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Philosopher is a fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. It is also a depencency-free wraper of Trans-Proteomic Pipeline (PeptideProphet, iProphet, PTMProphet, and ProteinProphet).

How to Use

Philosopher is part of FragPipe which has a user-friendly GUI.


See the documentation for more details about the available commands.

Questions, requests and bug reports

If you have any questions or remarks please use the Discussion board. If you want to report a bug, please use the Issue tracker.

How to cite

da Veiga Leprevost F, Haynes SE, Avtonomov DM, Chang HY, Shanmugam AK, Mellacheruvu D, Kong AT, Nesvizhskii AI. Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods. 2020 Sep;17(9):869-870. doi: 10.1038/s41592-020-0912-y. PMID: 32669682; PMCID: PMC7509848.

About the authors

Alexey Nesvizhskii’s research group