workflow-development-interest-group / fragpipe-proteomics-pipeline-tutorial

CWL descriptions for FragPipe Proteomics Pipline

FragPipe Proteomics Pipeline Tutorial

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FragPipe is a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger - an ultrafast proteomic search engine suitable for both conventional and "open" (wide precursor mass tolerance) peptide identification. FragPipe includes the Philosopher toolkit for downstream post-processing of MSFragger search results (PeptideProphet, iProphet, ProteinProphet), FDR filtering, label-based quantification, and multi-experiment summary report generation. Crystal-C and PTM-Shepherd are included to aid interpretation of open search results. Also included in FragPipe binary are TMT-Integrator for TMT/iTRAQ isobaric labeling-based quantification, IonQuant for label-free quantification with match-between-run (MBR) functionality, SpectraST and EasyPQP spectral library building modules, and DIA-Umpire SE module for direct analysis of data independent acquisition (DIA) data.

Goal: Use FragPipe Proteomics Pipeline to analyze the proteome of clear cell renal cell carcinoma samples.

Steps:

1. Run FragPipe Convert-Identify-PeptideProphet on 2 plexes
2. Run FragPipe ProteinProphet on all 23 plex workspaces in 1 task
3. Run FragPipe Filter-Quant-Report on 2 plex workspaces
4. Run FragPipe TMT-Integrator and QC on all 23 PSM files
5. Use RStudio to interactively QC the outputs of TMT-Integrator and cluster (?)

Please reach out during or after the workshop with any questions
[email protected]
[email protected]

CGC Proteomics Workshop - April 21, 2021 · Discussion Board· Nesvilab/FragPipe