Implementing the MSFragger Search Engine as a Node in Proteome Discoverer

Hui Yin Chang, Sarah E. Haynes, Fengchao Yu, Alexey I. Nesvizhskii

Research output: Contribution to journalArticlepeer-review


Here, we describe the implementation of the fast proteomics search engine MSFragger as a processing node in the widely used Proteome Discoverer (PD) software platform. PeptideProphet (via the Philosopher tool kit) is also implemented as an additional PD node to allow validation of MSFragger open (mass-tolerant) search results. These two nodes, along with the existing Percolator validation module, allow users to employ different search strategies and conveniently inspect search results through PD. Our results have demonstrated the improved numbers of PSMs, peptides, and proteins identified by MSFragger coupled with Percolator and significantly faster search speed compared to the conventional SEQUEST/Percolator PD workflows. The MSFragger-PD node is available at

Original languageEnglish
Pages (from-to)520-525
Number of pages6
JournalJournal of Proteome Research
Issue number2
StatePublished - 3 Feb 2023


  • Proteome Discoverer
  • liquid chromatography coupled to tandem mass spectrometry
  • proteomics


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