cvn001 / msgfplus

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Overview

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+ 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).

Requirements

Java Runtime v1.6 or higher (use 64-bit Java)
At least 2GB of memory (recommended to use 4GB); larger FASTA files require more memory

Downloads / Updates

• https://github.com/MSGFPlus/msgfplus/releases
• https://omics.pnl.gov/software/ms-gf

Version number notes

As of January 20, 2016 (commit 375d462) the version numbering scheme changed. Previously the version number was the SVN commit number; git does not have simple commit numbers, so MSGFPlus was changed to a date-based version numbering scheme.

An example: v10282 became v2016.01.20

Installation

Unzip MSGFPlus.zip
Place MSGFPlus.jar in any folder

Usage Information

Type java -jar MSGFPlus.jar for command line arguments.

To convert an mzid output file into a tsv file, run java -cp MSGFPlus.jar edu.ucsd.msjava.ui.MzIDToTsv

Alternatively, use the Mzid-To-Tsv-Converter, which is a faster converter that supports larger result files. It is a C# application that works on Windows or on Linux using mono. Download the Mzid-To-Tsv-Converter from GitHub.

For detailed documentation, see the "doc" subfolder, or visit:

• GitHub repo HTML help pages
• (previously at https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355)

Contact Information

PNNL Proteomics [[email protected]]
Sangtae Kim [sangtae.kim (at) gmail.com]

Publications

MS-GF+ makes progress towards a universal database search tool for proteomics, Sangtae Kim and Pavel A. Pevzner, Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.
https://www.ncbi.nlm.nih.gov/pubmed/25358478

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases, Sangtae Kim, Nitin Gupta, and Pavel Pevzner, J Proteome Res. 2008 Aug;7(8):3354-63. doi: 10.1021/pr8001244.
https://www.ncbi.nlm.nih.gov/pubmed/18597511

Source

https://github.com/MSGFPlus/msgfplus