collision_energy name="Thermo TSQ Ultra" step_size="1" step_count="5">
          <regression_ce charge="2" slope="0.036" intercept="0.954" />
          <regression_ce charge="3" slope="0.037" intercept="3.525" />
        </predict_collision_energy>
      </transition_prediction>
      <transition_filter precursor_charges="2" product_charges="1" precursor_adducts="[M-3H],[M-2H],[M-H],[M-],[M+H],[M+],[M+2H],[M+3H]" product_adducts="[M-3],[M-2],[M-],[M+],[M+2],[M+3]" fragment_types="p,b,y" small_molecule_fragment_types="f,p" fragment_range_first="(m/z &gt; precursor) - 1" fragment_range_last="last ion - 3" precursor_mz_window="0" auto_select="true">
        <measured_ion name="TMT-131" ion_formula="C4C'4H16N'" mass_monoisotopic="131.1387288096" mass_average="131.1839682496" charge="1" optional="true" />
      </transition_filter>
      <transition_libraries ion_match_tolerance="0.05" min_ion_count="0" ion_count="6" pick_from="none" />
      <transition_integration integrate_all="true" />
      <transition_instrument dynamic_min="true" min_mz="350" max_mz="1550" mz_match_tolerance="0.02" />
      <transition_full_scan acquisition_method="DDA" product_mass_analyzer="orbitrap" product_res="60000" product_res_mz="400" precursor_isotopes="Count" precursor_isotope_filter="4" precursor_mass_analyzer="orbitrap" precursor_res="60000" precursor_res_mz="400" selective_extraction="true" retention_time_filter_type="scheduling_windows" retention_time_filter_length="5">
        <isotope_enrichments name="Default">
          <atom_percent_enrichment symbol="H'">0.98</atom_percent_enrichment>
          <atom_percent_enrichment symbol="C'">0.995</atom_percent_enrichment>
          <atom_percent_enrichment symbol="N'">0.995</atom_percent_enrichment>
          <atom_percent_enrichment symbol="O&quot;">0.99</atom_percent_enrichment>
          <atom_percent_enrichment symbol="O'">0.99</atom_percent_enrichment>
        </isotope_enrichments>
      </transition_full_scan>
    </transition_settings>
    <data_settings document_guid="1b8273e2-a425-49e9-8ef6-248892a48db5">
      <annotation name="Hela digest (ug)" targets="replicate" type="value_list">
        <value>1</value>
        <value>2</value>
      </annotation>
      <annotation name="PPRT (fmol)" targets="replicate" type="value_list">
        <value>250</value>
        <value>500</value>
        <value>1000</value>
      </annotation>
    </data_settings>
    <measured_results time_normal_area="true">
      <replicate name="20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_1">
        <sample_file id="_20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_1_f0" file_path="D:\MS_DATA_HFX\20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_1.raw" sample_name="20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_1" acquired_time="2021-10-18T13:03:24" modified_time="2021-10-18T14:18:26" tic_area="292105715712" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_2">
        <sample_file id="_20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_2_f0" file_path="D:\MS_DATA_HFX\20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_2.raw" sample_name="20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_2" acquired_time="2021-10-18T20:05:46" modified_time="2021-10-18T21:20:48" tic_area="398748418048" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_1">
        <sample_file id="_20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_1_f0" file_path="D:\MS_DATA_HFX\20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_1.raw" sample_name="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_1" acquired_time="2021-10-19T10:43:56" modified_time="2021-10-19T11:58:58" tic_area="659174719488" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_2">
        <sample_file id="_20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_2_f0" file_path="D:\MS_DATA_HFX\20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_2.raw" sample_name="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_2" acquired_time="2021-10-19T12:32:56" modified_time="2021-10-19T13:47:58" tic_area="620498452480" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_3">
        <sample_file id="_20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_3_f0" file_path="D:\MS_DATA_HFX\20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_3.raw" sample_name="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_3" acquired_time="2021-10-19T18:20:57" modified_time="2021-10-19T19:35:59" tic_area="740800397312" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_1">
        <sample_file id="_20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_1_f0" file_path="D:\MS_DATA_HFX\20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_1.raw" sample_name="20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_1" acquired_time="2021-10-21T13:30:37" modified_time="2021-10-21T14:45:39" tic_area="978892161024" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_2">
        <sample_file id="_20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_2_f0" file_path="D:\MS_DATA_HFX\20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_2.raw" sample_name="20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_2" acquired_time="2021-10-21T15:20:27" modified_time="2021-10-21T16:35:29" tic_area="1010311299072" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20220126_FPL_HFX_HeLaQC_500ng_1">
        <sample_file id="_20220126_FPL_HFX_HeLaQC_500ng_1_f0" file_path="D:\MS_DATA_HFX\20220126_FPL_HFX_HeLaQC_500ng_1.raw" sample_name="20220126_FPL_HFX_HeLaQC_500ng_1" acquired_time="2022-01-26T18:09:41" modified_time="2022-01-26T19:24:43" tic_area="998329090048" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
      <replicate name="20220329_HFX_HelaQC_500ng_1">
        <sample_file id="_20220329_HFX_HelaQC_500ng_1_f0" file_path="D:\MS_DATA_HFX\20220329_HFX_HelaQC_500ng_1.raw" sample_name="20220329_HFX_HelaQC_500ng_1" acquired_time="2022-03-29T23:56:50" modified_time="2022-03-30T01:11:52" tic_area="654180155392" ion_mobility_type="compensation_V">
          <instrument_info_list>
            <instrument_info>
              <model>Q Exactive</model>
              <ionsource>nanoelectrospray</ionsource>
              <analyzer>quadrupole/orbitrap</analyzer>
              <detector>inductive detector</detector>
            </instrument_info>
          </instrument_info_list>
        </sample_file>
      </replicate>
    </measured_results>
  </settings_summary>
  <peptide_list label_name="iRT Biognoys" websearch_status="X#Upeptides1" auto_manage_children="false">
    <peptide standard_type="iRT" sequence="LGGNEQVTR" modified_sequence="LGGNEQVTR" calc_neutral_pep_mass="972.498858" num_missed_cleavages="0" rt_calculator_score="2.1316282072803006E-14" predicted_retention_time="20" avg_measured_retention_time="19.8273735">
      <peptide_results>
        <peptide_result replicate="20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_1" peak_count_ratio="0.8" retention_time="20.0112381" predicted_retention_time="20.12" />
        <peptide_result replicate="20211018_FPL_HFX_EDDCLC_HeLaQC_500ng_2" peak_count_ratio="0.7" retention_time="19.9356136" predicted_retention_time="20.09" />
        <peptide_result replicate="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_1" peak_count_ratio="0.8" retention_time="20.2152233" predicted_retention_time="20.6" />
        <peptide_result replicate="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_2" peak_count_ratio="0.9" retention_time="20.3269577" predicted_retention_time="20.63" />
        <peptide_result replicate="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_3" peak_count_ratio="0.7" retention_time="19.7462864" predicted_retention_time="20.14" />
        <peptide_result replicate="20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_1" peak_count_ratio="0.4" retention_time="20.6968956" predicted_retention_time="20.97" />
        <peptide_result replicate="20211021_FPL_HFX_EDDCLC_HeLaQC_500ng_2" peak_count_ratio="0.9" retention_time="20.7060051" predicted_retention_time="20.92" />
        <peptide_result replicate="20220126_FPL_HFX_HeLaQC_500ng_1" peak_count_ratio="0.9" retention_time="18.1173153" predicted_retention_time="18.01" />
        <peptide_result replicate="20220329_HFX_HelaQC_500ng_1" peak_count_ratio="0.8" retention_time="18.690834" predicted_retention_time="18.56" />
      </peptide_results>
      <precursor charge="2" calc_neutral_mass="972.498858" precursor_mz="487.256705" auto_manage_children="false" collision_energy="18.495241" modified_sequence="LGGNEQVTR">
        <precursor_results>
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          <precursor_peak replicate="20211019_FPL_HFX_EDDCLC_HeLaQC_500ng_1" peak_count_ratio="0.8" retention_time="20.2152233" start_time="20.0032234" end_time="20.403223" fwhm="0.0748354" area="1.700109E+10" background="10032148" height="2.11346586E+09" mass_error_ppm="-0.175651178" truncated="0" identified="false" isotope_dotp="0.997639954" user_set="TRUE" />
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