Repositories list

• MuMDIA

  Public
  Clean-room Rust reimplementation of MuMDIA, a data-independent-acquisition (DIA) proteomics search engine.

  rustbioinformaticsproteomics+ 2

  rustbioinformaticsproteomicsdiamass-spectrometry

  Rust

  •

  Apache License 2.0

  •00 forks•44 stars•00 issues•1010 pull requests•Updated Oct 4, 2026Oct 4, 2026

• visDIA

  Public
  Interactive, read-only viewer for MuMDIA DIA proteomics results

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 3, 2026Oct 3, 2026

• MSqRobPy

  Public
  Python implementation of MSqRob2 R package

  Python

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 1, 2026Oct 1, 2026

• ThermoRawFileParser

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

  C#

  •

  Apache License 2.0

  •6060 forks•249249 stars•1515 issues•11 pull request•Updated Sep 30, 2026Sep 30, 2026

• peptide-shaker

  Public
  Interpretation of proteomics identification results

  javabioinformaticsproteomics+ 1

  javabioinformaticsproteomicsprotein-identification

  Java

  •2121 forks•5656 stars•4848 issues•11 pull request•Updated Sep 28, 2026Sep 28, 2026

• textmining

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 23, 2026Sep 23, 2026

• mumble

  Public
  Finding the perfect modification for your mass shift

  Python

  •

  Apache License 2.0

  •11 fork•66 stars•00 issues•00 pull requests•Updated Sep 23, 2026Sep 23, 2026

• ristretto

  Public
  Lean and fast PSM rescoring

  Python

  •

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Sep 23, 2026Sep 23, 2026

• DeepLC

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

  deep-learningproteomicspeptides+ 2

  deep-learningproteomicspeptidesretention-timepeptide-modification

  Python

  •

  Apache License 2.0

  •2626 forks•8080 stars•11 issue•00 pull requests•Updated Sep 22, 2026Sep 22, 2026

• ms2rescore-rs

  Public
  Rust functionality for the MS²Rescore package

  Rust

  •

  Apache License 2.0

  •44 forks•22 stars•11 issue•11 pull request•Updated Sep 22, 2026Sep 22, 2026

• ms2rescore

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

  proteomicspercolatorpeptide-identification+ 2

  proteomicspercolatorpeptide-identificationms2pipdeeplc

  Python

  •

  Apache License 2.0

  •2323 forks•6666 stars•1616 issues•00 pull requests•Updated Sep 22, 2026Sep 22, 2026

• agentic-metadata

  Public
  Python

  •00 forks•00 stars•00 issues•11 pull request•Updated Sep 22, 2026Sep 22, 2026

• MoDPAv1.0

  Public
  MoDPA repository for publication

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•22 stars•00 issues•00 pull requests•Updated Sep 21, 2026Sep 21, 2026

• HAMLET-annotations

  Public
  Python

  •

  Other

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 17, 2026Sep 17, 2026

• compomics.com

  Public
  HTML

  •00 forks•00 stars•11 issue•11 pull request•Updated Sep 16, 2026Sep 16, 2026

• CALLC3

  Public
  A command-line interface tool for training context-aware graph neural networks for chromatography.

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 16, 2026Sep 16, 2026

• OmicsFM_webview

  Public
  Interactive OmicsFM maps for proteomics and transcriptomics

  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 14, 2026Sep 14, 2026

• tabloidProteome

  Public
  HTML

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•33 pull requests•Updated Sep 11, 2026Sep 11, 2026

• OmicsFM

  Public
  Python

  •

  Apache License 2.0

  •11 fork•66 stars•00 issues•00 pull requests•Updated Sep 10, 2026Sep 10, 2026

• eluflow

  Public
  A python package for building powerful transformer models for SMILES.

  machine-learningdeep-learningkeras+ 2

  machine-learningdeep-learningkerastransformersmiles

  Python

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 8, 2026Sep 8, 2026

• IM2Deep

  Public
  Collisional cross-section prediction for modified and multiconformational peptides

  proteomicsmass-spectrometrypeptides+ 3

  proteomicsmass-spectrometrypeptidesion-mobilitycollisional-cross-sectiontimstof

  Python

  •

  Apache License 2.0

  •22 forks•1414 stars•00 issues•00 pull requests•Updated Aug 26, 2026Aug 26, 2026

• tutorials-imsc-2026

  Public
  Pre-congress workshop at the IMSC conference in Lyon, France on 22 August 2026.

  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 24, 2026Aug 24, 2026

• molcraft

  Public
  A python package for building powerful GNN models for molecules.

  machine-learningdeep-learningkeras+ 2

  machine-learningdeep-learningkerasmoleculesgraph-neural-network

  Python

  •

  MIT License

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 18, 2026Aug 18, 2026

• compomics-utilities

  Public
  Open source Java library for computational proteomics

  bioinformaticsproteomicscomputational-proteomics

  bioinformaticsproteomicscomputational-proteomics

  Java

  •1818 forks•3737 stars•88 issues•22 pull requests•Updated Aug 13, 2026Aug 13, 2026

• omssa-parser

  Public
  Java based parser for OMSSA OMX files

  bioinformaticsproteomicsomssa

  bioinformaticsproteomicsomssa

  Java

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• SCI

  Public
  Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

  Jupyter Notebook

  •

  Apache License 2.0

  •00 forks•33 stars•00 issues•00 pull requests•Updated Aug 13, 2026Aug 13, 2026

• target_peptides_lookup

  Public
  Rust

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 12, 2026Aug 12, 2026

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •4.1k4.1k forks•00 stars•00 issues•00 pull requests•Updated Jul 30, 2026Jul 30, 2026

• psm_utils

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

  pythonparsingproteomics+ 3

  pythonparsingproteomicsmass-spectrometrypeptide-identificationpeptide-spectrum-matches

  Python

  •

  Apache License 2.0

  •1111 forks•3131 stars•1111 issues•11 pull request•Updated Jul 16, 2026Jul 16, 2026

• peptide-gnn

  Public
  A graph-based deep learning model for predicting and explaining peptide LC-RT data.

  Python

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Jul 14, 2026Jul 14, 2026