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1. FragPipe FragPipe Public

   A cross-platform proteomics data analysis suite

   Java 284 46

2. MSFragger MSFragger Public

   Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

   HTML 128 10

3. MSBooster MSBooster Public

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

   Java 21 2

4. philosopher philosopher Public

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

   Go 125 20

5. PTM-Shepherd PTM-Shepherd Public

   A tool for summarizing open search results

   Java 16 7

6. IonQuant IonQuant Public

   A label free quantification tool.

   19 8