recipe peptide-shaker

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!

License:Apache License, Version 2.0
Links:biotools: peptide-shaker, doi: 10.1038/nbt.3109
package peptide-shaker

(downloads) docker_peptide-shaker


1.16.36-0, 1.16.35-1, 1.16.35-0, 1.16.32-1, 1.16.31-1, 1.16.30-1, 1.16.29-1, 1.16.26-1, 1.16.23-0, 1.16.22-0, 1.16.20-0, 1.16.17-0, 1.16.16-1, 1.16.16-0, 1.16.15-1, 1.16.15-0, 1.16.14-0, 1.16.13-1, 1.16.13-0, 1.16.4-1, 1.16.4-0, 1.16.3-1, 1.16.3-0, 1.16.0-1, 1.16.0-0, 1.15.1-0, 1.15.0-0, 1.14.6-0, 1.14.4-0, 1.13.6-1, 1.13.6-0, 1.13.3-1, 1.13.3-0, 1.11.0-1, 1.11.0-0, 1.1.3-3, 1.1.3-2, 1.1.3-1

Required By:


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

conda install peptide-shaker

and update with:

conda update peptide-shaker

or use the docker container:

docker pull<tag>

(see peptide-shaker/tags for valid values for <tag>)


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”