Computational Omics and Systems Biology Group

ThermoRawFileParser

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

DeepLC

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

ms2rescore

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

peptide-shaker

Interpretation of proteomics identification results

ms2pip

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

searchgui

Highly adaptable common interface for proteomics search and de novo engines

compomics-utilities

Open source Java library for computational proteomics

psm_utils

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

IM2Deep

Collisional cross-section prediction for modified and multiconformational peptides

ML-course-VIB-2024

lesSDRF

mumble

Finding the perfect modification for your mass shift

reporter

Protein quantification based on reporter ions

ms2rescore-rs

Rust functionality for the MS²Rescore package

MuMDIA

ecoli-peptideatlas-manuscript

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

intro-to-deep-learning

Practical introduction to neural networks with Pytorch and Lightning

Peptonizer2000

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

tabloidProteome

Tissue_prediction_manuscript

bioconda-recipes

Conda recipes for the bioconda channel.

compomics-rover

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

compomics.github.io

Compomics github website.

EUPA_2025_DIA

Analysis of limitations of DIA data analysis for EuPA 2025 presentation

iDeepLC

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

molcraft

Deep Learning on Molecules.

molexpress

Graph Neural Networks with Keras 3

oui-discovery

Collaboration between CompOmics & OpenProt group

search-all-assess-subset-paper

Workshop_Grenoble_2025

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