PeptideShaker

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.