PaxDb 5.0: Curated Protein Quantification Data Suggests Adaptive Proteome Changes in Yeasts

Area of Science:

• Proteomics
• Bioinformatics
• Evolutionary Biology

Background:

• Protein abundance data is crucial for understanding cellular functions and organismal biology.
• Existing databases often lack comprehensive, uniformly processed data across diverse species.
• The Protein Abundances Across Organisms (PaxDb) database aims to consolidate this information.

Purpose of the Study:

• To describe the latest version 5.0 of the PaxDb database.
• To highlight data integration methods, expanded organism/tissue coverage, and proteome depth.
• To present comparative analyses and evolutionary insights derived from the data.

Main Methods:

• Integration of diverse raw proteomic datasets.
• Uniform data reprocessing and quality scoring.
• Orthology relation computation for cross-species comparisons.

Main Results:

• PaxDb version 5.0 includes 831 datasets from 170 species (22 Archaea, 81 Bacteria, 67 Eukaryota).
• Comparative analysis of human proteome data against Human Protein Atlas and Genotype-Tissue Expression.
• Identification of an evolutionary trend in sulfur-containing amino acid usage in Fungi.

Conclusions:

• PaxDb version 5.0 is a valuable, expanded resource for cross-species proteomic comparisons.
• The database facilitates research into cellular functions, tissue-specific expression, and evolutionary patterns.
• Analysis of PaxDb data can uncover significant biological trends, such as amino acid usage evolution.