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).

• Database downloading and formatting.

• Peptide assignment validation with PeptideProphet.

• Multi-level integrative analysis with iProphet.

• PTM site localization with PTMProphet.

• Protein inference with ProteinProphet.

• 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.

• Label-free quantification via spectral counting and MS1 intensities.

• Label-based quantification using TMT and iTRAQ.

• Multi-level detailed reports for peptides, ions, and proteins.

• Support for REPRINT and MSstats.

How to Use

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

Documentation

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