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. Author manuscript; available in PMC: 2021 Sep 1.
Published in final edited form as: Nat Methods. 2020 Sep;17(9):869–870. doi: 10.1038/s41592-020-0912-y

Figure 1. Philosopher provides easy access to a complete suite of computational proteomics tools.

Figure 1.

Functions include protein sequence database download and formatting, database searching, peptide-spectrum match validation with PeptideProphet, peptide evidence integration with iProphet, post-translational modification (PTM) localization with PTMProphet, and protein inference with ProteinProphet. Philosopher has multiple options for FDR scoring; performs label-free and labeling-based quantification, PTM annotation, generation of multi-level reports, and quantification comparison between samples. MSFragger and TMT-Integrator must be downloaded separately.