Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome

Sun, Zhongzhi, Ning, Zhibin, Wu, Qing, Li, Leyuan, Doxey, Andrew C. and Figeys, Daniel (2025) Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome. npj Biofilms and Microbiomes, 11 (1). ISSN 2055-5008

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Abstract

Mass spectrometry (MS)-based proteomics is widely used for quantitative protein profiling and protein interaction studies. However, most current research focuses on single-species proteomics, while protein interactions within complex microbiomes, composed of hundreds of bacterial species, remain largely unexplored. In this study, we analyzed peptide abundance correlations within a metaproteomics dataset derived from in vitro cultured human gut microbiomes subjected to various drug treatments. Our analysis revealed that peptides from the same protein or taxon exhibited correlated abundance changes. By using t-SNE for visualization, we generated a peptide correlation map in which peptides from the same taxon formed distinct clusters. Furthermore, peptide abundance correlations enabled genome-level taxonomic assignments for a greater number of peptides. For instance, 1880 (48.9%) of the 3845 peptides initially assigned only to the family Bacteroidaceae could now be assigned to a specific genome. In species representative genome subsets, peptide correlation networks based on taxon-normalized peptide abundance (TNPA) linked functionally related peptides and provided insights into uncharacterized proteins. Altogether, our study demonstrates that analyzing peptide abundance correlations enhances both taxonomic and functional analyses in human gut metaproteomics research.

Item Type:	Article
Additional Information:	Data availability: Metaproteomics raw files used to compile analysis were deposited at the ProteomeXchange Consortium59 via the PRIDE60 partner repository as described in our previous study26 (https://doi.org/10.1101/2025.02.13.637346). These files will be publicly available upon publication. Additionally, another dataset generated using a Q Exactive mass spectrometer is available with the data set identifiers PXD012724. Code availability: All codes to perform the analysis in this study are available on GitHub at https://github.com/northomics/Peptide_Abundance_Correlations.
Uncontrolled Keywords:	biotechnology,microbiology,applied microbiology and biotechnology ,/dk/atira/pure/subjectarea/asjc/1300/1305
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	19 Mar 2026 12:30
Last Modified:	22 Mar 2026 07:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102495
DOI:	10.1038/s41522-025-00801-y

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