pmultiqc

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🚀 What is pmultiqc?

pmultiqc is a MultiQC plugin for comprehensive quality control reporting of proteomics data. It generates interactive HTML reports with visualizations and metrics to help you assess the quality of your mass spectrometry-based proteomics experiments.

✨ Key Features

🌐 Public Services

You can use pmultiqc through our public web services:

Service URL Status Description
EBI PRIDE Service https://www.ebi.ac.uk/pride/services/pmultiqc/ PRIDE pmultiqc service Official EBI service with PRIDE integration
FU Berlin University Service https://pmultiqc.bsc.fu-berlin.de FU Berlin pmultiqc service pmultiqc service at Freie Universität Berlin
Tübingen University Service https://abi-services.cs.uni-tuebingen.de/pmultiqc/ Tübingen pmultiqc service pmultiqc service at Tübingen University

🎯 Service Features

📋 Supported Data Sources

pmultiqc supports the following data sources:

1. quantms pipeline output files:

2. MaxQuant result files:

3. DIA-NN result files:

4. ProteoBench file:

5. mzIdentML files:

💾 Installation

Install from PyPI

# To install the stable release from PyPI:
pip install pmultiqc

Install from Source (Without PyPI)

# Fork the repository on GitHub

# Clone the repository
git clone https://github.com/your-username/pmultiqc.git
cd pmultiqc

# Install the package locally
pip install .

# Now you can run pmultiqc on your own dataset

🛠️ Usage

pmultiqc is used as a plugin for MultiQC. After installation, you can run it using the MultiQC command-line interface.

Basic Usage

multiqc {analysis_dir} -o {output_dir}

Where:

Examples

For quantms pipeline results

# Basic usage
multiqc --quantms_plugin /path/to/quantms/results -o ./report

# With specific options
multiqc --quantms_plugin /path/to/quantms/results -o ./report --remove_decoy --condition factor

For MaxQuant results

multiqc --maxquant_plugin /path/to/maxquant/results -o ./report

For DIA-NN results

# Discover report inside a results folder
multiqc --diann_plugin /path/to/diann/results -o ./report

# Directly pass a DIA-NN report file (TSV or Parquet)
# Note: MultiQC requires an analysis directory argument; use '.' as a placeholder
multiqc --diann_plugin --diann_report /path/to/report.tsv . -o ./report
multiqc --diann_plugin --diann_report /path/to/report.parquet . -o ./report

For ProteoBench files

multiqc --proteobench_plugin /path/to/proteobench/files -o ./report

For mzIdentML files

multiqc --mzid_plugin /path/to/mzid/files -o ./report

Command-line Options

Option Description Default
--raw Keep filenames in experimental design output as raw False
--condition Create conditions from provided columns -
--remove_decoy Remove decoy peptides when counting True
--decoy_affix Pre- or suffix of decoy proteins in their accession DECOY_
--contaminant_affix The contaminant prefix or suffix CONT
--affix_type Location of the decoy marker (prefix or suffix) prefix
--disable_plugin Disable pmultiqc plugin False
--quantification_method Quantification method for LFQ experiment feature_intensity
--disable_table Disable protein/peptide table plots for large datasets False
--ignored_idxml Ignore idXML files for faster processing False
--quantms_plugin Generate reports based on Quantms results False
--diann_plugin Generate reports based on DIANN results False
--diann_report Path to DIA-NN main report (.tsv or .parquet). When provided with --diann_plugin, you can use . as the analysis directory placeholder. -
--maxquant_plugin Generate reports based on MaxQuant results False
--proteobench_plugin Generate reports based on ProteoBench result False
--mzid_plugin Generate reports based on mzIdentML files False
--disable_hoverinfo Disable interactive hover tooltips in the plots False

📊 QC Metrics and Visualizations

pmultiqc generates a comprehensive report with multiple sections:

📑 General Report

📚 Results Tables

📈 Identification Statistics

🔍 Example Reports

You can find example reports on the docs page. Here are the direct links to different example reports:

Example Type Description Link
LFQ Label-free quantification LFQ Example (disable_hoverinfo)
TMT Tandem mass tag TMT Example (disable_hoverinfo)
quantms DIA Data-independent acquisition quantms DIA Example (disable_hoverinfo)
DIA-NN Data-independent acquisition DIA-NN Example (disable_hoverinfo)
MaxQuant MaxQuant results MaxQuant Example (disable_hoverinfo)
MaxQuant DIA MaxQuant DIA results MaxQuant DIA Example (disable_hoverinfo)
ProteoBench ProteoBench results ProteoBench Example (disable_hoverinfo)
mzIdentML with mzML mzIdentML with mzML files mzIdentML with mzML Example (disable_hoverinfo)
mzIdentML with MGF mzIdentML with MGF files mzIdentML with MGF Example (disable_hoverinfo)

👥 Contributing

To contribute to pmultiqc:

  1. 🍴 Fork the repository
  2. 📥 Clone your fork: git clone https://github.com/YOUR-USERNAME/pmultiqc
  3. 🌿 Create a feature branch: git checkout -b new-feature
  4. ✏️ Make your changes
  5. 🔧 Install in development mode: pip install -e .
  6. 🧪 Test your changes: cd tests && multiqc resources/LFQ -o ./
  7. 💾 Commit your changes: git commit -am 'Add new feature'
  8. 📤 Push to the branch: git push origin new-feature
  9. 📩 Submit a pull request

📖 Documentation

For more detailed information, visit the pmultiqc GitHub repository or check the documentation site.

📜 License

This project is licensed under the terms of the LICENSE file included in the repository.

📝 Citation

If you use pmultiqc in your research, please cite our preprint:

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics
Qi-Xuan Yue, Chengxin Dai, Selvakumar Kamatchinathan, Chakradhar Bandla, Henry Webel, Asier Larrea, Wout Bittremieux, Julian Uszkoreit, Tom David Muller, Jinqiu Xiao, Juergen Cox, Philip Ewels, Vadim Demichev, Oliver Kohlbacher, Timo Sachsenberg, Chris Bielow, Mingze Bai, Yasset Perez-Riverol
bioRxiv 2025. DOI: 10.1101/2025.11.02.685980

Preprint: https://www.biorxiv.org/content/early/2025/11/03/2025.11.02.685980

BibTeX

@article{Yue2025.11.02.685980,
  author = {Yue, Qi-Xuan and Dai, Chengxin and Kamatchinathan, Selvakumar and Bandla, Chakradhar and Webel, Henry and Larrea, Asier and Bittremieux, Wout and Uszkoreit, Julian and Muller, Tom David and Xiao, Jinqiu and Cox, Juergen and Ewels, Philip and Demichev, Vadim and Kohlbacher, Oliver and Sachsenberg, Timo and Bielow, Chris and Bai, Mingze and Perez-Riverol, Yasset},
  title = {pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics},
  elocation-id = {2025.11.02.685980},
  year = {2025},
  doi = {10.1101/2025.11.02.685980},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2025/11/03/2025.11.02.685980},
  eprint = {https://www.biorxiv.org/content/early/2025/11/03/2025.11.02.685980.full.pdf},
  journal = {bioRxiv}
}

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