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

• DOI: 10.1128/spectrum.01755-24
• Publication Date: 2024-12-12T14:03:20Z
• Authors: Xiaowei Gao; Hewei Liang; Tongyuan Hu; Yuanqiang Zou; Liang Xiao
• Keywords: Metaproteomics; Human Microbiome Project; Identification; Database search engine

Metaproteomics offers a profound understanding of the functional dynamics gut microbiome, which is crucial for personalized healthcare strategies. The selection an appropriate database critical step identification peptides and proteins, as well provision accurate taxonomic annotations. matched metagenomic-derived considered to be best, but its limitations include low-abundance organisms resolution. Herein, we constructed protein (DBCGR2) based on Cultivated Genome Reference 2 (CGR2) developed complete peptide-centric analysis workflow searching annotation taxonomy function. This was subsequently appraised in comparison with metagenomics-derived databases metaproteomic data. Our findings suggested that performance DBCGR2 comparable improvement rates from species. results could fully annotated using pepTaxa approach this study, resolution enhanced strain level. Additionally, demonstrated sensitivity by employing DBCGR2. Overall, combined can alternative data superior performances.IMPORTANCEMass spectrometry-based metaproteomics microbial functionality. utilized are crucial, they determine proteins recognized linked overall human health, addition quality annotation. Among most effective approaches constructing utilization metagenomic sequencing create databases. However, database, derived isolated genomes, has yet undergo rigorous testing their efficacy accuracy Here, analysis. We compared performances indicated regarded databases, contribute