Q4SRMui usage - PNNL-Comp-Mass-Spec/Q4SRM GitHub Wiki

Q4SRMui is the graphical user interface version of Q4SRM.

Primary Inputs

• Thermo .RAW SRM file, mzML file, or folder containing multiple such files (tested on files from TSQ Vantage and TSQ Altis)
  • 64-bit OS: Thermo .RAW files are read using Thermo's RawFileReader library, more information available at Planet Orbitrap
    • A license document for use of this library is included in the source code folder 'Lib', and also will be included in the binary download/installer packages.
  • 32-bit OS: Thermo .RAW files are read using Thermo's MSFileReader library, which must be previously installed
  • NOTE: Currently does not support mzML chromatograms; if creating the mzML file with ProteoWizard/msconvert, specify the '--srmAsSpectra' option
• If reading mzML file(s): a CSV/TSV file with the following columns:
  • 'Compound Name': Name of the compound, also used to determine heavy compounds by finding "heavy" or "hvy" in the compound name
  • 'Precursor (m/z)': Precursor m/z
  • 'Product (m/z)': Product/transition m/z
  • 'Start Time (min)': Elution window start time
  • 'End Time (min)': Elution window end time
• Metrics controls
  • (Optional) A TSV file with compound and threshold columns, for custom thresholds for the specified compounds
  • A summed intensity minimum passing value (group of transitions); default is 10000
  • A minimum distance (in minutes) that a 'peak apex' must be from the edges of its elution window (single transition); default is 0.5 (minutes)
  • A maximum distance (in minutes) from the earliest 'peak apex' to the latest 'peak apex' in the compound (group of transitions); default is 0.5 (minutes)
  • A minimum difference of the max intensity point vs. the median of intensity (single transition); default is 10

Outputs

• A TSV file with compound and transition information, and values signifying whether the compound/transitions passed or failed a metric
• An image file (default is PNG format, can also be JPEG, SVG, or PDF) showing a scatterplot of compounds with marks showing if they failed certain metrics, with axes of 'max intensity time' and 'max intensity'.
• A PDF that includes the scatterplot mentioned above, and also showing the chromatograms of each transition in each group.
• HeavySummary.tsv, which is a short summary file listing total heavy peptides and the number that passed the metrics for each dataset

Usage

Double-click Q4SRMui.exe to run the program.

Screenshots

Data processing

Viewing result plot interactively