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.
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.
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.