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PeptideShaker free download for Mac


Version 1.16.41

Visualization of peptide and protein identification results from multiple search engines.

PeptideShaker overview

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!

PeptideShaker currently supports nine different analysis tasks:

  • Overview: get a simple yet detailed overview of all the proteins, peptides and PSMs in your dataset.
  • Spectrum IDs: compare the search engine performance and see how the search engine results are combined.
  • Fractions: inspect from which fractions proteins and peptides are likely to come from.
  • Modifications: get a detailed view of the post-translational modifications in the dataset.
  • 3D Structure: map the detected peptides and modifications onto corresponding PDB structures.
  • GO Enrichment: perform GO enrichment and find enriched GO terms in your dataset.
  • Validation: inspect and fine tune the validation process.
  • QC Plots: examine the quality of the results with Quality Control plots.
  • Reshake PRIDE: re-analyze public datasets in PRIDE as if they were your own.

All data can also easily be exported for follow up analysis in other tools.

What’s new in version 1.16.41

Updated on Jul 09 2019

Version 1.16.41:
  • Feature improvement: Re-implemented the PRIDE Reshake to not show all projects but rather the results of the user’s search.
  • Library update: updated utilities to version 4.12.15.





110.7 MB



App requirements

  • Intel 64
  • OS X 10.7.3 or later
  • Java version 7 or newer
  • 4 GB of RAM is recommended
  • Monitor with 1280 x 800 resolution or higher
  • For more information please visit this page
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