(How to migrate from MS-GFDB to MS-GF)
Usage: java -Xmx3500M -jar MSGFPlus.jar -s SpectrumFile (*.mzML, *.mzXML, *.mgf, *.ms2, *.pkl or *_dta.txt) Spectra should be centroided. Profile spectra will be ignored. -d DatabaseFile (*.fasta or *.fa) [-o OutputFile (*.mzid)] (Default: SpectrumFileName.mzid) [-t PrecursorMassTolerance] (e.g. 2.5Da, 20ppm or 0.5Da,2.5Da, Default: 20ppm) Use comma to set asymmetric values. E.g. "-t 0.5Da,2.5Da" will set 0.5Da to the minus (expMass<theoMass) and 2.5Da to plus (expMass>theoMass) [-ti IsotopeErrorRange] (Range of allowed isotope peak errors, Default:0,1) Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation. On Windows, put the range inside "" (e.g. "0,1"). The combination of -t and -ti determins the precursor mass tolerance. E.g. "-t 20ppm -ti -1,2" tests abs(exp-calc-n*1.00335Da)<20ppm for n=-1, 0, 1, 2. [-thread NumThreads] (Number of concurrent threads to be executed, Default: Number of available cores) [-tda 0/1] (0: don't search decoy database (Default), 1: search decoy database) [-m FragmentMethodID] (0: As written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD) [-inst InstrumentID] (0: Low-res LCQ/LTQ (Default), 1: High-res LTQ, 2: TOF, 3: Q-Exactive) [-e EnzymeID] (0: unspecific cleavage, 1: Trypsin (Default), 2: Chymotrypsin, 3: Lys-C, 4: Lys-N, 5: glutamyl endopeptidase, 6: Arg-C, 7: Asp-N, 8: alphaLP, 9: no cleavage) [-protocol ProtocolID] (0: NoProtocol (Default), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho) [-ntt 0/1/2] (Number of Tolerable Termini, Default: 2) E.g. For trypsin, 0: non-tryptic, 1: semi-tryptic, 2: fully-tryptic peptides only. [-mod ModificationFileName] (Modification file, Default: standard amino acids with fixed C+57) [-minLength MinPepLength] (Minimum peptide length to consider, Default: 6) [-maxLength MaxPepLength] (Maximum peptide length to consider, Default: 40) [-minCharge MinCharge] (Minimum precursor charge to consider if charges are not specified in the spectrum file, Default: 2) [-maxCharge MaxCharge] (Maximum precursor charge to consider if charges are not specified in the spectrum file, Default: 3) [-n NumMatchesPerSpec] (Number of matches per spectrum to be reported, Default: 1) [-addFeatures 0/1] (0: output basic scores only (Default), 1: output additional features) [-ccm ChargeCarrierMass] (Mass of charge carrier, Default: mass of proton (1.00727649)) Example (high-precision): java -Xmx3500M -jar MSGFPlus.jar -s test.mzXML -d IPI_human_3.79.fasta -t 20ppm -ti -1,2 -ntt 0 -tda 1 -o testMSGFPlus.mzid Example (low-precision): java -Xmx3500M -jar MSGFPlus.jar -s test.mzXML -d IPI_human_3.79.fasta -t 0.5Da,2.5Da -ntt 0 -tda 1 -o testMSGFPlus.mzid
If multiple MS-GF+ processes access the same database file, it is strongly recommended to index the database prior to the database search by running BuildSA (see below).
If -tda 1 is specified, MS-GF+ automatically creates a combined target/reversed database file (DBFileName.revConcat.fasta). Thus, when specifying "-d" parameter, DatabaseFile must contain only target proteins.
The meaning and the default value have changed as of version 8442 (Sept. 2012).
MS-GF+ outputs results as an mzIdentML (version 1.1) file. See http://www.psidev.info/mzidentml/ for details on the mzIdentML format. For every PSM, MS-GF+ reports the scores.
Using MzIDToTsv one can convert MS-GF+ output (*.mzid) into the tsv format
#SpecFile | SpecID | ScanNum | FragMethod | Precursor | IsotopeError | PrecursorError(ppm) | Charge | Peptide | Protein | DeNovoScore | MSGFScore | SpecEValue | EValue | QValue | PepQValue |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
test.mgf | index=0 | 26559 | CID | 1285.3457 | 1 | -5.049801 | 3 | K.IGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHK.T | test | 299 | 244 | 1.4807088E-31 | 3.2871733E-29 | 0.0 | 0.0 |
test.mgf | index=0 | 26559 | CID | 1285.3457 | 1 | -5.049801 | 3 | K.IGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTSTTHK.T | test_isoform | 299 | 244 | 1.4807088E-31 | 3.2871733E-29 | 0.0 | 0.0 |
test.mgf | index=1 | -1 | CID | 870.11743 | 0 | 0.14029178 | 3 | K.NLANPTSVILASIQM+15.995LEYLGMADK.A | test2 | 156 | 136 | 2.2559852E-22 | 4.4217308E-20 | 0.0 | 0.0 |