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Sarah Haynes edited this page Nov 8, 2019 · 5 revisions

Welcome to the Philosopher wiki!

Philosopher provides easy access to third-party tools and custom algorithms for proteomics analysis, from database searching to functional protein reports. Philosopher is also well-equipped for open search analysis, providing extended versions of PeptideProphet and ProteinProphet for peptide validation and protein inference. To date, Philosopher is the only proteomics toolkit that allows you to process and analyze closed and open search results.

  • Sequence database downloading and formatting

  • Peptide-spectrum matching with Comet, compatibility with other search engines such as MSFragger

  • Peptide assignment validation with PeptideProphet

  • Multi-level integrative analysis with iProphet

  • Localization of post-translational modifications with PTMProphet

  • Protein inference with ProteinProphet

  • Open search result validation

  • 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

  • Clustering analysis for proteomics results

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

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