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README.md

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 ## Introduction
 [MSFragger](http://msfragger.nesvilab.org/) is an ultrafast database search tool for peptide identification in mass spectrometry-based proteomics. While we provide a stand-alone Graphical User interface [FragPipe](https://fragpipe.nesvilab.org) for running MSFragger, here we describe the implementation of MSFragger as a processing node in the Thermo Scientific Proteome Discoverer (PD) environment. We also provide PeptideProphet (via [Philosopher](https://nesvilab.github.io/philosopher/)) as part of the PD processing node, enabling downstream processing of MSFragger search results in PD using either Percolator or PeptideProphet.