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1. FragPipe FragPipe Public

   A cross-platform proteomics data analysis suite

   Java 239 42

2. MSFragger MSFragger Public

   Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

   HTML 119 7

3. MSBooster MSBooster Public

   MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

   Java 19 2

4. philosopher philosopher Public

   PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

   Go 117 20

5. PTM-Shepherd PTM-Shepherd Public

   A tool for summarizing open search results

   Java 16 6

6. IonQuant IonQuant Public

   A label free quantification tool.

   17 8