MetaXtract/config.yml at main · Rappsilber-Laboratory/MetaXtract · GitHub

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io:
  input:
    - "C:/Users/yynk1/Desktop/thermo_reader/github/MetaXtract/data/MS2_MS1_orbitrap.raw"
    - "C:/Users/yynk1/Desktop/thermo_reader/github/MetaXtract/data/small.raw"
    - "C:/Users/yynk1/Desktop/thermo_reader/data/B240103_02_Astral_ZC_QC_51_Hela.raw"
  output_dir: "C:/Users/yynk1/Desktop/thermo_reader/github/MetaXtract/output/cli/"

outputs:
  file_based_details: true
  ms_method: true
  lc_method: true
  ms2_peaklist_export: true
  ms1_peaklist_export: true
  ms2_technical_details_export: false
  ms1_technical_details_export: false

visualisation:
  enabled: true
  export_format: "html"

multi_comparison:
  enabled: true
  samples: [1, 2]       # 1-based indices into io.input (file1 + file3)

scan_header:
  MS1:
    select_all: true
    columns:
      Ion Injection Time (ms): true
      Total Number of Peaks: true
      Total Ion Current: false
      Scan Start Time (min): false
      Base Peak Intensity: false
      Base Peak m/z: false
      Scan Mode: false
      thermo_Multi Inject Info: false
      thermo_Multiple Injection: false

  MS2:
    select_all: true
    columns:
      Total Ion Current: true
      Total Number of Peaks: true
      thermo_Number of Channels: false
      Sampling Frequency: false
      Collision Energy: false
      Scan Start Time (min): false
      Scan Window m/z Range: false
      Scan Mode: false
      Selected Ion Intensity: false
      Filter String: false
      thermo_AGC: false
      thermo_Micro Scan Count: false
      Ion Injection Time (ms): false
      thermo_Elapsed Scan Time (sec): false
      Dissociation Method: false
      Mass Analyzer Type: false
      Detector Type: false
      Base Peak m/z: false
      thermo_Average Scan by Inst: false
      thermo_Orbitrap Resolution: false
      thermo_API Process Delay: true
      thermo_Dependency Type: false
      thermo_Multi Inject Info: false
      Base Peak Intensity: false
      thermo_Master Scan Number: false
      Experimental Precursor Monoisotopic m/z: false
      Charge State: false
      Normalized Collision Energy (%): false
      Collision Energy (eV): false
      Isolation Window Width (m/z): false
      thermo_Access ID: false
      thermo_Conversion Parameter I: false
      thermo_Conversion Parameter A: false
      thermo_Conversion Parameter B: false
      thermo_Conversion Parameter C: false
      thermo_Conversion Parameter D: false
      thermo_Conversion Parameter E: false
      thermo_Temperature Comp. (ppm): false
      thermo_RF Comp. (ppm): false
      thermo_Space Charge Comp. (ppm): false
      thermo_Resolution Comp. (ppm): false
      thermo_Number of LM Found: false
      thermo_LM Correction (ppm): false
      thermo_RawOvFtT: false
      thermo_Injection t0: false
      thermo_Reagent Ion Injection Time (ms): false
      thermo_FAIMS Voltage On: false
      FAIMS Compensation Voltage: false