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).
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Database downloading and formatting.
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Peptide assignment validation with PeptideProphet.
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Multi-level integrative analysis with iProphet.
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PTM site localization with PTMProphet.
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Protein inference with ProteinProphet.
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FDR filtering with custom algorithms.
- Two-dimensional filtering for simultaneous control of PSM and Protein FDR levels.
- Sequential FDR estimation for large data sets using filtered PSM and proteins lists.
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Label-free quantification via spectral counting and MS1 intensities.
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Label-based quantification using TMT and iTRAQ.
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Multi-level detailed reports for peptides, ions, and proteins.
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Support for REPRINT and MSstats.
Philosopher is part of FragPipe which has a user-friendly GUI.
See the documentation for more details about the available commands.
If you have any questions or remarks please use the Discussion board. If you want to report a bug, please use the Issue tracker.
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.