Repositories list

• PTM-Shepherd

  Public
  A tool for summarizing open search results

  Java

  •

  Apache License 2.0

  •7•16•0•0•Updated Aug 1, 2025Aug 1, 2025

• FragPipeAnalystR

  Public
  R

  •

  GNU General Public License v3.0

  •2•5•11•0•Updated Jul 31, 2025Jul 31, 2025

• philosopher

  Public
  PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

  gobioinformaticsdata-analysis+ 3proteomicsmass-spectrometryms-data

  Go

  •

  GNU General Public License v3.0

  •20•117•40•0•Updated Jul 29, 2025Jul 29, 2025

• FragPipe-Analyst

  Public
  An easy-to-use and interactive web application for FragPipe

  3•8•8•0•Updated Jul 28, 2025Jul 28, 2025

• FragPipe

  Public
  A cross-platform proteomics data analysis suite

  guiproteomicsmass-spectrometry+ 5label-free-quantificationcommand-line-interfaceisobaric-quantificationdata-independent-acquisitiondata-dependent-acquisition

  Java

  •

  Other

  •42•242•52•1•Updated Jul 25, 2025Jul 25, 2025

• alphapeptdeep

  Public
  Deep learning framework for proteomics

  Jupyter Notebook

  •

  Apache License 2.0

  •22•0•0•0•Updated Jul 23, 2025Jul 23, 2025

• MSBooster

  Public
  MSBooster allows users to add deep learning-based features to .pin files before Percolator PSM rescoring

  Java

  •

  GNU Lesser General Public License v3.0

  •2•19•0•0•Updated Jul 16, 2025Jul 16, 2025

• FragPipe-PDV

  Public
  A forked PDV for FragPipe

  Java

  •

  GNU General Public License v3.0

  •20•1•0•0•Updated Jul 13, 2025Jul 13, 2025

• MSFragger

  Public
  Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

  bioinformaticsdatabase-searchproteomics+ 1mass-spectrometry

  HTML

  •9•120•4•0•Updated Jun 30, 2025Jun 30, 2025

• diaTracer

  Public
  A diaPASEF spectrum-centric analysis tool

  proteomicsdiadiapasef

  2•13•1•0•Updated Jun 30, 2025Jun 30, 2025

• IonQuant

  Public
  A label free quantification tool.

  Other

  •8•17•2•0•Updated Jun 30, 2025Jun 30, 2025

• Crystal-C

  Public
  Crystal-C: A computational tool for refinement of open search results

  Java

  •

  Apache License 2.0

  •3•5•2•0•Updated Jun 26, 2025Jun 26, 2025

• easypqp

  Public
  EasyPQP: Simple library generation for OpenSWATH

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •15•0•0•0•Updated Jun 16, 2025Jun 16, 2025

• DIA-Umpire

  Public
  Computational analysis for mass spectrometry-based proteomics data

  Java

  •

  GNU General Public License v3.0

  •10•20•2•0•Updated May 24, 2025May 24, 2025

• FragPipe-to-coADAPTr

  Public
  Standalone script to add FPOP/oxidative modifications column to FragPipe psm tables

  Python

  •

  Apache License 2.0

  •0•0•1•0•Updated May 13, 2025May 13, 2025

• ProteoBench

  Public
  ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/

  Jupyter Notebook

  •

  Apache License 2.0

  •19•0•0•0•Updated May 6, 2025May 6, 2025

• OpenMS

  Public
  The codebase of the OpenMS project

  C++

  •

  Other

  •358•0•0•0•Updated Apr 26, 2025Apr 26, 2025

• clean-storage

  Public
  A shell script to clean the Storage. Internal use only. DISCLAIMER: not responsible for loss of data.

  Shell

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 6, 2025Apr 6, 2025

• PepCentric-manuscript

  Public
  Scripts to generate the results in the PepCentric paper

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• MSFragger-DDAPlus-Manuscript

  Public
  Python and R scripts to generate the figures in the MSFragger-DDA+ paper

  Jupyter Notebook

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• PIP-ECHOanalysis

  Public
  A repository accompanying the manuscript "Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation"

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jan 23, 2025Jan 23, 2025

• diaTracer-manuscript

  Public
  R

  •0•0•0•0•Updated Dec 2, 2024Dec 2, 2024

• msconvert-scripts

  Public
  Some shell scripts related to Thermo Fisher raw format conversion using msconvert

  Shell

  •

  Apache License 2.0

  •2•10•0•0•Updated Nov 18, 2024Nov 18, 2024

• pwiz

  Public
  The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.

  C#

  •

  Apache License 2.0

  •106•0•0•0•Updated Oct 26, 2024Oct 26, 2024

• MSFragger-DIA-manuscript

  Public
  Python and R scripts to generate the figures in the MSFragger-DIA paper

  Python

  •

  Apache License 2.0

  •1•2•0•0•Updated Oct 14, 2024Oct 14, 2024

• OPair_FragPipe

  Public
  GDB

  •1•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• TMT-Integrator

  Public
  A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.

  1•12•1•0•Updated Aug 9, 2024Aug 9, 2024

• EntrapBench

  Public
  Generate entrapment database and calculate false discovery proportion (FDP)

  Java

  •

  Apache License 2.0

  •1•4•0•0•Updated Jul 17, 2024Jul 17, 2024

• FragPipeTPP

  Public
  Enables FragPipe Ouput from (TPP workflow) to be made compatible with TPP-R package

  R

  •

  Other

  •1•1•1•0•Updated May 10, 2024May 10, 2024

• PD-Nodes

  Public
  The implementation of MSFragger and Philosopher (PeptideProphet) as Proteome Discoverer nodes

  1•8•4•0•Updated Apr 20, 2024Apr 20, 2024