Introduction

The massspec-proteomics special interest group serves as a central hub for nf-core community members interested in mass spectrometry (MS) proteomics. Whether you are working on Label-Free Quantification (LFQ), Data-Independent Acquisition (DIA), Isobaric Labeling (TMT), or other MS-based techniques, this group is the place to coordinate efforts and share expertise.

The primary goal of this group is to put in place guidelines and standards tailored for MS data analysis pipelines for the nf-core community. This group also aims to channel the energy MS data analysis in the nf-core community into building a cohesive, modular ecosystem for mass spec-based proteomics data analysis.

Scope

The primary scope of this group includes:

  • Modular Pipeline Vision: Guiding the strategy for creating smaller, interoperable pipelines for specific data types (e.g., DDA, DIA, TMT) that can be chained together.

  • Shared Components: Coordinating the development and maintenance of shared nf-core/modules and nf-core/subworkflows. A key immediate focus is modularizing high-quality components from existing pipelines and implementing new pipelines for more refined analyses.

  • Standardization: Establishing best practices for proteomics data processing, quality control (QC), and benchmarking within the nf-core framework.

  • Collaboration: Acting as a forum to connect developers from different teams and individual contributors to prevent fragmentation and redundant effort.

Activities

  • Regular Meetings: We organize regular virtual meetings (e.g., monthly or bi-monthly) to discuss the roadmap, technical challenges, and community proposals.

  • Component Refactoring: Active collaboration on specific technical tasks, such as refactoring local modules from quantms into the official nf-core repositories.

  • New Workflow Development: Coordinating the implementation of requested features, such as FragPipe workflows and updated DIANN integration.
On this page
  • Proteomics