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    19 repositories

    • simba

      Public
      Python
      •
      Apache License 2.0
      •0•8•1•2•Updated Aug 25, 2026Aug 25, 2026

    • spectrum_utils

      Public
      Python package for efficient mass spectrometry data processing and visualization
      mass-spectrometry
      mass-spectrometry
      Python
      •
      Apache License 2.0
      •34•169•9•5•Updated Aug 18, 2026Aug 18, 2026

    • denovo_benchmarks

      Public
      Python
      •12•23•7•4•Updated Aug 14, 2026Aug 14, 2026

    • lab-website

      Public
      Bittremieux lab website
      TeX
      •0•0•0•7•Updated Aug 12, 2026Aug 12, 2026

    • metabo-depthcharge

      Public
      Metabolomics-focused depthcharge extension: spectrum processing, molecular fingerprints, and similarity metrics
      Python
      •0•2•0•0•Updated Jul 23, 2026Jul 23, 2026

    • falcon

      Public
      Large-scale tandem mass spectrum clustering using fast nearest neighbor searching.
      clusteringnearest-neighbor-searchmass-spectrometry
      clusteringnearest-neighbor-searchmass-spectrometry
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •13•36•8•2•Updated Jun 13, 2026Jun 13, 2026

    • cassava_cocoyam_fermentation_study

      Public
      South African cassava and cocoyam fermentation study
      Jupyter Notebook
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 4, 2026Jun 4, 2026

    • pu_ms2_identifiability

      Public
      Deep learning model for MS2 spectral quality assessment using PU learning
      Python
      •
      Apache License 2.0
      •0•4•0•0•Updated May 6, 2026May 6, 2026

    • gnps-rdd-app

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • TreeMS2

      Public
      TreeMS2 is a Python-based tool for efficient comparison of large-scale tandem mass spectrometry (MS/MS) datasets.
      Python
      •0•5•1•0•Updated Apr 2, 2026Apr 2, 2026

    • denovo-benchmarks-runner

      Public
      Python
      •0•0•0•0•Updated Mar 31, 2026Mar 31, 2026

    • casanovo-xl

      Public
      De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
      Python
      •
      Apache License 2.0
      •80•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • workshop_phl2026

      Public
      0•0•0•0•Updated Feb 11, 2026Feb 11, 2026

    • ANN-SoLo

      Public
      Spectral library searching using approximate nearest neighbor techniques.
      Jupyter Notebook
      •
      Apache License 2.0
      •21•50•2•1•Updated Feb 11, 2026Feb 11, 2026

    • gnps-rdd

      Public
      Reference data-driven metabolomics using the GNPS platform
      Jupyter Notebook
      •
      Apache License 2.0
      •2•3•5•0•Updated Jan 17, 2026Jan 17, 2026

    • positional-isomer-distinguishability

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

    • MassIVE-KB-spectra-extractor

      Public
      A Nextflow pipeline for extracting spectra from MassIVE-KB
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 14, 2025Oct 14, 2025

    • MTL-peptide-property-prediction

      Public
      All scripts to reproduce the results from the 'Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics' study. Data and pret…
      Python
      •
      Other
      •1•1•0•0•Updated Jul 16, 2024Jul 16, 2024

    • GLEAMS

      Public
      GLEAMS is a Learned Embedding for Annotating Mass Spectra.
      deep-learningclusteringmass-spectrometry
      deep-learningclusteringmass-spectrometry
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•29•2•0•Updated Aug 16, 2023Aug 16, 2023
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