Q4SRMcmd usage - PNNL-Comp-Mass-Spec/Q4SRM GitHub Wiki
Q4SRMcmd is the command-line 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
- 64-bit OS: Thermo .RAW files are read using Thermo's RawFileReader library, more information available at Planet Orbitrap
- 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
Syntax & Usage
Q4SRMcmd.exe -raw file.raw [other options]
Full usage information:
-?, -help Show this help screen
-raw Required. Path to .raw file, or directory containing .raw
files
-recurse If raw file path is a folder, whether to find .raw files
in subfolders (Default: False)
-filter If raw file path is a folder, a file filter string
(supports '*' wildcard) (Default: *.raw)
-method For mzML files, the method file path
-t Peak area threshold for a compound to be considered
"passing" (Default: 10000, Min: 0)
-m Time (in minutes) that a peak must be away from the edge
of the target window for it to be considered "passing"
(Default: 0.5, Min: 0)
-ec Threshold (in minutes) for elution concurrence of the
transition peaks for the same compound; smaller is
stricter. (Default: 0.5, Min: 0)
-sn Threshold for the Signal-to-Noise heuristic; larger is
stricter; value is calculated as max intensity / median
intensity (Default: 10, Min: 1)
-tpc A TSV file with compound and threshold columns, for
custom thresholds for the specified compounds
(Default: "")
-out Folder where the result files should be written (default:
written to same folder as .raw)
-threads Maximum number of threads to use (files processed
simultaneously), '0' for automatic (Default: 0, Min: 0)
-ow, -overwrite If specified, all files will be processed, even if
existing output was created with the same settings.
(Default: False)
-outThresholds If specified, creates a per-compound thresholds file for
all compounds that pass the minimum threshold (averaged
across processed files) (Default: False)
-outThresholdsPct The percentage of the averaged total intensity that
should be output as the threshold (Default: 0.5,
Min: 0.01, Max: 0.99)
-outThresholdsPath The path where the output threshold file should be
created
-summaryPath Path where processing summary tsv should be written.
Default is [out folder/raw file folder]\HeavySummary.tsv
-img Format for the saved total intensity vs. time plot
(Default: PNG (or 0))
Possible values are:
0 or 'PNG'
1 or 'PDF'
2 or 'SVG'
3 or 'JPEG'
-1 or 'NoImageExport': Don't save an image
-all If specified, metrics are computed for all compounds in
the file (not just heavy compounds) (Default: False)