PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms
Qingyao Huang1,2, Damian Szklarczyk1,2, John Oehninger2
1Swiss Institute of Bioinformatics, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
Nucleic Acids Research
|November 3, 2025
Summary
The PaxDb v6.0 database offers a standardized protein abundance reference for 392 species, improving reproducibility and data reuse from mass spectrometry (MS) experiments. This resource enhances biological insights by integrating reprocessed public MS data with consistent metadata.
Area of Science:
- Proteomics
- Bioinformatics
- Systems Biology
Background:
- Mass spectrometry (MS) data reuse is hindered by inconsistent processing and metadata, limiting biological discovery.
- Standardized, high-coverage reference resources are crucial for reproducibility and cross-study integration in proteomics.
- PaxDb provides organism- and tissue-level protein abundance data for the healthy, wild-type state.
Purpose of the Study:
- To enhance the PaxDb database with updated and expanded protein abundance data.
- To develop a standardized, automated pipeline for reprocessing public mass spectrometry data.
- To improve the accessibility and utility of public proteomics data for biological research.
Main Methods:
- Integrated 1639 datasets from 392 species into PaxDb v6.0.
- Developed an end-to-end MS data processing pipeline using the FragPipe framework for consistent re-analysis.
- Implemented standardized metadata integration, orthology mappings, and quality scoring.
- Utilized large-language model ensemble classifiers for semi-automated curation of ProteomeXchange projects.
- Created a user-facing tool for peptide-level abundance calculation and dataset comparison.
Main Results:
- PaxDb v6.0 significantly expands coverage across all kingdoms of life, nearly doubling previous dataset integration.
- A novel automated pipeline ensures consistent reprocessing of raw MS data, enhancing data quality and reliability.
- The updated database includes standardized metadata, orthology information, and quality scores for integrated datasets.
- New tools facilitate direct comparison of user data with PaxDb reference proteomes.
Conclusions:
- PaxDb v6.0 represents a significant advancement in creating a standardized, high-coverage protein abundance reference resource.
- The automated reprocessing pipeline and enhanced data integration overcome key limitations in public MS data reuse.
- This updated resource facilitates new biological insights by improving reproducibility and enabling cross-study data integration.
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