Repositories list

• qpx

  Public
  qpx (Quantitative Proteomics eXchange) format (aka quantms.io) a format to capture a full proteomics experiment

  Python

  •

  Apache License 2.0

  •88 forks•2626 stars•1616 issues•11 pull request•Updated Aug 6, 2026Aug 6, 2026

• quantms

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

  proteomicsmass-spectrometryproteogenomics+ 2

  proteomicsmass-spectrometryproteogenomicstmtlfq

  Nextflow

  •

  MIT License

  •5757 forks•8282 stars•5555 issues•11 pull request•Updated Aug 6, 2026Aug 6, 2026

• quantmsdiann

  Public
  quantms workflow for DIANN tool including DIA and DDA analysis

  Nextflow

  •

  MIT License

  •66 forks•1818 stars•77 issues•22 pull requests•Updated Aug 6, 2026Aug 6, 2026

• nf-modules

  Public
  quantms and other bigbio workflows modules in nf-core, nextflow standards

  Nextflow

  •

  MIT License

  •55 forks•11 star•00 issues•00 pull requests•Updated Aug 6, 2026Aug 6, 2026

• mokume

  Public
  Integrated library to perform feature normalization and multiple abundance computing based on qpx

  Python

  •

  MIT License

  •33 forks•22 stars•44 issues•44 pull requests•Updated Aug 6, 2026Aug 6, 2026

• sdrf-pipelines

  Public
  SDRF official validator and converts SDRF to pipeline configuration files

  proteomicsmass-spectrometryopenms+ 5

  proteomicsmass-spectrometryopenmsmaxquantmsstatsmultiomicssdrfproteomics-data-analysis

  Python

  •

  Apache License 2.0

  •3232 forks•3636 stars•1111 issues•11 pull request•Updated Aug 6, 2026Aug 6, 2026

• hvantk

  Public
  Hail variant annotation toolkit

  big-datagenomicshail+ 1

  big-datagenomicshailvariant-analysis

  Python

  •

  MIT License

  •00 forks•00 stars•1111 issues•22 pull requests•Updated Aug 6, 2026Aug 6, 2026

• sdrf-annotated-datasets

  Public
  A repository of datasets in ProteomeXchange annotated in SDRF, previously part of the specification

  Python

  •

  Apache License 2.0

  •1414 forks•88 stars•11 issue•22 pull requests•Updated Aug 6, 2026Aug 6, 2026

• proteomics-sample-metadata

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

  metadataproteomicsproteomics-datasets+ 9

  metadataproteomicsproteomics-datasetsmultiomicsproteomexchangesdrfpride-metadatamsrun-metadatasdrf-proteomicsproteomics-community+ 2

  HTML

  •

  GNU General Public License v2.0

  •115115 forks•115115 stars•4040 issues•00 pull requests•Updated Aug 6, 2026Aug 6, 2026

• sdrf-skills

  Public
  Agentic plugins to annotate SDRF using Claude; Codex; Cursor; Gemini

  metadataproteomicsmetadata-extraction+ 2

  metadataproteomicsmetadata-extractionsdrfproteomics-sample-metadata

  Python

  •

  MIT License

  •99 forks•1111 stars•77 issues•00 pull requests•Updated Aug 5, 2026Aug 5, 2026

• quantms-portal

  Public
  Tooling and frontend for portal.quantms.org — AI-first proteomics data portal

  Vue

  •11 fork•00 stars•33 issues•00 pull requests•Updated Jul 28, 2026Jul 28, 2026

• quantms-rescoring

  Public
  quantms and ms2rescore helper functions and scripts

  Python

  •

  Apache License 2.0

  •22 forks•11 star•00 issues•00 pull requests•Updated Jul 28, 2026Jul 28, 2026

• pmultiqc

  Public
  A library for QC report based on MultiQC framework

  proteomicsmass-spectrometryproteomics-data+ 2

  proteomicsmass-spectrometryproteomics-dataqcqc-proteomics

  Python

  •

  MIT License

  •2727 forks•3434 stars•99 issues•00 pull requests•Updated Jul 27, 2026Jul 27, 2026

• andes

  Public
  Rust

  •

  Apache License 2.0

  •22 forks•22 stars•11 issue•11 pull request•Updated Jul 25, 2026Jul 25, 2026

• rawQC

  Public
  This library enables to compute idfree QC metrics for mzML files using pyopenms

  Jupyter Notebook

  •

  MIT License

  •22 forks•33 stars•00 issues•00 pull requests•Updated Jul 24, 2026Jul 24, 2026

• DLEAMSE

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

  Python

  •

  Apache License 2.0

  •44 forks•1212 stars•33 issues•11 pull request•Updated Jul 17, 2026Jul 17, 2026

• sdrf-templates

  Public
  SDRF templates and validation yaml files from specification proteomics-sample-metadata

  Python

  •

  Apache License 2.0

  •1010 forks•55 stars•55 issues•33 pull requests•Updated Jul 10, 2026Jul 10, 2026

• quantms-containers

  Public
  DIANN docker container and OpenMS release for quantms

  Dockerfile

  •

  Apache License 2.0

  •88 forks•55 stars•11 issue•00 pull requests•Updated Jul 10, 2026Jul 10, 2026

• relink

  Public
  A nextflow workflow for the analysis of large-scale crosslinking experiments

  Nextflow

  •

  MIT License

  •11 fork•00 stars•66 issues•11 pull request•Updated Jul 9, 2026Jul 9, 2026

• onsite

  Public
  onsite: posttranslation modification site localization

  Python

  •

  MIT License

  •33 forks•44 stars•22 issues•00 pull requests•Updated Jun 27, 2026Jun 27, 2026

• quantms-test-datasets

  Public
  Python

  •

  MIT License

  •22 forks•22 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• pgatk

  Public
  Python tools for proteogenomics analysis toolkit

  pythonvcfensembl+ 4

  pythonvcfensemblproteomicsmass-spectrometryproteogenomicsproteogenomics-analysis-toolkit

  Python

  •

  Apache License 2.0

  •1414 forks•1717 stars•33 issues•00 pull requests•Updated May 23, 2026May 23, 2026

• MSScout

  Public
  MSScout fork in bigbio for relink

  C#

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

• pyspectrafuse

  Public
  Python library with utility scripts for spectrafuse pipeline

  Python

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 19, 2026May 19, 2026

• quantms-utils

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

  cloudnextflowbigdata+ 3

  cloudnextflowbigdataproteomicsmass-spectrometryproteogenomics

  Python

  •

  MIT License

  •55 forks•77 stars•00 issues•22 pull requests•Updated May 19, 2026May 19, 2026

• spectrafuse

  Public
  Incremental clustesting pipeline from quantms data.

  Nextflow

  •

  MIT License

  •00 forks•11 star•22 issues•00 pull requests•Updated May 18, 2026May 18, 2026

• sdrfedit

  Public
  SDRF lightweight, self hosted javascript editor

  TypeScript

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•11 pull request•Updated Apr 30, 2026Apr 30, 2026

• pIR

  Public
  Estimation of isoelectric point of peptides and proteins using support vector machines (SVM).

  machine-learningproteinspeptides+ 1

  machine-learningproteinspeptidesisoelectric-point

  R

  •66 forks•1010 stars•00 issues•00 pull requests•Updated Apr 15, 2026Apr 15, 2026

• quantms.org

  Public
  Web page storing all the datasets renalyzed with quantms

  HTML

  •

  MIT License

  •44 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• fslite

  Public
  Lightweight Feature selection Python library

  scikit-learnfeature-selectionmultiomics

  scikit-learnfeature-selectionmultiomics

  Python

  •

  Apache License 2.0

  •11 fork•22 stars•44 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026