Repositories list

• ThermoRawFileParser

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

  C#

  •

  Apache License 2.0

  •52•212•14•1•Updated Jun 19, 2025Jun 19, 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

• lesSDRF

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •8•6•5•1•Updated Jun 12, 2025Jun 12, 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•27•7•5•Updated Jun 11, 2025Jun 11, 2025

• mumble

  Public
  Finding the perfect modification for your mass shift

  Python

  •

  Apache License 2.0

  •1•4•1•3•Updated Jun 11, 2025Jun 11, 2025

• ms2rescore

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

  proteomicspercolatorpeptide-identification+ 2ms2pipdeeplc

  Python

  •

  Apache License 2.0

  •19•58•16•3•Updated Jun 10, 2025Jun 10, 2025

• DeepLC

  Public
  DeepLC: Retention time prediction for (modified) peptides using Deep Learning.

  deep-learningproteomicspeptides+ 2retention-timepeptide-modification

  Python

  •

  Apache License 2.0

  •22•65•0•1•Updated Jun 6, 2025Jun 6, 2025

• molcraft

  Public
  Deep Learning on Molecules.

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

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 2, 2025Jun 2, 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

• searchgui

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

  proteomicsprotein-identificationjava+ 1bioinformatics

  Java

  •15•44•16•0•Updated May 14, 2025May 14, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.5k•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

• IM2Deep

  Public
  Collisional cross-section prediction for modified and multiconformational peptides

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

  Python

  •

  Apache License 2.0

  •2•10•1•0•Updated May 5, 2025May 5, 2025

• peptide-shaker

  Public
  Interpretation of proteomics identification results

  proteomicsprotein-identificationjava+ 1bioinformatics

  Java

  •18•48•38•0•Updated Apr 7, 2025Apr 7, 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

• ms2rescore-rs

  Public
  Rust functionality for the MS²Rescore package

  Rust

  •

  Apache License 2.0

  •3•2•0•1•Updated Apr 1, 2025Apr 1, 2025

• Peptonizer2000

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

  Python

  •

  Apache License 2.0

  •0•1•3•0•Updated Mar 26, 2025Mar 26, 2025

• 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

  •18•43•6•3•Updated Mar 12, 2025Mar 12, 2025

• MuMDIA

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•1•1•0•Updated Feb 20, 2025Feb 20, 2025

• molexpress

  Public
  Graph Neural Networks with Keras 3

  Python

  •

  MIT License

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

• compomics-utilities

  Public
  Open source Java library for computational proteomics

  proteomicscomputational-proteomicsbioinformatics

  Java

  •17•33•4•0•Updated Dec 20, 2024Dec 20, 2024

• ML-course-VIB-2024

  Public archive
  Jupyter Notebook

  •50•9•0•0•Updated Nov 26, 2024Nov 26, 2024

• search-all-assess-subset-paper

  Public archive
  HTML

  •0•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• Tissue_prediction_manuscript

  Public archive
  Jupyter Notebook

  •1•1•0•0•Updated Nov 18, 2024Nov 18, 2024

• electron-vue-python-boilerplate

  Public
  Boilerplate to create desktop applications with electron, Vue3 and FastAPI

  Vue

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• reporter

  Public
  Protein quantification based on reporter ions

  bioinformaticsproteomicsprotein-quantification+ 1reporter-ions

  Java

  •2•4•5•0•Updated Sep 10, 2024Sep 10, 2024

• ThermoRawFileParserGUI

  Public
  Graphical user interface for the ThermoRawFileParser

  conversionproteomicsraw+ 1java

  Java

  •

  Apache License 2.0

  •1•23•2•0•Updated Jul 5, 2024Jul 5, 2024

• tabloidProteome

  Public
  HTML

  •

  Apache License 2.0

  •0•1•0•3•Updated Mar 21, 2024Mar 21, 2024

• denovogui

  Public
  Graphical user interface for de novo sequencing of tandem mass spectra

  proteomicsdenovographical-user-interface+ 1de-novo-sequencing

  Java

  •7•15•6•0•Updated Mar 11, 2024Mar 11, 2024