PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
Database downloading and formatting.
Peptide-spectrum matching with MSFragger and Comet.
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.
Quantification based on functional protein groups.
Multi-level detailed reports for peptides, ions, and proteins.
Support for REPRINT and MSstats.
Download the latest version here.
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.