MS-GF+ peptide search engine#

MS-GF+: MS-GF+ (aka MSGF+ or MSGFPlus) [KIM2014] performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. MSG-GF+ is released under specific License from California University.

Note

In quantms, msgf+ has proved to identified more than 15% PSMs than Comet search engine. However, users of cloud infrastructure needs to consider that msgf+ may slow the data processing and consume more memory than Comet search engine.

_images/resources-search-engine.png

In quantms, PSMs are exported from the search engine into .idXML (read more Formats in quantms) without filtering for the re-scoring (see Peptide identification from fragment spectra) step with percolator. The pipeline stores these original file results in the result folder under searchenginemsgf.

References#

[KIM2014]

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