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, 1.16.3|
|License||Apache License, Version 2.0|
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 https://quay.io/repository/biocontainers/peptide-shaker.