🧬 Project 29: Repository-Scale Quality Control in Proteomics

ELIXIR BioHackathon 2025

Important

Let's make public proteomics data FAIR and re-usable — at repository scale.

Mass spectrometry proteomics has generated an enormous global resource: >31,000 datasets in PRIDE alone, representing millions of biological samples. Yet, much of this treasure trove remains underused because quality information is inconsistent or missing.

This project tackles that head-on. Together, we'll build an automated, standardized quality control (QC) framework that can operate directly on public data repositories — producing machine-readable QC summaries (mzQC) linked with rich experimental metadata (SDRF-Proteomics).

By the end of the week, our prototype will:

• Generate mzQC outputs directly from pMultiQC.
• Define a core QC metric ontology adopted across tools.
• Leverage metadata to inform and contextualize QC analyses.
• Pave the way for FAIR, ML-ready proteomics data reuse.
• Provide an ID-free QC module for raw-data assessment.

If you're excited about open science, reproducible bioinformatics, and hands-on development with real impact on the global proteomics community — join us!

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Project Goals

Main objective: Build an end-to-end framework to enrich public proteomics datasets with standardized quality control (QC) information.

Key components:

• mzQC: HUPO-PSI JSON format for standardized QC reporting.
• pMultiQC: modular, multi-workflow QC tool for proteomics pipelines.
• SDRF-Proteomics: standardized experimental metadata schema.

Expected outcomes by the end of the hackathon:

• pMultiQC extended to export results in mzQC format.
• A refined and tiered QC metric ontology.
• Broader workflow coverage via new adapters.
• Enhanced SDRF integration for metadata-driven QC.
• Prototype ID-free QC modules for raw-data assessment.
• Documentation and examples for repository integration.

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Documentation & Resources

• Tasks Overview: Summary of all hackathon tasks and roles
• Task 1 — mzQC Export in pMultiQC: Implement mzQC output generation
• Task 2 — Tiered QC Metrics: Curate and define core/extended metrics
• Task 3 — Workflow Adapters: Add support for new tools
• Task 4 — SDRF Integration: Link sample metadata to QC analyses
• Task 5 — ID-Free QC: Develop raw-level QC modules
• Optional Extensions: Dashboards, benchmark datasets, ML exploration
• Reference Material: Links to mzQC, pMultiQC, and SDRF docs
• Example Outputs: Example .mzQC files + validation tips

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Schedule

We will follow the official BioHackathon Europe daily programme: https://biohackathon-europe.org/programme/

Stand-up: Every day at 09:00. We'll use Slack for quick updates and alignments; checkpoints and demos follow the event's program.

Collaboration & Contribution

• BioHackEU Slack channel: #29-towards-repository-scale-quality-control.
• Daily stand-up: 09:00.
• Ideas or questions? Use Discussions.
• Bugs / progress updates? Open Issues.
• Code changes: via Pull Requests.

Contribution Workflow

We welcome all contributions during the hackathon! To keep collaboration efficient and transparent:

1. Open an Issue first — describe your planned feature or task, tag everyone involved, and be detailed so others can follow or join. → This avoids duplicate efforts and keeps everyone aligned.
2. Create a branch named feature/<short-description> for your work.
3. Commit and reference your issue, e.g. Fixes #12.
4. Open a Pull Request (PR) when ready — add a short summary and test results.
5. Discuss & merge during the daily sync sessions.

See the CONTRIBUTING.md for coding style, testing, and detailed workflow instructions.