Proteomics software frameworks

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Open source

  1. TPP
  2. CPAS
  3. LabKey server (derived from CPAS)
  4. Prequips (on top of TPP)
  5. OpenMS/TOPP
  6. ProteoWizard
  7. XCMS. Written in R
  8. Corra
  9. Mass++
  10. mspire
  11. proteios
  12. msInspect
  13. Insilicos Proteomics Pipeline
  14. PatternLab

Commercial

  1. Scaffold
  2. PEAKS
  3. Rosseta Biosoftware
  4. ProteinPilot For ABI
  5. ProteinCenter From Proxeon (formerly Protana)
  6. ViPDAC. It runs on Amazon Elastic Cloud, have to run an instance in Amazon but the source code is available.