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MSPathFinder Usage
MSPathFinderT finds peptides in top-down LC-MS/MS datasets. Similar to database search engines for bottom-up, it takes a fasta file, a spectrum file, and a list of modifications as an input and reports proteoform spectrum matches (PsSMs) and their scores. These results are output in a tab-separated format and in a MzIdentML file.
- An instrument file or previously created .pbf file
- A previously created .ms1ft file (optional)
- Can also read .msalign from MS-Align+, or _isos.csv from ICR2LS or Decon2LS
- Command line options
- A *_IcTarget.tsv file (if target search done)
- A *_IcDecoy.tsv file (if decoy search done)
- A *_IcTda.tsv file (if target and decoy searches done)
- A *.mzid file
- A *.ms1ft (if feature file not provided)
- A *_ms1ft.png image of features (if feature file not provided)
- A *.pbf file (if a .pbf file was not provided)
MSPathFinderT version 1.0.7569 (September 21, 2020)
Usage: MSPathFinderT.exe
-?, -help Show this help screen
-s, -specFile, arg#1 Required. Spectrum File (*.raw)
-d, -database Required. Database File (*.fasta or *.fa or *.faa)
-o, -outputDir Output Directory
-ic Search Mode (Default: SingleInternalCleavage (or 1))
Possible values are:
0 or 'NoInternalCleavage': No Internal Cleavage
1 or 'SingleInternalCleavage': Single Internal Cleavage
2 or 'MultipleInternalCleavages': Multiple Internal
Cleavages
-tagSearch Include Tag-based Search (use true or false;
or use '0' for false or '1' for true) (Default: True)
-n, Number of results to report for each mass spectrum
-NumMatchesPerSpec (Default: 1)
-IncludeDecoy, Include decoy results in the _IcTda.tsv file
-IncludeDecoys (Default: False)
-mod Path to modification file that defines static and dynamic
modifications. Modifications can alternatively be defined
in a parameter file, as specified by /ParamFile or
-ParamFile
Modifications defined using the -mod switch take
precedence over modifications defined in a parameter file
(Default: empty string, meaning no modifications)
-tda Database search mode:
0: don't search decoy database,
1: search shuffled decoy database
(Default: 0, Min: -1, Max: 1)
-t, -precursorTol, Precursor Tolerance (in PPM) (Default: 10)
-PMTolerance
-f, -fragmentTol, Fragment Ion Tolerance (in PPM) (Default: 10)
-FragTolerance
-minLength Minimum Sequence Length (Default: 21, Min: 0)
-maxLength Maximum Sequence Length (Default: 500, Min: 0)
-minCharge Minimum precursor ion charge (Default: 2, Min: 1)
-maxCharge Maximum precursor ion charge (Default: 50, Min: 1)
-minFragCharge Minimum fragment ion charge (Default: 1, Min: 1)
-maxFragCharge Maximum fragment ion charge (Default: 20, Min: 1)
-minMass Minimum sequence mass in Da (Default: 3000)
-maxMass Maximum sequence mass in Da (Default: 50000)
-feature *.ms1ft, *_isos.csv, or *.msalign (Default: Run ProMex)
-threads Maximum number of threads, or 0 to set automatically
(Default: 0, Min: 0)
-act, Activation Method (Default: Unknown (or 6))
-ActivationMethod Possible values are:
0 or 'CID'
1 or 'ETD'
2 or 'HCD'
3 or 'ECD'
4 or 'PQD'
5 or 'UVPD'
6 or 'Unknown'
-scansFile Text file with MS2 scans to process
-flip If specified, FLIP scoring code will be used
(supports UVPD spectra) (Default: False)
-ParamFile Path to a file containing program parameters. Additional
arguments on the command line can supplement or override
the arguments in the param file. Lines starting with '#'
or ';' will be treated as comments; blank lines are
ignored. Lines that start with text that does not match a
parameter will also be ignored.
-CreateParamFile Create an example parameter file. Can supply a path; if
path is not supplied, the example parameter file content
will output to the console.
NOTE: arg#1, arg#2, etc. refer to positional arguments, used
like "AppName.exe [arg#1] [arg#2] [other args]".
Different command line options can result in drastically different runtimes, particularly the -m SearchMode parameter.
- If the SearchMode is 2, the search will be relatively fast (<1 hour usually); for SearchMode 1, it is slower due to the added complexity (1-12 hours usually); for SearchMode 0, it will be significantly slower, especially for larger protein collections and richer datasets (runtime is usually on the order of days, but can reach weeks).
- Enabling tag-based searching with
-tagSearch 1can give 5% to 10% more matches, but can increase the runtime by 30% to 50%.
With previously created .pbf and .ms1ft files:
MSPathFinderT.exe -s MyDataset.pbf -feature MyDataset.ms1ft -d C:\FASTA\ProteinList.fasta -o C:\WorkFolder -t 10 -f 10 -m 1 -tda 1 -minLength 21 -maxLength 300 -minCharge 2 -maxCharge 30 -minFragCharge 1 -maxFragCharge 15 -minMass 3000 -maxMass 50000 -mod MSPathFinder_Mods.txt
With a instrument/spectra file:
MSPathFinderT.exe -s MyDataset.raw -d C:\FASTA\ProteinList.fasta -o C:\WorkFolder -t 10 -f 10 -m 1 -tda 1 -minLength 21 -maxLength 300 -minCharge 2 -maxCharge 30 -minFragCharge 1 -maxFragCharge 15 -minMass 3000 -maxMass 50000 -mod MSPathFinder_Mods.txt
MSPathFinderT.exe -s MyDataset.raw -d C:\FASTA\ProteinList.fasta -o C:\WorkFolder -t 10 -f 10 -m 1 -tda 1 -minLength 21 -maxLength 300 -minCharge 2 -maxCharge 30 -minFragCharge 1 -maxFragCharge 15 -minMass 3000 -maxMass 50000 -mod MSPathFinder_Mods.txt
Using a parameter file:
MSPathFinderT.exe -s C:\WorkDir\Dataset.pbf -feature C:\WorkDir\Dataset.ms1ft -d C:\WorkDir\Proteins.fasta -o C:\WorkDir /ParamFile:C:\WorkDir\MSPF_MetOx_CysDehydro_NTermAcet_SingleInternalCleavage_ReportTop2.txt
Minimum required:
- .NET 4.7.2
Minimum recommended:
- 2.4 GHz, quad-core CPU
- 16 GB RAM
- Windows 7 or newer
- 250 GB hard drive