PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data!

Versions 1.1.3, 1.11.0, 1.13.3, 1.13.6, 1.14.4, 1.14.6, 1.15.0, 1.15.1, 1.16.0, 1.16.13, 1.16.14, 1.16.15, 1.16.16, 1.16.17, 1.16.20, 1.16.22, 1.16.23, 1.16.26, 1.16.29, 1.16.3, 1.16.30, 1.16.31, 1.16.32, 1.16.35, 1.16.4
License Apache License, Version 2.0
Links biotools: peptide-shaker, doi: 10.1038/nbt.3109


With an activated Bioconda channel (see 2. Set up channels), install with:

conda install peptide-shaker

and update with:

conda update peptide-shaker


PeptideShaker is Java program that comes with a custom wrapper shell script. This shell wrapper is called “opsin” and is on $PATH by default. By default “-Xms512m -Xmx1g” is set in the wrapper. If you want to overwrite it you can specify these values directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with “peptide-shaker -Xms512m -Xmx1g”


A Docker container is available at