Repositories list

• oui-discovery

  Public
  Collaboration between CompOmics & OpenProt group

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 5, 2026Jan 5, 2026

• ms2rescore

  Public
  Modular and user-friendly platform for AI-assisted rescoring of peptide identifications

  proteomicspercolatorpeptide-identification+ 2ms2pipdeeplc

  Python

  •

  Apache License 2.0

  •20•62•12•2•Updated Jan 5, 2026Jan 5, 2026

• ms2rescore-rs

  Public
  Rust functionality for the MS²Rescore package

  Rust

  •

  Apache License 2.0

  •4•2•0•1•Updated Jan 5, 2026Jan 5, 2026

• ms2pip

  Public
  MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.

  machine-learningproteomicsmass-spectrometry+ 3peptide-identificationspectrum-predictionpeptide-spectrum

  HTML

  •

  Apache License 2.0

  •19•47•7•3•Updated Dec 23, 2025Dec 23, 2025

• psm_utils

  Public
  Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

  pythonparsingproteomics+ 3mass-spectrometrypeptide-identificationpeptide-spectrum-matches

  Python

  •

  Apache License 2.0

  •10•29•8•1•Updated Dec 22, 2025Dec 22, 2025

• compomics-utilities

  Public
  Open source Java library for computational proteomics

  bioinformaticsproteomicscomputational-proteomics

  Java

  •16•34•8•0•Updated Dec 20, 2025Dec 20, 2025

• omssa-parser

  Public
  Java based parser for OMSSA OMX files

  bioinformaticsproteomicsomssa

  Java

  •0•0•0•0•Updated Dec 20, 2025Dec 20, 2025

• tabloidProteome

  Public
  HTML

  •

  Apache License 2.0

  •0•1•0•3•Updated Dec 18, 2025Dec 18, 2025

• ecoli-peptideatlas-manuscript

  Public
  Code used to produce figures in the E. coli PeptideAtlas Paper

  Jupyter Notebook

  •

  Apache License 2.0

  •0•1•0•0•Updated Dec 18, 2025Dec 18, 2025

• IM2Deep

  Public
  Collisional cross-section prediction for modified and multiconformational peptides

  proteomicsmass-spectrometrypeptides+ 3ion-mobilitycollisional-cross-sectiontimstof

  Python

  •

  Apache License 2.0

  •2•13•1•0•Updated Dec 11, 2025Dec 11, 2025

• molcraft

  Public
  Deep learning on molecules: Minimalistic and powerful implementations of molecular graphs and graph neural networks.

  pythonmachine-learningdeep-learning+ 4tensorflowkerasgraph-neural-networkmolecular-machine-learning

  Python

  •

  MIT License

  •0•1•0•0•Updated Dec 11, 2025Dec 11, 2025

• DeepLC

  Public
  DeepLC: Retention time prediction for peptides carrying any modification.

  deep-learningproteomicspeptides+ 2retention-timepeptide-modification

  Python

  •

  Apache License 2.0

  •24•72•0•1•Updated Dec 10, 2025Dec 10, 2025

• mumble

  Public
  Finding the perfect modification for your mass shift

  Python

  •

  Apache License 2.0

  •1•5•1•2•Updated Dec 3, 2025Dec 3, 2025

• protean-viz

  Public
  Tool to visualize user input such as modifications and peptides, including custom input files and search engine input files

  JavaScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 2, 2025Dec 2, 2025

• peptide-shaker

  Public
  Interpretation of proteomics identification results

  javabioinformaticsproteomics+ 1protein-identification

  Java

  •18•53•45•0•Updated Nov 26, 2025Nov 26, 2025

• lsabd-machine-learning-tutorials

  Public
  Tutorials machine learning for the Large Scale Analysis of Biomedical Data course

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •0•0•0•0•Updated Nov 4, 2025Nov 4, 2025

• Peptonizer2000

  Public
  Confidence for taxonomic analysis in metaproteomics. Get ready to peptonize!

  Python

  •

  Apache License 2.0

  •0•1•3•0•Updated Nov 3, 2025Nov 3, 2025

• iDeepLC

  Public
  iDeepLC: A deep Learning-based retention time predictor for unseen modified peptides with a novel encoding system

  Python

  •

  Apache License 2.0

  •2•1•0•0•Updated Oct 29, 2025Oct 29, 2025

• ThermoRawFileParser

  Public
  Thermo RAW file parser that runs on Linux/Mac and all other platforms that support Mono

  C#

  •

  Apache License 2.0

  •54•233•11•0•Updated Oct 27, 2025Oct 27, 2025

• MuMDIA

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•2•20•1•Updated Oct 24, 2025Oct 24, 2025

• lesSDRF

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •9•7•3•1•Updated Oct 15, 2025Oct 15, 2025

• reporter

  Public
  Protein quantification based on reporter ions

  bioinformaticsproteomicsprotein-quantification+ 1reporter-ions

  Java

  •2•4•5•0•Updated Aug 15, 2025Aug 15, 2025

• searchgui

  Public
  Highly adaptable common interface for proteomics search and de novo engines

  javabioinformaticsproteomics+ 1protein-identification

  Java

  •15•46•17•0•Updated Aug 15, 2025Aug 15, 2025

• EUPA_2025_DIA

  Public
  Analysis of limitations of DIA data analysis for EuPA 2025 presentation

  Jupyter Notebook

  •

  Apache License 2.0

  •1•0•0•0•Updated Jun 16, 2025Jun 16, 2025

• intro-to-deep-learning

  Public
  Practical introduction to neural networks with Pytorch and Lightning

  tutoriallightningpytorch+ 3recurrent-neural-networksneural-networksconvolutional-neural-networks

  Jupyter Notebook

  •

  Creative Commons Attribution 4.0 International

  •0•1•0•0•Updated May 20, 2025May 20, 2025

• compomics.github.io

  Public
  Compomics github website.

  SCSS

  •

  MIT License

  •1•0•0•0•Updated May 15, 2025May 15, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.7k•0•0•0•Updated May 8, 2025May 8, 2025

• compomics-rover

  Public archive
  A tool to visualize and validate quantitative proteomics data from different sources.

  Java

  •0•0•2•0•Updated May 8, 2025May 8, 2025

• Workshop_Grenoble_2025

  Public archive
  Workshop on MS²Rescore for data-driven peptide identification rescoring (Grenoble, 2025)

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

• molexpress

  Public
  Graph Neural Networks with Keras 3

  Python

  •

  MIT License

  •1•0•0•1•Updated Jan 31, 2025Jan 31, 2025