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pmultiqc: An Open-Source, Lightweight, and Metadata-Oriented QC Reporting Library for MS Proteomics.
Qi-Xuan Yue1, Chengxin Dai2, Selvakumar Kamatchinathan3
1Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China.
Molecular & Cellular Proteomics : MCP
|February 19, 2026
Summary
pmulti-qc is a new Python package for quality control in proteomics. It generates standardized, web-based reports across multiple analysis platforms, improving data reliability and reproducibility.
Area of Science:
- Proteomics
- Bioinformatics
- Data Science
Background:
- The growing scale and complexity of proteomics data necessitate advanced quality control (QC) frameworks.
- Ensuring data reliability and reproducibility is crucial for advancing proteomics research.
Purpose of the Study:
- To introduce pmultiqc, an open-source Python package for standardizing and generating web-based QC reports for proteomics data.
- To provide a scalable and interpretable QC framework across diverse proteomics data analysis platforms.
Main Methods:
- Developed pmultiqc as an extension of the MultiQC framework with specialized modules for mass spectrometry workflows.
- Integrated support for quantms, DIA-NN, MaxQuant/MaxDIA, FragPipe, and mzIdentML/mzML-based pipelines.
- Implemented metadata-aware QC using sample metadata in the SDRF format for standardized reporting.
Main Results:
- pmultiqc computes key QC metrics including intensity distributions, identification rates, retention time consistency, and missing value patterns.
- Generates interactive, publication-ready reports with metadata-guided QC metrics.
- Offers a modular architecture for easy extension to new workflows and formats.
Conclusions:
- pmultiqc provides a robust, scalable, and interpretable QC solution for the proteomics community.
- The package enhances data reliability and reproducibility through standardized, metadata-aware reporting.
- Accessible via local installation or a cloud-based service for broad user adoption.
