Software

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Program Paper Availability Authors Description
Byonic/Preview paper $$$ Marshall Bern and Yong Kil
Protein Metrics
Peptide/protein identificaiton and data visualization. Stand alone or part of Proteome Discoverer.
Crux paper FREE Christopher Park / Aaron Klammer
William Noble / Michael MacCoss
University of Washington
Crux is a software toolkit for tandem mass spectrometry analysis, with a focus on peptide identification.
GPMAW $$$ Mainly for single-protein analysis, but has an interface for X!Tandem and a lot of protein analysis and planning tools.
GreyLag FREE Mike Coleman Greylag is a suite of programs for MS/MS peptide identification by sequence database search.
Mascot paper $$$ David Perkins
John Cotrell
Matrix Science
Widely used commercial database searching software which has been around since at least 1999.
MassMatrix paper FREE Hua Xu
Michael Freitas
the Ohio State University
MassWiz paper FREE Amit Kumar Yadav
Debasis Dash
Institute of Genomics and Integrative Biology
MassWiz is an open-source integrated solution for Mass Spectrometry based protein and peptide identifications.
MaxQuant/Andromeda paper FREE J├╝rgen Cox
Matthias Mann
Max Planck Institute of Biochemistry
Identifies peptides and proteins, performs PTM localization, and quantifies SILAC labeled peptides.
MyriMatch paper FREE David Tabb
Vanderbilt University
MyriMatch is a tool designed to take experimental data from shotgun proteomics experiments and compare those spectra against sequences in a known database of proteins.
OMSSA paper FREE Lewis Geer
NIH
Freely available open source software for database searching from NCBI.
Peaks Studio paper $$$ Bioinformatics Solutions It performs de novo sequencing to generate sequence tags to assist its search engine. Useful if working on organisms will little or no genome information as you can look through the unmatched de novo spectra and BLAST search those.
pFind paper FREE Dequan Li
Wen Gao
Chinese Academy of Sciences
Phenyx $$$ GeneBio
ProbID paper FREE Ning Zhang
Benno Schwikowski / Ruedi Aebersold
Institute for Systems Biology
ProLuCID paper FREE Tao Xu
John Yates
The Scripps Research Institute
Protein Lynx Global Server (PLGS) $$$ Waters Corporation Database search software and full data analysis package
ProteinProspector FREE Alma Burlingame
University of California, San Francisco
Lots of useful utilities (protein digestion, isotope simulator, etc.) but also batch MS/MS searching capabilities.
ProteinPilot $$$ AB Sciex
Sequest paper $$$ Jimmy Eng
John Yates
University of Washington
Published in 1994. It was the first search engine and is still widely used. Currently distributed by Thermo Scientific.
Spectrum Mill $$$ Agilent Technologies
SPIRE FREE Eugene Kolker The SPIRE (Systematic Protein Investigative Research Environment) proteomics analysis pipeline provides experiment-specific analysis of mass spectrometry data in order to identify proteins and peptides, as well as to conduct label-free expression and relative expression analyses.
X!Tandem paper FREE Robertson Craig
Ronald Beavis
University of Manitoba
Freely available open source software for database searching.
ZCore paper $$$ Rovshan Sadygov
Thermo Fisher Scientific
for ETD spectra search