Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics

• Published in: Microbiology spectrum Vol. 13; no. 2; p. e0175524
• Main Authors: Gao, Xiaowei, Liang, Hewei, Hu, Tongyuan, Zou, Yuanqiang, Xiao, Liang
• Format: Journal Article
• Language: English
• Published: United States American Society for Microbiology 04.02.2025
• Subjects: Bacteria - classification; Bacteria - genetics; Bacterial Proteins - genetics; Computational Biology; Databases, Protein; functional analysis; Gastrointestinal Microbiome - genetics; Genome, Bacterial; Humans; Metagenomics - methods; metaproteomics; Molecular Sequence Annotation; protein database; Proteomics - methods; Research Article; taxonomic analysis; protein database; metaproteomics; functional analysis; taxonomic analysis
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.01755-24

Mass spectrometry-based metaproteomics offers a profound understanding of the gut microbial taxonomy and functionality. The databases utilized in the analysis of metaproteomic data are crucial, as they determine the identification of proteins that can be recognized and linked to overall human health, in addition to the quality of taxonomic and functional annotation. Among the most effective approaches for constructing protein databases is the utilization of metagenomic sequencing to create matched databases. However, the database, derived from isolated genomes, has yet to undergo rigorous testing for their efficacy and accuracy in protein identification and taxonomic and functional annotation. Here, we constructed a protein database DBCGR2 derived from Cultivated Genome Reference 2 (CGR2) and a complete workflow for data analysis. We compared the performances of DBCGR2 and metagenomics-derived databases. Our results indicated that DBCGR2 can be regarded as an alternative to metagenomics-derived databases, which contribute to metaproteomic data analysis.