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    48 repositories

    • FragPipe

      Public
      A cross-platform proteomics data analysis suite
      guiproteomicsmass-spectrometrylabel-free-quantificationcommand-line-interfaceisobaric-quantificationdata-independent-acquisitiondata-dependent-acquisition
      Java
      •
      Other
      •42•255•46•2•Updated Oct 9, 2025Oct 9, 2025

    • PTM-Shepherd

      Public
      A tool for summarizing open search results
      Java
      •
      Apache License 2.0
      •7•16•0•0•Updated Oct 9, 2025Oct 9, 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 Oct 9, 2025Oct 9, 2025

    • FragPipe-PDV

      Public
      A forked PDV for FragPipe
      Java
      •
      GNU General Public License v3.0
      •21•1•0•0•Updated Oct 7, 2025Oct 7, 2025

    • philosopher

      Public
      PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
      gobioinformaticsdata-analysisproteomicsmass-spectrometryms-data
      Go
      •
      GNU General Public License v3.0
      •20•118•44•0•Updated Sep 22, 2025Sep 22, 2025

    • easypqp

      Public
      EasyPQP: Simple library generation for OpenSWATH
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •15•0•0•0•Updated Sep 21, 2025Sep 21, 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•11•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
      bioinformaticsdatabase-searchproteomicsmass-spectrometry
      HTML
      •9•121•3•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•0•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•6•2•0•Updated Jun 26, 2025Jun 26, 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•11•0•0•Updated Nov 18, 2024Nov 18, 2024