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1. FragPipeFragPipePublic

   A cross-platform proteomics data analysis suite

   Java 314 47

2. MSFraggerMSFraggerPublic

   Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

   HTML 132 12

3. MSBoosterMSBoosterPublic

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

   Java 22 2

4. philosopherphilosopherPublic

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

   Go 128 22

5. PTM-ShepherdPTM-ShepherdPublic

   A tool for summarizing open search results

   Java 16 8

6. IonQuantIonQuantPublic

   A label free quantification tool.

   20 9