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.