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ToolsSun, Zhongzhi, Ning, Zhibin and Figeys, Daniel (2024) The landscape and perspectives of the human gut metaproteomics. Molecular & Cellular Proteomics, 23 (5). ISSN 1535-9484
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Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability: Additional data are available upon request. Funding and additional information: Substantial financial support was provided by the Natural Sciences and Engineering Research Council of Canada (NSERC) through the discovery grant (to D. F.). Z. S. was funded by a stipend from the NSERC CREATE in Technologies for Microbiome Science and Engineering (TECHNOMISE) Program. |
| 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: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 02 Sep 2025 09:30 |
| Last Modified: | 02 Sep 2025 09:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/100252 |
| DOI: | 10.1016/j.mcpro.2024.100763 |
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