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Welcome to the Philosopher wiki!

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).

• Sequence database downloading and formatting

• Peptide assignment validation with PeptideProphet

• Multi-level integrative analysis with iProphet

• Localization of post-translational modifications 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
  • PickedFDR for scalable estimations.
  • Razor peptide assignment for better quantification and interpretation

• Label-free quantification via spectral counting and MS1 intensities

• Label-based quantification using TMT isobaric tags

• Multi-level detailed reports including peptides, ions, and proteins