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Philosopher is fast, easy-to-use, scalable, and versatile data analysis software for mass spectrometry-based proteomics. Philosopher is dependency-free and can analyze both traditional database searches and open searches for post-translational modification (PTM) discovery.


Download the latest version here.

How to Use


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 developers

Felipe da Veiga Leprevost

Sarah Haynes

Alexey Nesvizhskii’s research group