MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. It supports the HUPO PSI standard input file (mzML) and saves results in the mzIdentML format, though results can easily be transformed to TSV. ProteomeXchange supports Complete data submissions using MS-GF+ search results.
MS-GF+ identifies peptides in LC-MS/MS datasets. It is optimized for a variety of spectral types, i.e., combinations of fragmentation method, instrument, enzyme, and experimental protocols. It supports a variety of input file formats, including mzML, mzXML, Mascot Generic File (mgf), MS2 files, Micromass Peak List files (pkl), and Concatenated DTA files (_dta.txt)
Latest version; zip file contains:
| File | Description | Requirements |
|---|---|---|
| MSGFPlus.jar | MS-GF+ search engine | Java Runtime |
| MzidToTsvConverter.exe | Converts .mzid files to a tab-delimited text file | .NET Runtime 4.6.2 or newer |
| Documentation files | HTML files explaining how to use the software | n/a |
| Example files | Example modification files and example results | n/a |
Pages describing the use of MS-GF+, the Mzid to TSV Converter, and the Suffix Array Builder (BuildSA) are hosted on GitHub, see the MS-GF+ Documentation
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