Repositories list

• pmultiqc

  Public
  A library for QC report based on MultiQC framework

  Python

  •

  MIT License

  •13•15•9•1•Updated Jul 30, 2025Jul 30, 2025

• quantms

  Public
  Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

  proteomicsmass-spectrometryproteogenomics+ 2tmtlfq

  Nextflow

  •

  MIT License

  •44•52•59•0•Updated Jul 29, 2025Jul 29, 2025

• quantms-rescoring

  Public
  quantms and ms2rescore helper functions and scripts

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Jul 25, 2025Jul 25, 2025

• quantms-containers

  Public
  DIANN docker container and OpenMS release for quantms

  Dockerfile

  •

  Apache License 2.0

  •2•2•0•0•Updated Jul 17, 2025Jul 17, 2025

• quantms-ms2rescore-paper

  Public
  TeX

  •

  Creative Commons Zero v1.0 Universal

  •6•0•2•2•Updated Jul 14, 2025Jul 14, 2025

• SDRFscribe

  Public
  AI assistant of SDRF annotations.

  Apache License 2.0

  •1•0•0•0•Updated Jul 11, 2025Jul 11, 2025

• pmultiqc-paper

  Public
  1•0•0•0•Updated Jul 10, 2025Jul 10, 2025

• quantms.io

  Public
  The proteomics quantification format, extending mzTab for large scale datasets.

  Python

  •

  Other

  •4•10•25•1•Updated Jun 30, 2025Jun 30, 2025

• quantms-readthedocs

  Public
  This repository contains the documentation of quantms workflow

  Batchfile

  •

  MIT License

  •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

• DLEAMSE

  Public
  A Deep LEArning-based Mass Spectra Embedder for spectral similarity scoring

  Python

  •

  Apache License 2.0

  •4•11•3•1•Updated Jun 18, 2025Jun 18, 2025

• quantms.org

  Public
  Web page storing all the datasets renalyzed with quantms

  Vue

  •

  MIT License

  •4•0•0•0•Updated Jun 2, 2025Jun 2, 2025

• hvantk

  Public
  Hail variant annotation toolkit

  big-datagenomicsbigdata+ 2hailvariant-analysis

  Python

  •

  MIT License

  •0•0•3•0•Updated May 23, 2025May 23, 2025

• sdrf-pipelines

  Public
  `sdrf-pipelines` is the official SDRF file validator and converts SDRF to pipeline configuration files

  proteomicsmass-spectrometryopenms+ 5maxquantmsstatsmultiomicssdrfproteomics-data-analysis

  Python

  •

  Apache License 2.0

  •25•20•32•3•Updated May 16, 2025May 16, 2025

• quantms-test-datasets

  Public
  Nextflow

  •

  MIT License

  •0•0•0•0•Updated May 15, 2025May 15, 2025

• quantms-utils

  Public
  A python library with scripts and helpers classes for quantms workflow

  cloudnextflowbigdata+ 3proteomicsmass-spectrometryproteogenomics

  Python

  •

  MIT License

  •3•5•0•0•Updated May 14, 2025May 14, 2025

• ibaqpy

  Public
  Absolute quantification package based on quantms.io

  proteomicsmass-spectrometryquantification+ 2absolute-quantificationibaq

  HTML

  •

  MIT License

  •12•14•2•0•Updated May 14, 2025May 14, 2025

• quantms-ptms

  Public
  quantms-ptms

  Python

  •

  MIT License

  •1•0•0•1•Updated Apr 14, 2025Apr 14, 2025

• proteomics-sample-metadata

  Public
  The Proteomics sample metadata: Standard for experimental design annotation in proteomics datasets

  metadataproteomicsproteomics-datasets+ 9multiomicsproteomexchangesdrfpride-metadatamsrun-metadatasdrf-proteomicsproteomics-community+ 2

  GNU General Public License v2.0

  •110•92•65•6•Updated Apr 10, 2025Apr 10, 2025

• .github

  Public
  MIT License

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

• sdrf-cellline-metadata-db

  Public
  SDRF Cell Line Metadata Database

  metadataannotationsproteomics+ 5mass-spectrometryhupo-psisdrfsdrf-proteomicscelllines

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

• sdrf-utils

  Public
  sdrf-cls

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Dec 18, 2024Dec 18, 2024

• spectrafuse

  Public
  Incremental clustesting pipeline from quantms data.

  Python

  •

  MIT License

  •0•1•4•0•Updated Nov 18, 2024Nov 18, 2024

• pgatk-io

  Public archive
  High performance io library for proteogenomics

  sparkparquetproteomics+ 3mass-spectrometryproteogenomicsfileformats

  Java

  •

  Apache License 2.0

  •0•1•1•1•Updated Oct 8, 2024Oct 8, 2024

• fslite

  Public
  Lightweight Feature selection Python library

  scikit-learnfeature-selectionmultiomics

  Python

  •

  Apache License 2.0

  •1•1•4•1•Updated Sep 26, 2024Sep 26, 2024

• pyspectrafuse

  Public
  Python library with utility scripts for spectrafuse pipeline

  Python

  •

  Apache License 2.0

  •1•0•0•1•Updated Jun 26, 2024Jun 26, 2024

• pgt-pangenome

  Public
  Protegenomics analysis based on Pangenome references

  proteinvariantsproteomics+ 6mass-spectrometrypangenomeproteogenomicsnon-canonicalquantmspublic-proteomics

  Jupyter Notebook

  •

  BSD 2-Clause "Simplified" License

  •0•1•0•0•Updated May 25, 2024May 25, 2024

• py-pgatk

  Public
  Python tools for proteogenomics analysis toolkit

  pythonvcfensembl+ 4proteomicsmass-spectrometryproteogenomicsproteogenomics-analysis-toolkit

  Python

  •

  Apache License 2.0

  •12•13•9•0•Updated Apr 26, 2024Apr 26, 2024

• msgfplus

  Public
  MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

  search-engineproteomicsmass-spectrometry+ 1sequential-algorithm

  Java

  •

  Other

  •37•0•1•0•Updated Mar 26, 2024Mar 26, 2024

• mad_decoy

  Public
  Mad decoy is a decoy simulation tool to assess large-scale merge of q-values.

  Python

  •

  Apache License 2.0

  •2•0•0•0•Updated Nov 4, 2023Nov 4, 2023

• tdf2mzml

  Public
  quantms bruker to mzml

  Python

  •

  Other

  •16•0•0•0•Updated Oct 2, 2023Oct 2, 2023