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1. FragPipe FragPipe Public

   A cross-platform proteomics data analysis suite

   Java 311 47

2. MSFragger MSFragger Public

   Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

   HTML 132 12

3. MSBooster MSBooster Public

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

   Java 22 2

4. philosopher philosopher Public

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

   Go 128 21

5. PTM-Shepherd PTM-Shepherd Public

   A tool for summarizing open search results

   Java 16 8

6. IonQuant IonQuant Public

   A label free quantification tool.

   20 9