# MS-GF+ Documentation

### Contacts

PNNL Proteomics [proteomics@pnnl.gov]
Sangtae Kim [sangtae.kim (at) gmail.com]

### Summary

- MS-GF+ is an MS/MS database search tool that is sensitive (it identifies more peptides than other database search tools and as many peptides as spectral library search tools) and universal (works well for diverse types of spectra, different configurations of MS instruments and different experimental protocols).
- MS-GF+ supports the HUPO PSI standard input (mzML) and output (mzIdentML).

### Usage and help

MS-GF+ Usage (ChangeLog)

MS-GF+ Parameter files (aka config files)

MS-GF+ Mzid to Tsv output converter

MS-GF+ Suffix Array builder

Training new MS-GF+ scoring models

MS-GFDB (obsolete; differences from MS-GFDB to MS-GF+)

### Publications

MS-GF+ makes progress towards a universal database search tool for proteomics.
Kim S, Pevzner PA. Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.
PubMed ID 25358478

Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases.
Kim S, Gupta N, Pevzner PA. J Proteome Res. 2008 Aug;7(8):3354-63. doi: 10.1021/pr8001244.
PubMed ID 18597511