Repositories list

• IM2Deep

  Public
  Collisional cross-section prediction for modified and multiconformational peptides

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

  Python

  •

  Apache License 2.0

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

• lesSDRF

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •8•6•4•0•Updated Apr 28, 2025Apr 28, 2025

• DeepLC

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

  deep-learningproteomicspeptides+ 2retention-timepeptide-modification

  Python

  •

  Apache License 2.0

  •21•63•0•1•Updated Apr 24, 2025Apr 24, 2025

• ms2rescore

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

  proteomicspercolatorpeptide-identification+ 2ms2pipdeeplc

  Python

  •

  Apache License 2.0

  •18•57•15•3•Updated Apr 16, 2025Apr 16, 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•6•3•Updated Apr 15, 2025Apr 15, 2025

• ThermoRawFileParser

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

  C#

  •

  Apache License 2.0

  •52•209•13•1•Updated Apr 9, 2025Apr 9, 2025

• compomics.github.io

  Public
  Compomics github website.

  SCSS

  •

  MIT License

  •1•0•0•0•Updated Apr 8, 2025Apr 8, 2025

• searchgui

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

  proteomicsprotein-identificationjava+ 1bioinformatics

  Java

  •15•43•16•0•Updated Apr 7, 2025Apr 7, 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
  Workshop_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•2•Updated Mar 12, 2025Mar 12, 2025

• iDeepLC_Zenodo

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Mar 11, 2025Mar 11, 2025

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.5k•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• MuMDIA

  Public
  Jupyter Notebook

  •

  Apache License 2.0

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

• mumble

  Public
  Finding the perfect modification for your mass shift

  Python

  •

  Apache License 2.0

  •1•4•1•3•Updated Feb 14, 2025Feb 14, 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
  Jupyter Notebook

  •50•8•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•21•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•14•6•0•Updated Mar 11, 2024Mar 11, 2024

• workshop-BioscienceSnapshot

  Public
  Dockerfile

  •

  Creative Commons Attribution Share Alike 4.0 International

  •1•0•0•0•Updated Oct 9, 2023Oct 9, 2023

• COSS

  Public
  COSS: CompOmics Spectral Searching

  Java

  •3•8•5•4•Updated Apr 18, 2023Apr 18, 2023

• moff-gui

  Public
  A graphical user interface for the Modest Feature Finding algorithm (moFF)

  Java

  •2•2•0•1•Updated Mar 11, 2023Mar 11, 2023