PeptideShaker is a platform for the interpretation of proteomics identification results obtained from various search and de novo engines. Currently, it supports X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, OMSSA, Andromeda, Mascot, MetaMorpheus, Novor, Sage, DirecTag, and mzidentML.

This tool can import results obtained from searchGUI, which is a GUI for running proteomics identification search engines. Once imported, these results are aggregated into a single identification set. PeptideShaker annotates spectra, calculates a consensus score, handles mapping of sequences and protein inference, scores post-translational modification localization, performs statistical validation, along with quality control, and finally annotates the results using several sources of information.

The utility can be used from the command-line and allows you to visualize the results using navigational tools. It supports both local data sets and those stored in the ProteomeXchange PRIDE repository.

PeptideShaker supports nine analysis tasks that give you an overview of proteins, peptides, and PSMs in your data set while also allowing for more in-depth analysis. You can analyze search engine performance and results, inspect fractions and modifications, map 3D structures, perform GO enrichment, fine-tune the validation process, analyze results with quality control plots, and re-analyze public datasets in PRIDE.