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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. Database downloading and formatting.

Peptide-spectrum matching with 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.

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.

Quantification based on functional protein groups.

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