This manual describes all of the commandline functionality available in msInspect. To access any of these commands, type the java command that you use to start msInspect (e.g., 'java -Xmx1G -jar viewerApp.jar'), followed by ' --<command>' (the name of the command), followed by any arguments. Argument names are not case-sensitive.
To access a graphical interface for entering arguments for any command (with graphical help for choosing files, etc.), use the command '--interactive', followed by the name of the command you wish to execute.
All commandline functions may also be accessed through the msInspect graphical user interface using the 'Run Command' menu item under the 'File' menu.
For more information about msInspect, as well as help with the graphical user interface, go to the official msInspect webpage at http://proteomics.fhcrc.org/CPL/msinspect.html
Required arguments for each command are indicated in bold text in the arguments table. In some cases, additional arguments may be required if certain arguments are specified. Some commands have 'advanced' arguments, which are never required; it is not recommended to specify values for those arguments unless you know exactly what you're doing.
In addition to the arguments discussed below for each particular command, msInspect accepts two special arguments for all commands:
This document automatically generated on August 12, 2009 by msInspect revision 382. If you are running a newer version of msInspect, you may generate the current version of this document with the 'usermanual' command.
GeneralGeneral msInspect tools | ||||||||||||||||||||||||||||||||||||||||||||||||
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QuantitationTools related to labeled and unlabeled quantitation | ||||||||||||||||||||||||||||||||||||||||||||||||
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AlignmentTools for aligning multiple runs, including Peptide Arrays | ||||||||||||||||||||||||||||||||||||||||||||||||
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MS/MSTools related to tandem mass spectrometry and the file formats used for tandem MS | ||||||||||||||||||||||||||||||||||||||||||||||||
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AMTAccurate Mass and Time analysis tools | ||||||||||||||||||||||||||||||||||||||||||||||||
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MRMThe MRMer tools for Multiple Reaction Monitoring | ||||||||||||||||||||||||||||||||||||||||||||||||
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Quality AssuranceQuality Assurance tools | ||||||||||||||||||||||||||||||||||||||||||||||||
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--analyzehydroalg --fasta=<filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| fasta | <filepath> | null | fasta file containing database to digest |
--calibratefeaturemasses [--initialfilterppm=<integer>] [--maxpairs=<integer>] [--out=<filepath>] [--outdir=<filepath>] [--partitions=<integer>] [--showcharts=<true | false>] [--theoreticalwavelength=<decimal>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input feature file(s) |
| initialfilterppm | <integer> | 0 | Initial ppm value used as a pre-calibration cutoff. Features deviating from theoretical clusters (BEFORE calibration) will be filtered out during calibration. However, those features WILL appear in the recalibrated featureset, with corrected masses. Default = no filter |
| maxpairs | <integer> | 500000 | Maximum number of mass pairs to be considered (higher numbers may increase accuracy, but will take much longer) |
| out | <filepath> | null | Output file (for single input files) |
| outdir | <filepath> | null | Output directory (for multiple input files) |
| partitions | <integer> | 1 | Number of partitions to break the file into (higher numbers are more expensive) |
| showcharts | <true | false> | false | Show charts |
| theoreticalwavelength | <decimal> | 1.000476 | Theoretical mass cluster wavelength |
--calibratemzxmlmasses [--features=<filepath>] [--featuresdir=<filepath>] [--initialfilterppm=<integer>] [--offset=<decimal>] [--onlyms2precursormasses=<true | false>] [--out=<filepath>] [--outdir=<filepath>] [--outfeatures=<filepath>] [--partitions=<integer>] [--scanchargefeatures=<filepath>] [--scanchargefeaturesdir=<filepath>] [--wavelength=<decimal>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input mzXML file(s) |
| features | <filepath> | null | Feature file to use in recalibration |
| featuresdir | <filepath> | null | Directory of feature files to use in recalibration |
| initialfilterppm | <integer> | 0 | Initial ppm value used as a pre-calibration cutoff. Features deviating from theoretical clusters (BEFORE calibration) will be filtered out during calibration. However, those features WILL appear in the recalibrated featureset, with corrected masses. Default = no filter |
| offset | <decimal> | null | Offset |
| onlyms2precursormasses | <true | false> | false | Only recalibrate MS2 precursor masses |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for multiple inputs) |
| outfeatures | <filepath> | null | Output recalibrated feature file |
| partitions | <integer> | 1 | Number of partitions by scan |
| scanchargefeatures | <filepath> | null | Feature file to use to assign charges to MS/MS scans |
| scanchargefeaturesdir | <filepath> | null | Directory of feature files to use for determining charge states |
| wavelength | <decimal> | null | Wavelength |
--consensusfeaturefile [--minfeatureruns=<integer>] [--out=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | input feature files |
| minfeatureruns | <integer> | 2 | minimun number of runs a feature must appear in |
| out | <filepath> | null | output file |
--convertfeaturefile --outformat=<msinspect | pepxml | specarraytsv | apml | hardklor | multimsinspect> [--dumpwindow=<true | false>] [--fasta=<filepath>] [--forcepeptideprophetvalue=<decimal>] [--informat=<msinspect | pepxml | specarraytsv | apml | hardklor | multimsinspect>] [--mzxml=<filepath>] [--out=<filepath>] [--outdir=<filepath>] [--specarrayversion=<1.0 | 1.2>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input feature file(s) |
| outformat | <msinspect | pepxml | specarraytsv | apml | hardklor | multimsinspect> | null | output file format |
| dumpwindow | <true | false> | null | (no details provided) |
| fasta | <filepath> | null | FASTA filepath to include in pepXML file (for outformat=pepxml only) |
| forcepeptideprophetvalue | <decimal> | null | Set the PeptideProphet probability of all features to this (for pepxml output) |
| informat | <msinspect | pepxml | specarraytsv | apml | hardklor | multimsinspect> | msinspect | input file format. To force loading of an ambiguous file as a specific file type |
| mzxml | <filepath> | null | (no details provided) |
| out | <filepath> | null | output file |
| outdir | <filepath> | null | output directory (for multiple inputs) |
| specarrayversion | <1.0 | 1.2> | null | specArray version, for specArray conversions (default 1.2) |
--createindex <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | A series of feature files to index |
--deconvolute [--deltamass=<mass value>da|ppm] [--deltatime=<decimal>] [--heavytagweight=<decimal>] [--intensitytype=<total | max | recalculated>] [--labeledresidue=<value>] [--lighttagweight=<decimal>] [--masswindow=<decimal>] [--maxlabelcount=<integer>] [--msfile=<filepath>] [--out=<filepath>] [--outdir=<filepath>] [--quant=<true | false>] [--scanwindow=<integer>] [--showcharts=<true | false>] [--sumintensities=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input File(s) |
| deltamass | <mass value>da|ppm | 0.2da | Mass Tolerance |
| deltatime | <decimal> | 10.0 | Time Tolerance |
| heavytagweight | <decimal> | -1.0 | Heavy tag weight |
| intensitytype | <total | max | recalculated> | null | Intensity type |
| labeledresidue | <value> | null | Labeled Residue |
| lighttagweight | <decimal> | -1.0 | Light tag weight |
| masswindow | <decimal> | 0.4 | Mass Window |
| maxlabelcount | <integer> | 3 | Maximum Label Count |
| msfile | <filepath> | null | mzXml File |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for multiple files) |
| quant | <true | false> | false | Quantitate |
| scanwindow | <integer> | 6 | Scan Window |
| showcharts | <true | false> | false | Show Charts |
| sumintensities | <true | false> | true | If true, deconvoluted feature intensities reflect the sum of all component feature intensities. If false, intensity of most-intense feature is kept. |
--detectadducts [--deltamass=<mass value>da|ppm] [--masswavelength=<decimal>] [--maxrelativedaltons=<integer>] [--maxrelativeseconds=<integer>] [--minrelativedaltons=<integer>] [--minrelativeseconds=<integer>] [--scanwindowsize=<integer>] [--secondsincrement=<integer>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Feature File of features to interrogate |
| deltamass | <mass value>da|ppm | 10.0ppm | Mass tolerance around each Dalton increment |
| masswavelength | <decimal> | 1.000476 | Mass wavelength |
| maxrelativedaltons | <integer> | 100 | Maximum Daltons, relative to original mass |
| maxrelativeseconds | <integer> | 60 | (no details provided) |
| minrelativedaltons | <integer> | 0 | Minimum Daltons, relative to original mass |
| minrelativeseconds | <integer> | -60 | (no details provided) |
| scanwindowsize | <integer> | 1 | Size of the scan window (including identity scan) |
| secondsincrement | <integer> | 1 | (no details provided) |
--dumpwindow2d --features=<filepath> [--leadingpeaks=<integer>] [--leadingscans=<integer>] [--out=<filepath>] [--trailingpeaks=<integer>] [--trailingscans=<integer>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | mzXML File |
| features | <filepath> | null | Feature file |
| leadingpeaks | <integer> | 1 | Leading Peaks |
| leadingscans | <integer> | 4 | Leading Scans |
| out | <filepath> | null | output file |
| trailingpeaks | <integer> | 1 | Leading Peaks |
| trailingscans | <integer> | 4 | Trailing Scans |
----filter [--out=filename] [--outdir=directory] [--minMz=float] [--maxMz=float] [--minMass=float] [--maxMass=float] [--minPeaks=int] [--maxPeaks=int] [--minCharge=int] [--maxCharge=int] [--maxKL=float] [--minIntensity=float] [--minTotalIntensity=float] [--minTime=float] [--maxTime=float] [--scanFirst=int] [scanLast=int] [--minScans=int] [--minpprophet=float] [--maxmassdeviationppm] [--outputpepxml] [--maxsumsquaresdist=float] [--minsearchscore=float] [--maxsearchscore=float] [--searchscorename=string] [--accmz=true|false] [--outformat=msinspect|pepxml] featurefile [featurefile] [featurefile] ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input feature file(s) |
| accmz | <true | false> | null | Accurate m/z only? |
| maxcharge | <integer> | null | Maximum charge |
| maxkl | <decimal> | null | Maximum K/L score |
| maxmass | <decimal> | null | Maximum mass |
| maxmassdeviationppm | <integer> | null | Maximum deviation from nearest theoretical mass cluster, in PPM |
| maxmz | <decimal> | null | Maximum M/Z value |
| maxpeaks | <integer> | null | Maximum number of peaks |
| maxsearchscore | <decimal> | 3.4028234663852886E38 | Maximum search score |
| maxsumsquaresdist | <decimal> | null | Maximum sum-squares distance score |
| maxtime | <decimal> | null | Maximum time |
| mincharge | <integer> | null | Minimum charge |
| minintensity | <decimal> | null | Minimum intensity |
| minmass | <decimal> | null | Minimum mass |
| minmz | <decimal> | null | Minimum M/Z value |
| minpeaks | <integer> | null | Minimum number of peaks |
| minpprophet | <decimal> | null | Minimum PeptideProphet score |
| minscans | <integer> | null | Minimum number of scans covered |
| minsearchscore | <decimal> | 1.401298464324817E-45 | Minimum search score |
| mintime | <decimal> | null | Minimum time |
| mintotalintensity | <decimal> | null | Minimum total intensity |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for filtering multiple files) |
| outformat | <msinspect | pepxml> | null | msinspect: msInspect .tsv format pepxml: pepXML format |
| scanfirst | <integer> | null | Minimum scan number |
| scanlast | <integer> | null | Maximum scan number |
| searchscorename | <value> | null | Search score name (for minsearchscore or maxsearchscore) |
----findPeptides [--dumpWindow=windowSize] [--out=outfilename] [--outdir=outdirpath] [--start=startScan] [--count=scanCount] [--minMz=minMzVal] [--maxMz=maxMzVal] [--strategy=className] [--noAccurateMass] [--accurateMassScans=<int>] [--walkSmoothed] mzxmlfile
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input mzXML file(s) |
| count | <integer> | 2147483647 | Number of scans to search |
| maxmz | <decimal> | null | Maximum M/Z Value (default: the maximum m/z value in the file) |
| minmz | <decimal> | null | Minimum M/Z Value (default: the minimum m/z value in the file) |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for finding features in multiple files) |
| start | <integer> | 1 | Minimum scan number |
| strategy | <value> | null | Class name of a feature-finding strategy implementation |
| Argument | Usage | Default | Description |
|---|---|---|---|
| accuratemassscans | <integer> | 3 | When attempting to improve mass-accuracy, consider a neighborhood of <int> scans |
| dumpwindow | <integer> | 0 | Number of scans around each feature to dump to the file |
| maxkl | <decimal> | 3.0 | Maximum K/L quality score |
| minpeaks | <integer> | 2 | Maximum K/L quality score |
| noaccuratemass | <true | false> | false | Do NOT attempt mass-accuracy adjustment after default peak finding strategy (by default, adjustment is done) |
| nofilter | <true | false> | false | Perform no filtering on identified features. By default, only features with at least 2 peaks and a K/L score less than 3.0 are kept. (overrides maxkl and minpeaks) |
| plotstats | <true | false> | false | Plot statistics related to feature-finding |
| walksmoothed | <true | false> | false | When calculating feature extents, use smoothed rather than wavelet-transformed spectra) |
--massaccuracy --ms1features=<filepath> --ms2features=<filepath> --mzxml=<filepath> [--deltamass=<mass value>da|ppm] [--deltatime=<decimal>] [--minpprophet=<decimal>]
| Argument | Usage | Default | Description |
|---|---|---|---|
| ms1features | <filepath> | null | MS1 features |
| ms2features | <filepath> | null | MS2 features |
| mzxml | <filepath> | null | mzXML file |
| deltamass | <mass value>da|ppm | 5.0ppm | Maximum mass difference between matched features (in units of da [Daltons] or ppm [parts per million] |
| deltatime | <decimal> | null | Maximum time between matched features |
| minpprophet | <decimal> | null | Minimum PeptideProphet score |
--matchfeatures --ms1features=<filepath> [--align=<true | false>] [--amtdbtoexclude=<filepath>] [--deltamass=<mass value>da|ppm] [--deltascan=<integer>] [--deltatime=<decimal>] [--fasta=<filepath>] [--matchonhydro=<true | false>] [--minpprophet=<decimal>] [--mode=<ms1ms2 | ms1ms2dir>] [--modifications=<residue><massdiff>[V][,...]] [--ms2dir=<filepath>] [--ms2features=<filepath>] [--mzxml=<filepath>] [--out=<filepath>] [--outallms2marked=<filepath>] [--outunmatchedms2=<filepath>] [--showcharts=<true | false>] [--stripmultiplems2=<true | false>] [--writeunmatched=<true | false>]
| Argument | Usage | Default | Description |
|---|---|---|---|
| ms1features | <filepath> | null | MS1 feature file |
| align | <true | false> | false | align all MS2 runs to the MS1 run being matched |
| amtdbtoexclude | <filepath> | null | an AMT database whose peptides should be excluded from protein matching |
| deltamass | <mass value>da|ppm | 5.0ppm | Maximum mass difference between matched features (in units of da [Daltons] or ppm [parts per million] |
| deltascan | <integer> | 3 | Maximum number of scans between matched features |
| deltatime | <decimal> | 20.0 | Maximum time between matched features |
| fasta | <filepath> | null | Fasta database for matching |
| matchonhydro | <true | false> | false | under the hood, perform matching based on hydrophobicity |
| minpprophet | <decimal> | 0.0 | Minimum PeptideProphet score |
| mode | <ms1ms2 | ms1ms2dir> | ms1ms2 | Mode of operation, default ms1ms2 |
| modifications | <residue><massdiff>[V][,...] | null | a list of modifications to use when creating features to represent peptide sequences |
| ms2dir | <filepath> | null | MS2 feature file directory |
| ms2features | <filepath> | null | MS2 feature file (usually pepXml) |
| mzxml | <filepath> | null | mzXML file |
| out | <filepath> | null | Output File |
| outallms2marked | <filepath> | null | Output File for all MS2, with unmatched having 'unmatched' in description |
| outunmatchedms2 | <filepath> | null | Output File for unmatched MS2 |
| showcharts | <true | false> | false | show useful charts created when matching |
| stripmultiplems2 | <true | false> | true | Strip subsequent MS2 identifications for the same peptide out of the file when matching |
| writeunmatched | <true | false> | true | Write out unmatched features |
--modelpeptide --daltons=<decimal>
| Argument | Usage | Default | Description |
|---|---|---|---|
| daltons | <decimal> | null | peptide mass |
--plotfeatureattributes --attribute=<pprophet | fracdeltamass | intensity | time | ratio | lightarea | charge | sumsquaresdist | kl | peaks | searchscore | fval | mass | mz> [--attribute2=<pprophet | fracdeltamass | intensity | time | ratio | lightarea | charge | sumsquaresdist | kl | peaks | searchscore | fval | mass | mz>] [--breaks=<integer>] [--logmode=<true | false>] [--out=<filepath>] [--outdir=<filepath>] [--plottype=<histogram | scatter | boxplot>] [--searchscore=<value>] [--showcharts=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Feature file(s) |
| attribute | <pprophet | fracdeltamass | intensity | time | ratio | lightarea | charge | sumsquaresdist | kl | peaks | searchscore | fval | mass | mz> | null | pprophet: PeptideProphet probabilities fracdeltamass: Fractional Delta Mass intensity: (Maximum) Intensity time: Retention Time ratio: Ratio lightarea: Light Area (quantitated peptides) charge: Charge sumsquaresdist: Sum-of-squares distance kl: K/L Score peaks: Number of peaks searchscore: Search score (must provide score name) fval: fval mass: mass mz: mz |
| attribute2 | <pprophet | fracdeltamass | intensity | time | ratio | lightarea | charge | sumsquaresdist | kl | peaks | searchscore | fval | mass | mz> | null | pprophet: PeptideProphet probabilities fracdeltamass: Fractional Delta Mass intensity: (Maximum) Intensity time: Retention Time ratio: Ratio lightarea: Light Area (quantitated peptides) charge: Charge sumsquaresdist: Sum-of-squares distance kl: K/L Score peaks: Number of peaks searchscore: Search score (must provide score name) fval: fval mass: mass mz: mz |
| breaks | <integer> | 100 | Number of breaks |
| logmode | <true | false> | false | Log mode |
| out | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
| plottype | <histogram | scatter | boxplot> | null | histogram: Histogram scatter: Scatterplot boxplot: Box and whiskers plot |
| searchscore | <value> | null | Search score name (for searchscore mode) |
| showcharts | <true | false> | true | Show charts? |
--plotmasscalibration [--indir=<filepath>] [--out=<filepath>] [--outboxwhiskersplot=<filepath>] [--ppmline=<decimal>] [--showcharts=<true | false>] [--theoreticalwavelength=<decimal>] [--usemz=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| indir | <filepath> | null | Directory containing input files, all of which will be used |
| out | <filepath> | null | (no details provided) |
| outboxwhiskersplot | <filepath> | null | File to save box-and-whiskers plot to |
| ppmline | <decimal> | -1.0 | PPM cutoff to display on plot (default none) |
| showcharts | <true | false> | true | Show charts? |
| theoreticalwavelength | <decimal> | 1.000476 | Theoretical mass cluster wavelength |
| usemz | <true | false> | false | Plot m/z instead of mass |
--plotms1ms2scancounts [--mzxmldir=<filepath>] [--out=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| mzxmldir | <filepath> | null | directory of mzXml Files |
| out | <filepath> | null | (no details provided) |
--runcommandfile <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | Macro file to run |
--saveimage [--includetic=<true | false>] [--maxheight=<integer>] [--maxwidth=<integer>] [--out=<filepath>] [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input mzXml file(s) |
| includetic | <true | false> | false | Include Total Ion Chromatogram? |
| maxheight | <integer> | 2147483647 | Maximum height of output image |
| maxwidth | <integer> | 2147483647 | Maximum width of output image |
| out | <filepath> | null | Output image file |
| outdir | <filepath> | null | Output image directory |
--savemzxmlwindow [--excludems1=<true | false>] [--maxmz=<decimal>] [--maxscan=<integer>] [--minmz=<decimal>] [--minscan=<integer>] [--out=<filepath>] [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input mzXML file(s) |
| excludems1 | <true | false> | false | Exclude MS1 scans from output |
| maxmz | <decimal> | null | Maximum M/Z value |
| maxscan | <integer> | null | Maximum scan number |
| minmz | <decimal> | null | Minimum M/Z value |
| minscan | <integer> | null | Minimum scan number |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for multiple inputs |
--spreadsheetmerge --mergecolumn=<value> [--compareout=<filepath>] [--file2column=<value>] [--keepallfile1values=<true | false>] [--multiplemergecolvaluessfirstfile=<true | false>] [--newcolname=<value>] [--out=<filepath>] [--outunique2file=<filepath>] [--plotcolumn=<value>] [--plotlog=<true | false>] [--presenceannotation=<value>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | input spreadsheets |
| mergecolumn | <value> | null | column to merge on |
| compareout | <filepath> | null | output file for comparing values of plotcolumn |
| file2column | <value> | null | column to add from the second file. If not specified, all columns added |
| keepallfile1values | <true | false> | false | Keep all values from the first file, even if they don't occur in other files? |
| multiplemergecolvaluessfirstfile | <true | false> | false | check for multiple merge-column values in the first file, separated by ';' |
| newcolname | <value> | null | New column name, for presence annotations |
| out | <filepath> | null | output file |
| outunique2file | <filepath> | null | output file for rows unique to the second spreadsheet |
| plotcolumn | <value> | null | column to plot, one vs. the other |
| plotlog | <true | false> | false | Plot in log scale |
| presenceannotation | <value> | null | Rather than adding columns from second file, add this string as the value for all matching mergecolumn rows, as a new column with name 'newcolname' |
--usermanual [--gui=<true | false>] [--out=<filepath>] <value>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <value> | null | Single command to document (leave blank for full manual) |
| gui | <true | false> | true | Open in a GUI window? (otherwise HTML output is simply written to a file or to standard output |
| out | <filepath> | null | Output file |
--viewspectrum --maxmz=<decimal> --maxscan=<integer> --minmz=<decimal> --minscan=<integer> [--height=<integer>] [--maxscansimageheight=<integer>] [--out=<filepath>] [--outscans=<filepath>] [--resolution=<integer>] [--scanline1=<integer>] [--scanline2=<integer>] [--scansfileimageheight=<integer>] [--showcharts=<true | false>] [--showscans=<true | false>] [--static=<true | false>] [--width=<integer>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | mzXML file |
| maxmz | <decimal> | null | maximum m/z |
| maxscan | <integer> | null | maximum scan number |
| minmz | <decimal> | null | minimum m/z |
| minscan | <integer> | null | minimum scan number |
| height | <integer> | 1000 | Window height (also used for spectrum file) |
| maxscansimageheight | <integer> | 4000 | Maximum overall height for the all-scans line plot image (overrides scansfileimageheight) |
| out | <filepath> | null | Output image file for heatmap |
| outscans | <filepath> | null | Output image file for single-scan line plots |
| resolution | <integer> | 100 | resolution (number of breaks per Thompson |
| scanline1 | <integer> | 0 | Line for marking a particular scan |
| scanline2 | <integer> | 0 | Another line for marking a particular scan |
| scansfileimageheight | <integer> | 100 | Height of EACH per-scan image, in the output file |
| showcharts | <true | false> | true | Show charts at all? |
| showscans | <true | false> | true | Show individual scan spectra? |
| static | <true | false> | false | Only show static image? For remote invocation |
| width | <integer> | 1000 | Window width |
--icat [--deconvolute=<true | false>] [--deltamass=<mass value>da|ppm] [--deltatime=<decimal>] [--heavytagweight=<decimal>] [--intensitytype=<total | max | recalculated>] [--labeledresidue=<value>] [--lighttagweight=<decimal>] [--masswindow=<decimal>] [--maxlabelcount=<integer>] [--msfile=<filepath>] [--out=<filepath>] [--outdir=<filepath>] [--scanwindow=<integer>] [--showcharts=<true | false>] [--sumintensities=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input File(s) |
| deconvolute | <true | false> | false | Deconvolute |
| deltamass | <mass value>da|ppm | 0.2da | Mass Tolerance |
| deltatime | <decimal> | 10.0 | Time Tolerance |
| heavytagweight | <decimal> | -1.0 | Heavy tag weight |
| intensitytype | <total | max | recalculated> | null | Intensity type |
| labeledresidue | <value> | null | Labeled Residue |
| lighttagweight | <decimal> | -1.0 | Light tag weight |
| masswindow | <decimal> | 0.4 | Mass Window |
| maxlabelcount | <integer> | 3 | Maximum Label Count |
| msfile | <filepath> | null | mzXml File |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for multiple files) |
| scanwindow | <integer> | 6 | Scan Window |
| showcharts | <true | false> | false | Show Charts |
| sumintensities | <true | false> | true | If true, deconvoluted feature intensities reflect the sum of all component feature intensities. If false, intensity of most-intense feature is kept. |
--peptideratiovariation --out=<filepath> [--minpprophet=<decimal>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | input files |
| out | <filepath> | null | output file |
| minpprophet | <decimal> | 0.8999999761581421 | min peptideprophet |
--proteinquantcharts --mzxmldir=<filepath> --outdir=<filepath> --pepxml=<filepath> --protxml=<filepath> [--appendoutput=<true | false>] [--minproteinprophet=<decimal>] [--out=<filepath>] [--protein=<value>] [--protgenefile=<filepath>]
| Argument | Usage | Default | Description |
|---|---|---|---|
| mzxmldir | <filepath> | null | Directory with mzXML files |
| outdir | <filepath> | null | Output Directory |
| pepxml | <filepath> | null | PepXML file |
| protxml | <filepath> | null | ProtXML file |
| appendoutput | <true | false> | true | Append output to file, if already exists? |
| minproteinprophet | <decimal> | 0.8999999761581421 | Minimum ProteinProphet score for proteins (if protein not specified) |
| out | <filepath> | null | Output File |
| protein | <value> | null | Protein name |
| protgenefile | <filepath> | null | File associating gene symbols with protein accession numbers |
--q3new [--alternatemzxmldir=<value>] [--compat=<true | false>] [--d=<value>] [--debug=<true | false>] [--forceoutput=<true | false>] [--labeledresidue=<value>] [--m=<mass value>da|ppm] [--massdiff=<decimal>] [--maxfracdeltamass=<mass value>da|ppm] [--mimicxpress=<true | false>] [--minpeptideprophet=<decimal>] [--n=<value>] [--nosentinels=<true | false>] [--out=<filepath>] [--outdir=<filepath>] [--stripoldq3=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input file(s) |
| alternatemzxmldir | <value> | null | Alternate mzXML directory |
| compat | <true | false> | null | Match behavior of the original R code when the center scan has fewer than three matching isotopes (default false) |
| d | <value> | null | Alternate mzXML directory |
| debug | <true | false> | null | Output extra debugging information in the pepXML |
| forceoutput | <true | false> | null | Force output (default false) |
| labeledresidue | <value> | null | Labeled residue |
| m | <mass value>da|ppm | null | Mass tolerance |
| massdiff | <decimal> | null | Mass difference between heavy and light forms of the labeled residue |
| maxfracdeltamass | <mass value>da|ppm | null | Maximum fractional delta mass |
| mimicxpress | <true | false> | null | Mimic XPress? (default false) |
| minpeptideprophet | <decimal> | null | Minimum PeptideProphet score |
| n | <value> | null | Label definition (e.g. -nC,3.0100645 |
| nosentinels | <true | false> | null | No sentinels (default false) |
| out | <filepath> | null | Output file |
| outdir | <filepath> | null | Output Directory (for handling multiple files) |
| stripoldq3 | <true | false> | false | Strip existing analysis_results and Q3 analysis_summary elements from the file |
--quant [--deconvolute=<true | false>] [--deltamass=<mass value>da|ppm] [--deltatime=<decimal>] [--heavytagweight=<decimal>] [--intensitytype=<total | max | recalculated>] [--labeledresidue=<value>] [--lighttagweight=<decimal>] [--masswindow=<decimal>] [--maxlabelcount=<integer>] [--msfile=<filepath>] [--out=<filepath>] [--outdir=<filepath>] [--scanwindow=<integer>] [--showcharts=<true | false>] [--sumintensities=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input File(s) |
| deconvolute | <true | false> | false | Deconvolute |
| deltamass | <mass value>da|ppm | 0.2da | Mass Tolerance |
| deltatime | <decimal> | 10.0 | Time Tolerance |
| heavytagweight | <decimal> | -1.0 | Heavy tag weight |
| intensitytype | <total | max | recalculated> | null | Intensity type |
| labeledresidue | <value> | null | Labeled Residue |
| lighttagweight | <decimal> | -1.0 | Light tag weight |
| masswindow | <decimal> | 0.4 | Mass Window |
| maxlabelcount | <integer> | 3 | Maximum Label Count |
| msfile | <filepath> | null | mzXml File |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for multiple files) |
| scanwindow | <integer> | 6 | Scan Window |
| showcharts | <true | false> | false | Show Charts |
| sumintensities | <true | false> | true | If true, deconvoluted feature intensities reflect the sum of all component feature intensities. If false, intensity of most-intense feature is kept. |
--quantcharts --outdir=<filepath> --pepxml=<filepath> [--3dheight=<integer>] [--3drotation=<integer>] [--3dshowaxes=<true | false>] [--3dtilt=<integer>] [--3dwidth=<integer>] [--fractions=<value>] [--infooncharts=<true | false>] [--maxscansimageheight=<integer>] [--minpprophet=<decimal>] [--mzpadding=<decimal>] [--mzxml=<filepath>] [--mzxmldir=<filepath>] [--numpeaksaboveheavy=<integer>] [--outhtml=<filepath>] [--outtsv=<filepath>] [--paddingscans=<integer>] [--peakdistance=<decimal>] [--peakmasstoleranceppm=<decimal>] [--peptides=<value>] [--proteins=<value>] [--resolution=<integer>] [--scan=<integer>] [--scanimageheight=<integer>] [--show3dplots=<true | false>] [--spectrumimageheight=<integer>] [--width=<integer>]
| Argument | Usage | Default | Description |
|---|---|---|---|
| outdir | <filepath> | null | Output directory |
| pepxml | <filepath> | null | pepXML file |
| fractions | <value> | null | Fraction containing desired quantitation event |
| minpprophet | <decimal> | 0.0 | minimum PeptideProphet value |
| mzxml | <filepath> | null | mzXML file |
| mzxmldir | <filepath> | null | mzXML directory |
| outhtml | <filepath> | null | Output HTML file |
| outtsv | <filepath> | null | Output TSV file |
| peptides | <value> | null | comma-separated list of peptides to examine |
| proteins | <value> | null | comma-separated list of proteins to examine |
| scan | <integer> | 0 | Scan number of desired quantitation event |
| show3dplots | <true | false> | true | Show 3D plot? (takes more time) |
| Argument | Usage | Default | Description |
|---|---|---|---|
| 3dheight | <integer> | 900 | Image height for 3D plot |
| 3drotation | <integer> | 80 | Rotation angle for 3D plot |
| 3dshowaxes | <true | false> | true | Include axes on 3D plot? |
| 3dtilt | <integer> | 20 | Tilt angle for 3D plot |
| 3dwidth | <integer> | 900 | Image width for 3D plot |
| infooncharts | <true | false> | false | Write quantitation information directly on the charts? |
| maxscansimageheight | <integer> | 4000 | Maximum overall height for the all-scans line plot image (overrides scansfileimageheight) |
| mzpadding | <decimal> | 1.5 | amount of m/z space to display around quant |
| numpeaksaboveheavy | <integer> | 4 | number of peaks above the heavy-ion monoisotope to display |
| paddingscans | <integer> | 5 | number of scans before and after quant envelope to display |
| peakdistance | <decimal> | 1.0 | Distance, in Daltons, between peaks. This is configurable in Q3, so it has to be configurable here. Used in generating the intensity sum chart |
| peakmasstoleranceppm | <decimal> | 25.0 | Mass tolerance, in PPM, around each theoretical peak to consider part of the peptide being quantitated. Used in generating the intensity sum chart |
| resolution | <integer> | 100 | resolution (number of breaks per Thompson |
| scanimageheight | <integer> | 100 | Height of EACH per-scan image, in the output file |
| spectrumimageheight | <integer> | 700 | Image height (used for spectrum, scans, and sum scan intensities charts) |
| width | <integer> | 900 | Image width (used for spectrum, scans, and sum scan intensities charts) |
--qurate <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | Quantitation summary file |
--align --mode=<spline | quantile> [--deltamass=<mass value>da|ppm] [--mappingpolynomialdegree=<integer>] [--maxleverage=<decimal>] [--maxstudres=<decimal>] [--topn=<integer>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| mode | <spline | quantile> | null | spline: spline quantile: quantile |
| deltamass | <mass value>da|ppm | null | delta-mass for matching features for alignment |
| mappingpolynomialdegree | <integer> | 5 | The degree of the polynomial to fit when mapping time to hydrophobicity nonlinearly |
| maxleverage | <decimal> | 6.0 | Maximum NUMERATOR of the leverage of features used for regression |
| maxstudres | <decimal> | 3.0 | Maximum studentized residual for regression |
| topn | <integer> | -1 | topN argument for spline-based mapping |
--analyzepeparray --mode=<getinfo | createfeaturefilesallmatched | countmultiplyobservedpeptides | comparepeptideintensities | createconsensusfeaturefile | compareallintensities | compareallintensitiesadd1 | comparepeptideintensitiesadd1 | comparenonpeptideintensities> [--allowhalfmatched=<true | false>] [--caserun=<value>] [--caserunlistfile=<filepath>] [--controlrun=<value>] [--controlrunlistfile=<filepath>] [--minconsensusfeatureruns=<integer>] [--minfeaturesupport=<integer>] [--minpeptidesupport=<integer>] [--minrunspergroup=<integer>] [--minsignificantratio=<decimal>] [--out=<filepath>] [--outdir=<filepath>] [--showcharts=<true | false>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | (no details provided) |
| mode | <getinfo | createfeaturefilesallmatched | countmultiplyobservedpeptides | comparepeptideintensities | createconsensusfeaturefile | compareallintensities | compareallintensitiesadd1 | comparepeptideintensitiesadd1 | comparenonpeptideintensities> | null | getinfo: Get basic peptide array information createfeaturefilesallmatched: Create feature files, one per run, containing only those features matched across all runs countmultiplyobservedpeptides: Count the distinct peptides observed in multiple runs comparepeptideintensities: Compare peptide intensities matched across runs createconsensusfeaturefile: Create a 'consensus' feature file, containing features (with details from the first run) that align across at least minconsensusfeatureruns runs compareallintensities: Compare intensity in the case runs vs. intensity in the control runs compareallintensitiesadd1: Compare intensity in the case runs vs. intensity in the control runs, adding 1, so that logs can be used comparepeptideintensitiesadd1: Compare intensity in the case runs vs. the control runs for features mapped to the same peptide comparenonpeptideintensities: Compare intensity in the case runs vs. the control runs for features mapped to the same peptide, adding 1, so that logs can be used |
| allowhalfmatched | <true | false> | false | When determining whether peptide matches are made, should it be considered a match when one run has an ID and another run has an intensity but no ID? |
| caserun | <value> | null | Case run |
| caserunlistfile | <filepath> | null | File containing the names of runs in the case group, one per line |
| controlrun | <value> | null | Case run |
| controlrunlistfile | <filepath> | null | File containing the names of runs in the control group, one per line |
| minconsensusfeatureruns | <integer> | 2 | Minimum number of runs required for a feature to be included in the consensus feature set |
| minfeaturesupport | <integer> | 1 | Minimum number of runs for which a non-peptide-conflicting feature was identified |
| minpeptidesupport | <integer> | 1 | Minimum number of runs for which the same peptide was identified |
| minrunspergroup | <integer> | 1 | Minimum number of runs in each group in which a feature must be located to be counted |
| minsignificantratio | <decimal> | 3.0 | Minimum ratio of intensities considered interesting |
| out | <filepath> | null | output file |
| outdir | <filepath> | null | output directory |
| showcharts | <true | false> | false | show charts? |
--peptidearray --out=<filepath> [--accmz=<true | false>] [--align=<true | false>] [--alignbytags=<none | loose | strict>] [--alignmentmode=<spline | quantile>] [--alignminintensity=<decimal>] [--alignmztolerance=<decimal>] [--df=<integer>] [--featurepairselector=<mz | peptide | hybrid>] [--intensitytype=<sum | best>] [--massbuckets=<value>] [--masswindow=<decimal>] [--maxcharge=<integer>] [--maxkl=<decimal>] [--maxleverage=<decimal>] [--maxmass=<decimal>] [--maxmassdeviationppm=<integer>] [--maxmz=<decimal>] [--maxpeaks=<integer>] [--maxstudres=<decimal>] [--maxsumsquaresdist=<decimal>] [--maxtime=<decimal>] [--mincharge=<integer>] [--minintensity=<decimal>] [--minmass=<decimal>] [--minmz=<decimal>] [--minpeaks=<integer>] [--minpprophet=<decimal>] [--minscans=<integer>] [--mintime=<decimal>] [--mintotalintensity=<decimal>] [--normalize=<true | false>] [--optimize=<true | false>] [--optimizeonpeptideids=<true | false>] [--peptidematchscore=<integer>] [--peptidemismatchpenalty=<integer>] [--polynomialdegree=<integer>] [--scanbuckets=<value>] [--scanfirst=<integer>] [--scanlast=<integer>] [--scanwindow=<integer>] [--showcharts=<true | false>] [--tags=<filepath>] [--topn=<integer>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | A series of feature files to align |
| out | <filepath> | null | output file |
| accmz | <true | false> | null | Accurate m/z only? |
| align | <true | false> | true | should alignment be performed? |
| alignbytags | <none | loose | strict> | none | Request a pre-alignment within each group of tags. "None" indicates that no pre-alignment be done. "Loose" requests pre-alignment, preserving those features present in at least 3/4 of the runs in each group. "Strict" preserves those features present in all runs in each group. Unless "None", a tags file *must* be specified. |
| alignmentmode | <spline | quantile> | spline | spline: Use the spline regression algorithm for alignment. This is the original algorithm implemented. It runs a bit faster than the quantile regression and behaves less oddly at the very extremes of the data. quantile: Use quantile regression algorithm for alignment. This algorithm performs better with very noisy data. |
| alignminintensity | <decimal> | 100.0 | Minimum intensity used in picking pairs of features for alignment (if applicable) |
| alignmztolerance | <decimal> | 0.10000000149011612 | M/Z tolerance used in picking pairs of features for alignment (if applicable) |
| df | <integer> | 20 | Degrees of Freedom for alignment (spline mode) |
| featurepairselector | <mz | peptide | hybrid> | null | How features should be paired when performing alignment. Default is MZ |
| intensitytype | <sum | best> | sum | What type of intensity should we include in the array when there are conflicts? A sum of all matching features in the bucket, or the intensity of the best-looking feature? |
| massbuckets | <value> | null | comma-separated list of decimal values for the maximum mass bucket size |
| masswindow | <decimal> | 0.2 | number of Daltons to use as a window when aligning features |
| maxcharge | <integer> | null | Maximum charge |
| maxkl | <decimal> | null | Maximum K/L score |
| maxleverage | <decimal> | 100.0 | Maximum NUMERATOR of the leverage of features used for alignment (denominator is N). Default value is effectively no filtering. Use values < 8 for tighter filtering |
| maxmass | <decimal> | null | Maximum mass |
| maxmassdeviationppm | <integer> | null | Maximum deviation from nearest theoretical mass cluster, in PPM |
| maxmz | <decimal> | null | Maximum M/Z value |
| maxpeaks | <integer> | null | Maximum number of peaks |
| maxstudres | <decimal> | 100.0 | Maximum studentized residual for alignment. Default value is effectively no filtering. Use values < 3 for tighter filtering |
| maxsumsquaresdist | <decimal> | null | Maximum sum-squares distance score |
| maxtime | <decimal> | null | Maximum time |
| mincharge | <integer> | null | Minimum charge |
| minintensity | <decimal> | null | Minimum intensity |
| minmass | <decimal> | null | Minimum mass |
| minmz | <decimal> | null | Minimum M/Z value |
| minpeaks | <integer> | null | Minimum number of peaks |
| minpprophet | <decimal> | null | Minimum PeptideProphet score |
| minscans | <integer> | null | Minimum number of scans covered |
| mintime | <decimal> | null | Minimum time |
| mintotalintensity | <decimal> | null | Minimum total intensity |
| normalize | <true | false> | false | should the intensities be normalized after alignment? |
| optimize | <true | false> | false | Should we optimize the size of the mass and scan buckets based on the number of 'perfect buckets'? |
| optimizeonpeptideids | <true | false> | false | If optimizing, optimize based on the number of rows with agreeing peptide IDs, rather than the number of rows with one peptide (of any ID) from each row |
| peptidematchscore | <integer> | 1 | If optimizing based on rows with agreeing peptides, give this score for each agreeing row |
| peptidemismatchpenalty | <integer> | 1 | If optimizing based on rows with agreeing peptides, give this penalty for each mismatched row |
| polynomialdegree | <integer> | 5 | The degree of the polynomial to fit (for quantile mode) |
| scanbuckets | <value> | null | comma-separated list of integer values for the maximum scan bucket size |
| scanfirst | <integer> | null | Minimum scan number |
| scanlast | <integer> | null | Maximum scan number |
| scanwindow | <integer> | 50 | number of scans to use as a window when aligning features |
| showcharts | <true | false> | false | Optionally plot the warping functions for each aligned run |
| tags | <filepath> | null | optional file of tags for each run |
| topn | <integer> | 0 | if > 0, sets the number of highest-intensity features from each run to use when constructing the non-linear mapping |
--calcfdr [--bycharge=<true | false>] [--higherisbetter=<true | false>] [--maxfdr=<decimal>] [--out=<filepath>] [--outdir=<filepath>] [--outformat=<pepxml | msinspect | apml | input>] [--pprophetvalue=<decimal>] [--savechartsdir=<filepath>] [--scoretype=<pprophet | searchscore>] [--searchscorename=<value>] [--setpprophet1minusfdr=<true | false>] [--showcharts=<true | false>] [--targetdecoydbsizeratio=<decimal>] [--together=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input feature file(s) |
| bycharge | <true | false> | true | Calculate FDR separately by charge state? Charge states with too few identifications will be dropped |
| higherisbetter | <true | false> | false | Is a higher value better, for this score (for 'searchscore' mode)? |
| maxfdr | <decimal> | 0.05000000074505806 | Maximum FDR to keep in output file |
| out | <filepath> | null | Output file (for single file processing) |
| outdir | <filepath> | null | Output directory |
| outformat | <pepxml | msinspect | apml | input> | input | pepxml: PepXML msinspect: msInspect .tsv apml: APML input: Same as input format (PepXML or msInspect) |
| pprophetvalue | <decimal> | 0.949999988079071 | Set the PeptideProphet score of every passing feature to this value |
| savechartsdir | <filepath> | null | Directory to save charts to |
| scoretype | <pprophet | searchscore> | searchscore | pprophet: Use PeptideProphet probability searchscore: Use a search score (name must be provided) |
| searchscorename | <value> | expect | Name of the search score to use (for 'searchscore' mode) |
| setpprophet1minusfdr | <true | false> | false | Set PeptideProphet score to 1 - FDR? |
| showcharts | <true | false> | false | Plot an ROC curve? |
| targetdecoydbsizeratio | <decimal> | 1.0 | Ratio of the number of peptides in the target search database to the number of peptides in the decoy search database. |
| together | <true | false> | true | Calcualte FDR on all fractions together? Otherwise, calculate FDR separately for eachrun |
--combinepepxmlfiles --out=<filepath> <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | input files |
| out | <filepath> | null | Output file |
--comparefastas --fasta1=<filepath> --fasta2=<filepath> --out=<filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| fasta1 | <filepath> | null | FASTA file 1 |
| fasta2 | <filepath> | null | FASTA file 2 |
| out | <filepath> | null | output file |
--correctprecursormz --features=<filepath> [--calibrate=<true | false>] [--calibratespectra=<true | false>] [--featuresdir=<filepath>] [--fracmztolerance=<decimal>] [--initialfilterppm=<integer>] [--out=<filepath>] [--outdir=<filepath>] [--outfeatures=<filepath>] [--partitions=<integer>] [--peaksaboveprecursor=<integer>] [--peaksbelowprecursor=<integer>] [--showcharts=<true | false>] [--useinaccuratems1mz=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input mzXML file(s) |
| features | <filepath> | null | Feature file to use in correction |
| calibrate | <true | false> | false | Calibrate precursor masses? |
| calibratespectra | <true | false> | false | Calibrate spectra, as well as precursor masses (only valid with calibrate option)? |
| featuresdir | <filepath> | null | Directory of feature files to use in correction |
| fracmztolerance | <decimal> | 100.0 | fractional M/Z tolerance, in PPM, for associating MS1 features with precursor scans |
| initialfilterppm | <integer> | 0 | Initial ppm value used as a pre-calibration cutoff. Features deviating from theoretical clusters (BEFORE calibration) will be filtered out during calibration. However, those features WILL appear in the recalibrated featureset, with corrected masses.Default = no filter |
| out | <filepath> | null | Output File |
| outdir | <filepath> | null | Output Directory (for multiple inputs) |
| outfeatures | <filepath> | null | Output recalibrated feature file |
| partitions | <integer> | 1 | Number of partitions, by scan, to divide the run into, for calibration |
| peaksaboveprecursor | <integer> | 1 | Number of peaks above the precursor m/z to check for MS1 features |
| peaksbelowprecursor | <integer> | 3 | Number of peaks below the precursor m/z to check for MS1 features |
| showcharts | <true | false> | false | show charts? |
| useinaccuratems1mz | <true | false> | false | Use an MS1 feature if m/z not "accurate"? |
--extractrunsfrompepxml --outdir=<filepath> [--accmz=<true | false>] [--maxcharge=<integer>] [--maxkl=<decimal>] [--maxmass=<decimal>] [--maxmassdeviationppm=<integer>] [--maxmz=<decimal>] [--maxpeaks=<integer>] [--maxsumsquaresdist=<decimal>] [--maxtime=<decimal>] [--mincharge=<integer>] [--minintensity=<decimal>] [--minmass=<decimal>] [--minmz=<decimal>] [--minpeaks=<integer>] [--minpprophet=<decimal>] [--minscans=<integer>] [--mintime=<decimal>] [--mintotalintensity=<decimal>] [--mzxmldir=<filepath>] [--outformat=<tsv | pepxml>] [--populatetimes=<true | false>] [--scanfirst=<integer>] [--scanlast=<integer>] [--sourcefilename=<value>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | Input pepXml file |
| outdir | <filepath> | null | Output Directory |
| accmz | <true | false> | null | Accurate m/z only? |
| maxcharge | <integer> | null | Maximum charge |
| maxkl | <decimal> | null | Maximum K/L score |
| maxmass | <decimal> | null | Maximum mass |
| maxmassdeviationppm | <integer> | null | Maximum deviation from nearest theoretical mass cluster, in PPM |
| maxmz | <decimal> | null | Maximum M/Z value |
| maxpeaks | <integer> | null | Maximum number of peaks |
| maxsumsquaresdist | <decimal> | null | Maximum sum-squares distance score |
| maxtime | <decimal> | null | Maximum time |
| mincharge | <integer> | null | Minimum charge |
| minintensity | <decimal> | null | Minimum intensity |
| minmass | <decimal> | null | Minimum mass |
| minmz | <decimal> | null | Minimum M/Z value |
| minpeaks | <integer> | null | Minimum number of peaks |
| minpprophet | <decimal> | null | Minimum PeptideProphet score |
| minscans | <integer> | null | Minimum number of scans covered |
| mintime | <decimal> | null | Minimum time |
| mintotalintensity | <decimal> | null | Minimum total intensity |
| mzxmldir | <filepath> | null | Directory to search for mzXML files (for populating times) |
| outformat | <tsv | pepxml> | pepxml | Output format |
| populatetimes | <true | false> | false | Populate times using mzXML file |
| scanfirst | <integer> | null | Minimum scan number |
| scanlast | <integer> | null | Maximum scan number |
| sourcefilename | <value> | null | Source File Name (without .xml) |
--filterpeptideregexp --regexp=<value> [--out=<filepath>] [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| regexp | <value> | null | Regular expression that every peptide must match |
| out | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
--filterpepxml [--badprotprefix=<value>] [--goodprotprefix=<value>] [--out=<filepath>] [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| badprotprefix | <value> | null | Exclude any peptides with any associated proteins with this prefix to their names |
| goodprotprefix | <value> | null | Include any peptides with any associated proteins with this prefix to their names |
| out | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
--filterreversedbhits [--out=<filepath>] [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| out | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
--findindistinguishableproteins --protfile=<filepath> [--minpprophet=<decimal>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | protxml file |
| protfile | <filepath> | null | File with list of proteins to look for |
| minpprophet | <decimal> | 0.0 | Minimum ProteinProphet score. |
--flippepxmlratios [--out=<filepath>] [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | pepXML file(s) to flip |
| out | <filepath> | null | Output file |
| outdir | <filepath> | null | Output directory |
--guessproteinsfromfasta --fasta=<filepath> [--guessallproteins=<true | false>] [--out=<filepath>] [--outdir=<filepath>] [--outformat=<msinspect | pepxml>] [--refreshparser=<true | false>] [--striphighcharge=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Feature File to fix up |
| fasta | <filepath> | null | Fasta file |
| guessallproteins | <true | false> | false | Guess all proteins? If false, just guess one protein |
| out | <filepath> | null | output file (if not specified, alters in place |
| outdir | <filepath> | null | output directory (if not specified, alters in place |
| outformat | <msinspect | pepxml> | pepxml | msinspect: msinspect pepxml: pepxml |
| refreshparser | <true | false> | false | Run RefreshParser? RefreshParser executable must be on path. |
| striphighcharge | <true | false> | true | Strip high-charge features from output? (for ProteinProphet) |
--ms2scanviewer --mass=<decimal> [--masstoleranceppm=<decimal>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | mzXML file |
| mass | <decimal> | null | Mass to search for scans around |
| masstoleranceppm | <decimal> | 20.0 | PPM mass tolerance |
--peptidecompare --mode=<showoverlap | createfeaturefileforpeptideunion | plottimes | plotintensities | plottotalintensities | plotpprophet | plotfval | plotkscoreorxcorr | calcratios | plotratios | plotlightarea | idcluster | plotspectralcounts> [--fasta=<filepath>] [--featuresdir1=<filepath>] [--featuresdir2=<filepath>] [--includeunmatched=<true | false>] [--listallcommon=<true | false>] [--minpprophet=<decimal>] [--normalize=<true | false>] [--out=<filepath>] [--outformatpepxml=<true | false>] [--showcharts=<true | false>] [--summaryonly=<true | false>] [--withincharge=<true | false>] [--xaxislabel=<value>] [--yaxislabel=<value>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | input files |
| mode | <showoverlap | createfeaturefileforpeptideunion | plottimes | plotintensities | plottotalintensities | plotpprophet | plotfval | plotkscoreorxcorr | calcratios | plotratios | plotlightarea | idcluster | plotspectralcounts> | null | showoverlap: Show overlap between peptide identifications in two or more files createfeaturefileforpeptideunion: Create a feature file containing all the features in the first file whose peptides are found in all other files, as well plottimes: Plot time in one set vs. time in the other set, by peptide plotintensities: Plot intensity in one set vs. intensity in the other set, by peptide plottotalintensities: Plot total intensity in one set vs. total intensity in the other set, by peptide plotpprophet: Plot PeptideProphet probability vs. PeptideProphet probability in the other set, by peptide plotfval: Plot PeptideProphet fval vs. PeptideProphet fval in the other set, by peptide plotkscoreorxcorr: Plot kscore or xcorr score in one set (which is available) against kscore or xcorr score in the other set, by peptide calcratios: Calculate ratios (run 1 : run 2) for each peptide plotratios: Plot peptide ratios against each other plotlightarea: Plot light areas (for peptides with ratios) idcluster: Cluster runs by peptide identifications plotspectralcounts: Plot spectral counts |
| fasta | <filepath> | null | fasta file |
| featuresdir1 | <filepath> | null | First directory full of feature files |
| featuresdir2 | <filepath> | null | Second directory full of feature files |
| includeunmatched | <true | false> | true | include unmatched peptides (for ratio mode) |
| listallcommon | <true | false> | true | List all peptides common to all runs? |
| minpprophet | <decimal> | 0.0 | Minimum PeptideProphet score |
| normalize | <true | false> | true | normalize intensities (for ratio mode) |
| out | <filepath> | null | Output file |
| outformatpepxml | <true | false> | false | output to pepxml |
| showcharts | <true | false> | false | show charts |
| summaryonly | <true | false> | false | Summary-level info only? For directories |
| withincharge | <true | false> | false | Only compare peptides within charge states |
| xaxislabel | <value> | null | label for X axis |
| yaxislabel | <value> | null | label for Y axis |
--picktargetedms2candidates --fasta=<filepath> --modifications=<residue><massdiff>[V][,...] --out=<filepath> --protlistfile=<filepath> [--excluderesidue=<value>] [--maxmz=<decimal>] [--maxpeptidesperprotein=<integer>] [--minmz=<decimal>] [--minpprophet=<decimal>] [--minproteinprophet=<decimal>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | protxml file(s) |
| fasta | <filepath> | null | FASTA file |
| modifications | <residue><massdiff>[V][,...] | null | Modifications |
| out | <filepath> | null | output file |
| protlistfile | <filepath> | null | Protein list file |
| excluderesidue | <value> | null | Residue to exclude |
| maxmz | <decimal> | 1800.0 | Maximum m/z for targets |
| maxpeptidesperprotein | <integer> | 3 | Maximum peptides per protein |
| minmz | <decimal> | 400.0 | Minimum m/z for targets |
| minpprophet | <decimal> | 0.8999999761581421 | Minimum PeptideProphet probability |
| minproteinprophet | <decimal> | 0.8999999761581421 | Minimum ProteinProphet probability |
--plotdeltamasses [--fractional=<true | false>] [--out=<filepath>] [--ppmline=<decimal>] [--showregressionline=<true | false>] [--useppm=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| fractional | <true | false> | true | Fractional masses? |
| out | <filepath> | null | Output file for chart |
| ppmline | <decimal> | -1.0 | PPM cutoff to display on plot (default none) |
| showregressionline | <true | false> | false | Show a simple regression line through the data |
| useppm | <true | false> | false | Use PPM instead of Daltons |
--populatems2times --mzxmldir=<filepath> [--outdir=<filepath>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | (no details provided) |
| mzxmldir | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
--postprocesspepxml [--adjustquantzeroareas=<true | false>] [--badproteinprefix=<value>] [--bynumcysteines=<true | false>] [--filterbyproteinprefix=<true | false>] [--goodproteinprefix=<value>] [--label=<acrylamide | silac>] [--maxexpect=<decimal>] [--maxfracdeltamass=<mass value>da|ppm] [--maxquantexpect=<decimal>] [--mediancenter=<true | false>] [--minmediancenterratios=<integer>] [--minmedianpprophet=<decimal>] [--minpprophet=<decimal>] [--minquantpprophet=<decimal>] [--out=<filepath>] [--outdir=<filepath>] [--protprefixexcludequantonly=<true | false>] [--requirepepxmlextension=<true | false>] [--showcharts=<true | false>] [--strippeptidefile=<filepath>] [--stripquantmissingheavy=<true | false>] [--stripquantmissinglightorheavyacrossruns=<true | false>] [--stripquantmissinglightorheavywithinrun=<true | false>] [--stripquantzeroareas=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | PepXML files to process |
| adjustquantzeroareas | <true | false> | false | Adjust zero values for light or heavy areas in quantitation (and ratios) to the 1 percentile of all the (nonzero) values |
| badproteinprefix | <value> | null | Exclude any peptides with any associated proteins with this prefix to their names |
| bynumcysteines | <true | false> | false | Median-center ratios separately by number of Cysteines? |
| filterbyproteinprefix | <true | false> | false | Filter peptides based on prefixes of the protein names that they're associated with? |
| goodproteinprefix | <value> | null | Include any peptides with any associated proteins with this prefix to their names |
| label | <acrylamide | silac> | acrylamide | acrylamide: Acrylamide (3.0106Da on C) silac: SILAC Lycine labeling (134.115092 on K) |
| maxexpect | <decimal> | 3.4028234663852886E38 | Maximum expect score to keep |
| maxfracdeltamass | <mass value>da|ppm | null | Maximum fractional delta mass |
| maxquantexpect | <decimal> | 3.4028234663852886E38 | Maximum expect score for quantitation |
| mediancenter | <true | false> | false | Median-center ratios? |
| minmediancenterratios | <integer> | 10 | Minimum number of ratios necessary in order to perform median-centering |
| minmedianpprophet | <decimal> | 0.75 | Minimum PeptideProphet score to be counted in median calculation |
| minpprophet | <decimal> | 0.0 | Minimum PeptideProphet score to keep |
| minquantpprophet | <decimal> | 0.0 | Minimum PeptideProphet score for quantitation |
| out | <filepath> | null | Output file |
| outdir | <filepath> | null | Output directory |
| protprefixexcludequantonly | <true | false> | false | When excluding peptides based on protein prefix, exclude only quantitation? If false, excludes entire ID |
| requirepepxmlextension | <true | false> | false | When looking for files in a pepxmldir, require that they end with .pep.xml? |
| showcharts | <true | false> | false | Show charts? |
| strippeptidefile | <filepath> | null | File containing a list of peptides to strip from results, one per line, all caps |
| stripquantmissingheavy | <true | false> | false | Strip quantitation events in which the heavy isotope was never identified, in any run |
| stripquantmissinglightorheavyacrossruns | <true | false> | false | Strip peptides that we haven't seen in both light and heavy states, across all runs. This ONLY makes sense for multiple metabolically-labeled experiments with a label flip |
| stripquantmissinglightorheavywithinrun | <true | false> | false | Strip peptides that we haven't seen in both light and heavy states, within a single run |
| stripquantzeroareas | <true | false> | false | Strip quantitation with zero values for light or heavy areas |
--proteinfractionsspreadsheet --out=<filepath> --protxml=<filepath> [--grouplevel=<true | false>] [--minpprophet=<decimal>] [--minproteinprophet=<decimal>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | MS2 feature files |
| out | <filepath> | null | (no details provided) |
| protxml | <filepath> | null | ProtXML File |
| grouplevel | <true | false> | false | Group-level? (default is accesion-number level) |
| minpprophet | <decimal> | 0.0 | Minimum peptideprophet |
| minproteinprophet | <decimal> | 0.0 | Minimum proteinprophet |
--protxmlcompare [--listunique2proteins=<true | false>] [--minpprophet=<decimal>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | protxml files to compare |
| listunique2proteins | <true | false> | false | List the proteins unique to the second file |
| minpprophet | <decimal> | 0.0 | Minimum ProteinProphet score. |
--reversefasta --out=<filepath> <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | (no details provided) |
| out | <filepath> | null | (no details provided) |
--searchscorecutoff --maxfar=<decimal> --mode=<pprophet | searchscore> [--higherisbetter=<true | false>] [--out=<filepath>] [--plotroc=<true | false>] [--searchscorename=<value>] [--setpprophet=<true | false>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | (no details provided) |
| maxfar | <decimal> | null | maximum false assignment rate |
| mode | <pprophet | searchscore> | null | pprophet: Use PeptideProphet probability searchscore: Use a search score (name must be provided) |
| higherisbetter | <true | false> | true | Is a higher value better, for this score? |
| out | <filepath> | null | Output file |
| plotroc | <true | false> | false | Plot an ROC curve? |
| searchscorename | <value> | null | Name of the search score to use |
| setpprophet | <true | false> | false | Set the PeptideProphet score of every passing feature to 1 - the FAR at that score |
--spectralcount --mode=<peptide | gene | proteingroup> [--genelookupfile=<filepath>] [--out=<filepath>] [--protxml=<filepath>] [--showcharts=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | MS2 Feature file(s) |
| mode | <peptide | gene | proteingroup> | null | peptide: Peptide-level counts gene: Gene-level counts proteingroup: protein group-level counts |
| genelookupfile | <filepath> | null | Gene lookup file for IPI numbers |
| out | <filepath> | null | output file |
| protxml | <filepath> | null | ProtXML file |
| showcharts | <true | false> | false | show charts? |
--summarizeprotxml [--minpprophet=<decimal>] [--protgenefile=<filepath>] [--showcharts=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | protxml file(s) |
| minpprophet | <decimal> | 0.0 | Min proteinprophet for MA plot |
| protgenefile | <filepath> | null | File associating gene symbols with protein accession numbers |
| showcharts | <true | false> | false | show charts? |
--amtdiagnostic --mode=<compareobshcalch | comparecalchtime | plotthmaps | histhydrostddev | plotrunstddevs | saveallcharts | plotmassvsobshydro | basicinfo | histmasses | plotrunhvsmedian | peptidedetails | plotmassh | histidprobs> [--ms1features=<filepath>] [--out=<filepath>] [--outdir=<filepath>] [--peptide=<value>] [--showcharts=<true | false>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | AMT database file |
| mode | <compareobshcalch | comparecalchtime | plotthmaps | histhydrostddev | plotrunstddevs | saveallcharts | plotmassvsobshydro | basicinfo | histmasses | plotrunhvsmedian | peptidedetails | plotmassh | histidprobs> | null | compareobshcalch: Compare Observed vs. Calculated H, per run comparecalchtime: Compare Calculated H vs. Time, per run plotthmaps: Plot the T->H mappings for each run histhydrostddev: Histogram of the hydrophobicity standard deviations across all observations for each peptide plotrunstddevs: Bar chart of the mean difference between predicted and observed H, per run saveallcharts: Save all charts to image files in a specified directory plotmassvsobshydro: Plot peptide mass vs. observed hydrophobicity, per run basicinfo: Return basic AMT database information histmasses: Histogram all peptide masses plotrunhvsmedian: Plot observed hydrophobicity against median peptide hydrophobicity, by run peptidedetails: Show details about a single peptide plotmassh: Plot mass and H for every entry in the DB histidprobs: Histogram the probabilities of all peptide entry IDs' correctness |
| ms1features | <filepath> | null | MS1 feature file to show along with database entries (plotmassandh mode only) |
| out | <filepath> | null | output filepath (for individual charts) |
| outdir | <filepath> | null | output directory (for saving all charts) |
| peptide | <value> | null | Peptide to get details about (for mode peptidedetails only) |
| showcharts | <true | false> | false | show charts? |
--amtlabeledquant [--maxratio=<decimal>] [--minratio=<decimal>] [--minratiohighpprophet=<decimal>] [--minratiolowpprophet=<decimal>] [--othermods=<residue><massdiff>[V][,...]] [--out=<filepath>] [--outdir=<filepath>] [--percharge=<true | false>] [--residue=<value>] [--separation=<decimal>] [--showcharts=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | AMT matching result file(s) |
| maxratio | <decimal> | 15.0 | Maximum ratio to keep |
| minratio | <decimal> | 0.06666667014360428 | Minimum ratio to keep |
| minratiohighpprophet | <decimal> | 0.699999988079071 | Minimum AMT probability for consideration in a ratio: the higher of the two probabilities must be at least this high |
| minratiolowpprophet | <decimal> | 0.05000000074505806 | Minimum AMT probability for consideration in a ratio: the lower of the two probabilities must be at least this high |
| othermods | <residue><massdiff>[V][,...] | C57.021,M16.0V,C14.01557 | a list of other modifications applied to sample |
| out | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
| percharge | <true | false> | true | Calculate ratios per charge (vs. all charges together)? |
| residue | <value> | C | Labeled residue (leave blank for n-terminal) |
| separation | <decimal> | 3.0101 | light-heavy separation |
| showcharts | <true | false> | false | show charts? |
--combineamtms2 --ms2dir=<filepath> [--amtdir=<filepath>] [--fasta=<filepath>] [--guessproteins=<true | false>] [--out=<filepath>] [--outdir=<filepath>] [--outformat=<pepxml | feature>] [--refreshparser=<true | false>] [--restrictcharge=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | pepXml files from MS2 search (these can be specified individually or using the 'ms2dir' argument |
| ms2dir | <filepath> | null | Directory of pepXML files from MS2 search |
| amtdir | <filepath> | null | Directory of AMT matching results |
| fasta | <filepath> | null | Fasta file |
| guessproteins | <true | false> | false | Guess initial proteins for peptides? (Requires fasta) |
| out | <filepath> | null | (no details provided) |
| outdir | <filepath> | null | (no details provided) |
| outformat | <pepxml | feature> | pepxml | Output format |
| refreshparser | <true | false> | false | Run RefreshParser to assign all possible proteins to peptides? (RefreshParser must be on path, and fasta must be specified, and guessproteins must be specified) |
| restrictcharge | <true | false> | null | Cap feature charge in output files at 5? (the maximum allowed by ProteinProphet) |
--createamt --mode=<directories | ms2featurefile | amtxmls | randompeptides> [--accmz=<true | false>] [--align=<true | false>] [--deltamassppm=<decimal>] [--deltatime=<decimal>] [--fasta=<filepath>] [--maxcharge=<integer>] [--maxkl=<decimal>] [--maxmass=<decimal>] [--maxmassdeviationppm=<integer>] [--maxmz=<decimal>] [--maxpeaks=<integer>] [--maxsrforinclusion=<decimal>] [--maxsrforregression=<decimal>] [--maxsumsquaresdist=<decimal>] [--maxtime=<decimal>] [--mincharge=<integer>] [--minintensity=<decimal>] [--minmass=<decimal>] [--minmz=<decimal>] [--minpeaks=<integer>] [--minpprophet=<decimal>] [--minscans=<integer>] [--mintime=<decimal>] [--mintotalintensity=<decimal>] [--ms1dir=<filepath>] [--ms1features=<filepath>] [--ms2dir=<filepath>] [--ms2features=<filepath>] [--mzxml=<filepath>] [--mzxmldir=<filepath>] [--numpeptides=<integer>] [--out=<filepath>] [--scanfirst=<integer>] [--scanlast=<integer>] [--scanortimemode=<scan | time>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input file (for 'ms2features' mode) |
| mode | <directories | ms2featurefile | amtxmls | randompeptides> | null | directories: supply directories for MS2 and mzXML files ms2featurefile: create an AMT database from a single MS2 and mzXML file amtxmls: combine multiple existing AMT databases randompeptides: create a database of random peptides from a FASTA file |
| accmz | <true | false> | null | Accurate m/z only? |
| fasta | <filepath> | null | FASTA file to pull random peptides from ('randompeptides' mode only |
| maxcharge | <integer> | null | Maximum charge |
| maxkl | <decimal> | null | Maximum K/L score |
| maxmass | <decimal> | null | Maximum mass |
| maxmassdeviationppm | <integer> | null | Maximum deviation from nearest theoretical mass cluster, in PPM |
| maxmz | <decimal> | null | Maximum M/Z value |
| maxpeaks | <integer> | null | Maximum number of peaks |
| maxsumsquaresdist | <decimal> | null | Maximum sum-squares distance score |
| maxtime | <decimal> | null | Maximum time |
| mincharge | <integer> | null | Minimum charge |
| minintensity | <decimal> | null | Minimum intensity |
| minmass | <decimal> | null | Minimum mass |
| minmz | <decimal> | null | Minimum M/Z value |
| minpeaks | <integer> | null | Minimum number of peaks |
| minpprophet | <decimal> | null | Minimum PeptideProphet score |
| minscans | <integer> | null | Minimum number of scans covered |
| mintime | <decimal> | null | Minimum time |
| mintotalintensity | <decimal> | null | Minimum total intensity |
| ms1dir | <filepath> | null | Directory of MS1 feature files (for 'directories' mode) |
| ms1features | <filepath> | null | Input MS1 feature file (for 'ms1featurefile' mode) |
| ms2dir | <filepath> | null | Directory of MS2 feature files (for 'directories' mode) |
| ms2features | <filepath> | null | Input MS2 feature file (for 'ms2featurefile' mode) |
| mzxml | <filepath> | null | Input mzXml file (for 'ms2featurefile' mode), only necessary if retention times are not populated in the MS2 feature file |
| mzxmldir | <filepath> | null | Directory of mzXML files (for 'directories' mode), only necessary if retention times are not populated in the MS2 feature file |
| out | <filepath> | null | output file |
| scanfirst | <integer> | null | Minimum scan number |
| scanlast | <integer> | null | Maximum scan number |
| Argument | Usage | Default | Description |
|---|---|---|---|
| align | <true | false> | false | use nonlinear alignment when mapping time to hydrophobicity. This is not necessarily recommended, as the manageamt command has a mode ('alignallruns') for nonlinearly aligning all runs to a single scale that is much more effective. |
| deltamassppm | <decimal> | 10.0 | Mass tolerance for MS1 feature match with MS2 in order to retrieve MS1 feature times |
| deltatime | <decimal> | 25.0 | Time tolerance (in seconds) for MS1 feature match with MS2 in order to retrieve MS1 feature times |
| maxsrforinclusion | <decimal> | 2.0 | maximum studentized residual for inclusion in database. Any observation with a higher studentized residual, based on the RT->NRT regression, will be excluded |
| maxsrforregression | <decimal> | 2.0 | maximum studentized residual for use in regression calculation for transforming RT to NRT |
| numpeptides | <integer> | 50000 | Number of random peptides to use in database creation ('randompeptides' mode only) |
| scanortimemode | <scan | time> | null | Use scans or times from features (default 'time') |
--createamtfeatureset [--featuremassadjustment=<decimal>] [--modifications=<residue><massdiff>[V][,...]] [--out=<filepath>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | AMT database for matching |
| featuremassadjustment | <decimal> | 0.0 | Adjust the masses of all AMT database features by this amount (in Daltons; for false positive testing) |
| modifications | <residue><massdiff>[V][,...] | null | a list of modifications to match on |
| out | <filepath> | null | output filepath |
--manageamt --mode=<removeoutlierobservations | removepredictedhoutliers | removefewobservations | removerunswithoutmassmatches | alignallruns | adjustacrylamide | removepeptideswithresidue | removefastapeptides | filterobservationsbypprophet> [--alignmentdegree=<integer>] [--fasta=<filepath>] [--fromacryltonot=<true | false>] [--maxentries=<integer>] [--maxruns=<integer>] [--minmassmatchpercent=<integer>] [--minobservations=<integer>] [--minpprophet=<decimal>] [--ms1features=<filepath>] [--out=<filepath>] [--residue=<value>] [--showcharts=<true | false>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | AMT database file |
| mode | <removeoutlierobservations | removepredictedhoutliers | removefewobservations | removerunswithoutmassmatches | alignallruns | adjustacrylamide | removepeptideswithresidue | removefastapeptides | filterobservationsbypprophet> | null | removeoutlierobservations: Remove all individual observations that are at least 3 standard deviations from the median for that peptide, for peptides with at least three observations removepredictedhoutliers: Remove all peptides with only one observation, for which that observation is at least 2 standard deviations away from the prediction removefewobservations: Remove all peptides with fewer than minobservations observations removerunswithoutmassmatches: Make mass matches between each run's entries and an MS1 feature file. Remove all runs that don't mass-match at least minmassmatchpercent percent of peptides alignallruns: Nonlinearly align all runs in the database to a single run, starting with the run with the most peptide overlap with other runs in the database. This is an extremely important step. adjustacrylamide: Adjust all Cysteine-bearing observations to take the H contribution of acrylamide into account. Direction of adjustment depends on the 'fromacryltonot' parameter removepeptideswithresidue: Remove all peptides containing a given residue removefastapeptides: Remove all peptides that occur in a specified FASTA database filterobservationsbypprophet: Remove all observations below 'minpprophet' PeptideProphet probability |
| minobservations | <integer> | 2 | Minimum number of observations for features kept in the database |
| minpprophet | <decimal> | null | Minimum PeptideProphet score (for 'filterobservationsbypprophet' mode) |
| out | <filepath> | null | (no details provided) |
| residue | <value> | null | Residue (for 'removepeptideswithresidue' mode) |
| showcharts | <true | false> | false | Show charts? |
| Argument | Usage | Default | Description |
|---|---|---|---|
| alignmentdegree | <integer> | 5 | Degree of polynomial to use in alignment (for 'alignallruns' mode) |
| fasta | <filepath> | null | FASTA database (removefastapeptides mode only) |
| fromacryltonot | <true | false> | null | For mode adjustacrylamide. If true, adjusts all observations to _remove_ the effect of acrylamide. If false, adjusts observations to _add_ the effect. |
| maxentries | <integer> | 2147483647 | Maximum DB entries (removerunswithoutmassmatches mode only) |
| maxruns | <integer> | 2147483647 | Maximum DB runs (removerunswithoutmassmatches mode only) |
| minmassmatchpercent | <integer> | 20 | Minimum percent of peptides mass-matched to MS1, per run (removerunswithoutmassmatches mode only) |
| ms1features | <filepath> | null | MS1 features (removerunswithoutmassmatches mode only) |
--matchamt --mode=<singlems1 | ms1dir> [--amtdbstructure=<value>] [--calcfdr=<true | false>] [--calibratematches=<true | false>] [--deltamassms1ms2ppm=<decimal>] [--deltatimems1ms2=<decimal>] [--dummymatch=<true | false>] [--embeddedms2=<filepath>] [--loosedeltaelution=<decimal>] [--loosedeltamass=<mass value>da|ppm] [--mappingpolynomialdegree=<integer>] [--massmatchdeltamass=<mass value>da|ppm] [--maxemiterations=<integer>] [--maxfractionstokeep=<integer>] [--maxregressionleverage=<decimal>] [--maxregressionstudres=<decimal>] [--maxsecondbestprob=<decimal>] [--minemiterations=<integer>] [--minfractionstokeep=<integer>] [--minmatchprob=<decimal>] [--minpprophet=<decimal>] [--minsecondbestprobdiff=<decimal>] [--modifications=<residue><massdiff>[V][,...]] [--ms1=<filepath>] [--ms1dir=<filepath>] [--ms2dir=<filepath>] [--mzxml=<filepath>] [--mzxmldir=<filepath>] [--out=<filepath>] [--outdir=<filepath>] [--removefractions=<true | false>] [--savechartsdir=<filepath>] [--showcharts=<true | false>] [--usems1foralignment=<true | false>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | AMT database for matching |
| mode | <singlems1 | ms1dir> | null | singlems1: Match against a single MS1 feature file ms1dir: Match against a directory of MS1 files, one by one |
| calibratematches | <true | false> | true | Calibrate MS1 feature masses using AMT matches? This is a good idea if you suspect there might be a miscalibration in the MS1 data. Even a small miscalibration can have a significant effect on matching by breaking the assumption that mass match error is distributed normally. |
| embeddedms2 | <filepath> | null | Embedded MS2 feature file from the same run that the MS1 features from matching are from. This will be used to help develop the mapping between Retention Time and Retention Time and Normalized Retention Time (the scale of the AMT database) for this run. (for 'singlems1' mode) |
| loosedeltaelution | <decimal> | 0.15000000596046448 | A loose deltaElution value. The EM probability model will be fit using all AMT matches in the loose match. The appropriate value for this parameter may depend somewhat on data, so you should adjust it accordingly if you find true matches being excluded or all of the true matches clustering near the center of the RT distribution. |
| loosedeltamass | <mass value>da|ppm | 20.0ppm | A loose mass tolerance for the initial AMT match. The EM probability model will be fit using all AMT matches in the loose match. The appropriate value for this parameter is largely data-independent. |
| massmatchdeltamass | <mass value>da|ppm | 5.0ppm | A mass tolerance value to be used when developing the RT->NRT map based on mass-only matching. This value is not used if the 'embeddedms2' or 'ms2dir' argument is specified. |
| minmatchprob | <decimal> | 0.10000000149011612 | Minimum AMT match probability to keep in output |
| minpprophet | <decimal> | 0.9 | Minimum PeptideProphet score to use from the embedded MS2 feature file(s) in building the RT->NRT map |
| modifications | <residue><massdiff>[V][,...] | C57.021,M16.0V | A list of modifications to use in matching. This list should contain all of the expected modifications in your MS1 data. During matching, AMT feature masses will be adjusted to account for any static mods specified here, and multiple features will be created to account for any variable mods. The default value is appropriate for non-isotopically-labeled MS1 data with iodoacetylated Cysteine and possibly oxidized Methionine. |
| ms1 | <filepath> | null | Input MS1 feature file for matching (for 'singlems1' mode) |
| ms1dir | <filepath> | null | Directory full of ms1 feature files for matching (for 'ms1dir' mode) |
| ms2dir | <filepath> | null | Embedded MS2 feature file (e.g., pepxml) directory. For 'ms1dir' mode. For each MS1 file, the corresponding MS2 feature file will be located in this directory by filename and used to aid in the mapping between Retention Time and Normalized Retention Time for the run. |
| mzxml | <filepath> | null | mzXML file used to populate MS2 scan times, for use in developing the RT->NRT map. This argument is not necessary if the MS2 feature file already contains retention times (see the 'populatems2times' command). (for 'singlems1' mode) |
| mzxmldir | <filepath> | null | Directory containing mzXML files from the same runs as the MS1 feature files. For each embedded MS2 feature file, the corresponding mzXML file will be located by filename and used to populate MS2 scan times, for use in developing the RT->NRT map. This argument is not necessary if the MS2 feature files already contain retention times (see the 'populatems2times' command). (for 'ms1dir' mode) |
| out | <filepath> | null | Output filepath for matching results (for 'singlems1' mode) |
| outdir | <filepath> | null | Output directory for all matching result files (for 'ms1dir' mode) |
| savechartsdir | <filepath> | null | Directory to save charts to. This can be used with or without 'showcharts' |
| showcharts | <true | false> | false | Show useful charts created when matching? Not recommended when matching large numbers of files |
| usems1foralignment | <true | false> | true | Use MS1 times, rather than MS2 times, for alignment? This is done by matching MS1 and MS2 in a tight window |
| Argument | Usage | Default | Description |
|---|---|---|---|
| amtdbstructure | <value> | null | For multi-fraction AMT databases from one or more experiments. Defines the arrangement of runs within the AMT database. This is only used to produce fancy heatmap charts of matches. Of the format '#rows,#cols,row|col,#experiments', e.g., '12,11,col,2' for a database with two experiments, each with 12 rows and 11 columns, whose runs are in order by column within the database |
| calcfdr | <true | false> | false | Calculate FDR for all results. We do this by making half of the database into decoy features, then repeating with the other half. This is for purposes of evaluating the EM model _only_! The probabilities calculated this way are not as accurate as the probabilities calculated without the decoy hits, because the decoy hits add to the background complexity of the null distribution. |
| deltamassms1ms2ppm | <decimal> | 10.0 | Mass tolerance for MS1 feature match with MS2 in order to retrieve MS1 feature times |
| deltatimems1ms2 | <decimal> | 25.0 | Time tolerance (in seconds) for MS1 feature match with MS2 in order to retrieve MS1 feature times |
| dummymatch | <true | false> | false | Do a dummy match against a mass-shifted database, rather than a real match. This is only used for visualizing the false match density. |
| mappingpolynomialdegree | <integer> | 5 | The degree of the polynomial to fit when mapping time to hydrophobicity nonlinearly. If you notice the mapping overfitting, you may reduce this value. If you think the mapping is not capturing all of the nonlinear quirks of the data, try increasing it. |
| maxemiterations | <integer> | 200 | Maximum number of iterations for the EM algorithm deciding probability values |
| maxfractionstokeep | <integer> | 0 | Maximum number of fractions to keep (for "removefractions"). Default is actually the number of runs in the database |
| maxregressionleverage | <decimal> | 12.0 | Maximum leverage /numerator/ (denominator is N) for features included in the modal regression to map RT to Hydrophobicity. If you have spurious features at the beginning or end of the gradient, you may want to reduce this value. |
| maxregressionstudres | <decimal> | 3.0 | Maximum studentized residual for features included in the modal regression to map RT to Hydrophobicity. You may want to decrease this value if many spurious matches are throwing off the regression, or increase it if legitimate features are being excluded. |
| maxsecondbestprob | <decimal> | 0.5 | Maximum probability of the second-best AMT match, in order to keep best match |
| minemiterations | <integer> | 30 | Minimum number of iterations for the EM algorithm deciding probability values |
| minfractionstokeep | <integer> | 1 | Minimum number of fractions to keep (for "removefractions") |
| minsecondbestprobdiff | <decimal> | 0.10000000149011612 | Minimum difference between best and secodn-best probability, in order to keep best match |
| removefractions | <true | false> | false | Remove fractions from the database that are unlike the MS1 matching fraction. This is only recommended for very dense, extensively fractionated databases built from hundreds of runs. |
--proteinrollup --mode=<digestprotxml | tabfile | createpepxmlfromtabfile | collapsepeptides | rollupgenes | rollupgenesfrompeptides> [--amtxml=<filepath>] [--expanded=<true | false>] [--fasta=<filepath>] [--genelookupfile=<filepath>] [--indir=<filepath>] [--minpeptides=<integer>] [--minprotxmlprobability=<decimal>] [--minuniquepeptides=<integer>] [--out=<filepath>] [--outdir=<filepath>] [--peptidelistfile=<filepath>] [--pepxml=<filepath>] [--protxml=<file>,<file>,...] [--showcharts=<true | false>] <filepath> <filepath> ...
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed ...) | <filepath> | null | Input feature file(s) |
| mode | <digestprotxml | tabfile | createpepxmlfromtabfile | collapsepeptides | rollupgenes | rollupgenesfrompeptides> | null | digestprotxml: Digest the output of ProteinProphet tabfile: Take as input a single tab-delimited ratio file in a special format createpepxmlfromtabfile: Create a pepXML file, using an input tab-delimited ratio file collapsepeptides: collapse per-peptide row entries into one per protein rollupgenes: Roll up proteins to gene level rollupgenesfrompeptides: Rollup peptides to proteins and then to gene level in one step |
| amtxml | <filepath> | null | AMT database file (for spectral count info) |
| expanded | <true | false> | false | Peptide expanded format (for gene rollup) |
| fasta | <filepath> | null | Input protein database |
| genelookupfile | <filepath> | null | Gene lookup file for IPI numbers |
| indir | <filepath> | null | Directory of input files |
| minpeptides | <integer> | 1 | Minimum peptides for a protein to be collapsed |
| minprotxmlprobability | <decimal> | 0.0 | Minimum probability assigned by protXml required for the protein to be considered to be identified |
| minuniquepeptides | <integer> | 1 | Minimum number of unique peptides for a protein to be considered to be identified in a protXml file |
| out | <filepath> | null | output filepath |
| outdir | <filepath> | null | output directory |
| peptidelistfile | <filepath> | null | Input file containing one peptide sequence per line |
| pepxml | <filepath> | null | pepXml file for use in digesting protXml file |
| protxml | <file>,<file>,... | null | ProtXML file(s) |
| showcharts | <true | false> | false | Show charts |
--mrm [--auc_cutoff=<decimal>] [--peak_height_cutoff=<decimal>] [--peakstrategy=<BasicElutionCurveStrategy | BasicLowIntensityElutionCurveStrategy | ThermoElutionCurveStrategy>] [--precursor_tolerance=<decimal>] [--product_tolerance=<decimal>] [--selected_ion_monitoring=<true | false>] [--sic_tolerance=<decimal>] [--synclh=<true | false>] [--trace_all_fragments=<true | false>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | input mzXML file containing SRM/MRM scans |
| auc_cutoff | <decimal> | 0.0 | Use "AUC_CUTOFF=nnnnn" to define a minimum peak area to accept |
| peak_height_cutoff | <decimal> | 0.0 | Use "PEAK_HEIGHT_CUTOFF=nnnnn" to define minimum peak height (within best curve) to accept |
| peakstrategy | <BasicElutionCurveStrategy | BasicLowIntensityElutionCurveStrategy | ThermoElutionCurveStrategy> | BasicElutionCurveStrategy | Use peakstrategy to set the elution curve discovery and AUC determination algorithms |
| precursor_tolerance | <decimal> | 0.009999999776482582 | Use "PRECURSOR_TOLERANCE=nnnn" to set the tolerance for discriminating precursor mass sets |
| product_tolerance | <decimal> | 0.10000000149011612 | Use "PRODUCT_TOLERANCED=nnnn" to set the tolerance for discriminating between the masses of different product ions |
| selected_ion_monitoring | <true | false> | false | Set "SELECTED_ION_MONITORING" to TRUE if MS1 SIM scans are present and you want to use them exclusively for precursor chromatagrams |
| sic_tolerance | <decimal> | 1.0 | Use "SIC_TOLERANCE=nnnn" to set the tolerance around the precursor ion for MS1 single ion chromatograms |
| synclh | <true | false> | true | Set "SYNCHLH" to TRUE to synchronize heavy and light elution regions (applicable in AQUA/SILAC analyses; transition.tsv file must be present) |
| trace_all_fragments | <true | false> | true | Set "TRACE_ALL_FRAGMENTS" to TRUE to draw pale elution curves over all product ions, instead of gray spikes |
--qaexperiment --allpepxml=<filepath> --allprotxml=<filepath> --protgenefile=<filepath> --qadir=<filepath> [--force=<true | false>] [--labelmassdiff=<decimal>] [--minpeptideprophet=<decimal>] [--minproteinprophet=<decimal>] [--mzxmldir=<filepath>] [--noms1=<true | false>]
| Argument | Usage | Default | Description |
|---|---|---|---|
| allpepxml | <filepath> | null | all.pep.xml filepath |
| allprotxml | <filepath> | null | all.prot.xml filepath |
| protgenefile | <filepath> | null | File associating gene symbols with protein accession numbers |
| qadir | <filepath> | null | QA Output Root Directory |
| force | <true | false> | false | Force re-creation of output files if they exist? |
| labelmassdiff | <decimal> | 3.0 | Isotopic label mass difference |
| minpeptideprophet | <decimal> | 0.75 | Minimum PeptideProphet probability |
| minproteinprophet | <decimal> | 0.8999999761581421 | Minimum ProteinProphet probability |
| mzxmldir | <filepath> | null | mzXML Directory |
| noms1 | <true | false> | false | No MS1 analysis -- only pepXML and protXML |
--qaprotxml --out=<filepath> --protgenefile=<filepath> [--minpprophet=<decimal>] <filepath>
| Argument | Usage | Default | Description |
|---|---|---|---|
| (unnamed) | <filepath> | null | all.prot.xml filepath |
| out | <filepath> | null | Output File |
| protgenefile | <filepath> | null | File associating gene symbols with protein accession numbers |
| minpprophet | <decimal> | 0.0 | Minimum ProteinProphet score to keep in output |