U.S. Department of Energy

Pacific Northwest National Laboratory

MS-GF+

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.

Area of Research: 
Description: 

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)

Software Instructions: 

MSGF+ Download

Download MSGF+ from the MSGF+ releases page on GitHub: https://github.com/MSGFPlus/msgfplus/releases

Zip file MSGFPlus_v20181015.zip includes:

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

Documentation

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

Publications

  • MS-GF+: Universal Database Search Tool for Mass Spectrometry, Sangtae Kim, Pavel A. Pevzner,
    Nat Commun. 2014 Oct 31;5:5277. doi: 10.1038/ncomms6277.
    http://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.
    http://www.ncbi.nlm.nih.gov/pubmed/18597511

Source code

Acknowledgment

All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, as shown in the Readme file for the given application or on the website that more fully describes the application.

 

Disclaimer

These programs are primarily designed to run on Windows machines. Please use them at your own risk. This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights.

Portions of this research were supported by the NIH National Center for Research Resources (Grant RR018522), the W.R. Wiley Environmental Molecular Science Laboratory (a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at PNNL), and the National Institute of Allergy and Infectious Diseases (NIH/DHHS through interagency agreement Y1-AI-4894-01). PNNL is operated by Battelle Memorial Institute for the U.S. Department of Energy under contract DE-AC05-76RL0 1830.

We would like your feedback about the usefulness of the tools and information provided by the Resource. Your suggestions on how to increase their value to you will be appreciated. Please e-mail any comments to proteomics@pnl.gov

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