Repositories list

• 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 Oct 24, 2025Oct 24, 2025

• FragPipe

  Public
  A cross-platform proteomics data analysis suite

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

  Java

  •

  Other

  •43•261•52•2•Updated Oct 24, 2025Oct 24, 2025

• FragPipe-SpecLib

  Public
  FragPipe-SpecLib: Simple library generation for FragPipe

  proteomicsdata-independent-acquisitionspectral-library+ 1fragpipe

  Python

  •

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

  •0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

• PTM-Shepherd

  Public
  A tool for summarizing open search results

  Java

  •

  Apache License 2.0

  •7•16•0•0•Updated Oct 21, 2025Oct 21, 2025

• FragPipe-PDV

  Public
  A forked PDV for FragPipe

  Java

  •

  GNU General Public License v3.0

  •21•1•0•0•Updated Oct 16, 2025Oct 16, 2025

• Crystal-C

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

  Java

  •

  Apache License 2.0

  •3•6•2•0•Updated Oct 16, 2025Oct 16, 2025

• philosopher

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

  gobioinformaticsdata-analysis+ 3proteomicsmass-spectrometryms-data

  Go

  •

  GNU General Public License v3.0

  •20•119•45•0•Updated Sep 22, 2025Sep 22, 2025

• OPair_FragPipe

  Public
  GDB

  •1•0•0•0•Updated Sep 10, 2025Sep 10, 2025

• FDRBench

  Public
  Estimation of false discovery proportion for mass spectrometry proteomics data using entrapment

  Java

  •

  Apache License 2.0

  •3•0•0•0•Updated Sep 4, 2025Sep 4, 2025

• nesvilab.github.io

  Public
  Nesvilab website

  Less

  •

  Apache License 2.0

  •0•1•0•0•Updated Sep 3, 2025Sep 3, 2025

• PepCentric

  Public
  Search proteins and peptides against repository-scale MS/MS spectra within seconds

  proteomicsproteogenomics

  0•1•0•0•Updated Aug 28, 2025Aug 28, 2025

• CPTAC_AML

  Public
  R

  •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

• FDRBench_manuscript

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •2•0•0•0•Updated Aug 7, 2025Aug 7, 2025

• EntrapBench

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

  Java

  •

  Apache License 2.0

  •1•4•0•0•Updated Aug 6, 2025Aug 6, 2025

• FragPipeAnalystR

  Public
  R

  •

  GNU General Public License v3.0

  •3•5•12•0•Updated Jul 31, 2025Jul 31, 2025

• FragPipe-Analyst

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

  3•8•9•0•Updated Jul 28, 2025Jul 28, 2025

• alphapeptdeep

  Public
  Deep learning framework for proteomics

  Jupyter Notebook

  •

  Apache License 2.0

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

• MSFragger

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

  bioinformaticsproteomicsmass-spectrometry+ 1database-search

  HTML

  •9•121•4•0•Updated Jun 30, 2025Jun 30, 2025

• diaTracer

  Public
  A diaPASEF spectrum-centric analysis tool

  proteomicsdiadiapasef

  2•13•0•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

• 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

  •20•0•0•0•Updated May 6, 2025May 6, 2025

• OpenMS

  Public
  The codebase of the OpenMS project

  C++

  •

  Other

  •360•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•12•0•0•Updated Nov 18, 2024Nov 18, 2024