FragPipe is a comprehensive computational platform for analyzing mass spectrometry-based proteomics data. FragPipe comes with an easy to use Java Graphical User Interface (GUI) but can also be run in the command line mode, on Windows, Linux, or in the cloud environment. It is powered by [MSFragger](https://msfragger.nesvilab.org/) - an ultrafast proteomic search engine suitable for both conventional and "open" (wide precursor mass tolerance) peptide identification. FragPipe includes Percolator and the [Philosopher](https://nesvilab.github.io/philosopher/) toolkit for downstream post-processing of MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, label-based quantification, and multi-experiment summary report generation. FragPipe includes MSBooster module for deep-learning based rescoring of peptide identifications. [Crystal-C](https://www.nesvilab.org/Crystal-C/) and [PTM-Shepherd](https://github.com/Nesvilab/PTM-Shepherd) are included to aid interpretation of open search results. Also included in FragPipe binary are [TMT-Integrator](http://tmt-integrator.nesvilab.org/) for TMT/iTRAQ isobaric labeling-based quantification, [IonQuant](http://ionquant.nesvilab.org/) for label-free quantification with FDR-controlled match-between-run (MBR) functionality, spectral library building with EasyPQP, and MSFragger-DIA, DIA-Umpire SE, and diaTracer modules for direct ("library-free") analysis of data independent acquisition (DIA) data. FragPipe includes DIA-NN for extraction of quantification from DIA data.
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