Overview

Following the recent introduction of the Mass Spec Proteomics SIG, we held our official kickoff meeting to discuss the current landscape of proteomics in nf-core, module development, and our roadmap for pipeline integration. It is incredibly encouraging to see the growing interest and enthusiasm for standardizing mass spectrometry and proteomics workflows within the nf-core community.

Attendees

Key Discussion Points

1. Collaboration and Integration with quantms

We spent a significant portion of the meeting discussing the excellent work done by the bigbio organization on the quantms pipeline. While quantms is actively maintained in its own organization, we see a massive opportunity for mutual benefit by introducing their custom modules to the broader nf-core community.

Current Progress:

  • We have successfully implemented the diann module.
  • The dia_proteomics_analysis subworkflow is currently available in nf-core.
  • Validation Success: We confirmed that running the nf-core thermorawfileparser combined with the dia_proteomics_analysis subworkflow produces exactly the same results as quantms. This includes identical DIANN configurations and step-by-step outputs.
  • We are working on a comprehensive module and subworkflow collection for fragpipe as well. This will be released in the upcoming weeks and will be a PR to nf-core/modules.

2. Expanding the Module Library

Our immediate goal is to transfer more modules from quantms into nf-core/modules. Key targets include:

Objective: By migrating these components to nf-core/modules, we aim to demonstrate to the quantms team that the shared nf-core ecosystem is highly robust. Relying on community-maintained modules can significantly reduce the maintenance burden for their pipeline developers, creating a win-win scenario.

3. The Future of Archived nf-core Proteomics Pipelines

We reviewed the status of several legacy nf-core proteomics pipelines that are currently archived:

Next Steps: The SIG will evaluate these pipelines to determine the community appetite and technical feasibility of reviving them versus directing efforts entirely toward modular components and new workflows.
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