Assessing the Dark Field of Metaproteome

Duan, Haonan, Cheng, Kai, Ning, Zhibin, Li, Leyuan, Mayne, Janice, Sun, Zhongzhi and Figeys, Daniel (2022) Assessing the Dark Field of Metaproteome. Analytical Chemistry, 94 (45). pp. 15648-15654. ISSN 0003-2700

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Abstract

The human gut microbiome is a complex system composed of hundreds of species, and metaproteomics can be used to explore their expressed functions. However, many lower abundance species are not detected by current metaproteomic techniques and represent the dark field of metaproteomics. We do not know the minimal abundance of a bacterium in a microbiome(depth) that can be detected by shotgun metaproteomics. In this study, we spiked 15N-labeled E. coli peptides at different percentages into peptides mixture derived from the human gut microbiome to evaluate the depth that can be achieved by shotgun metaproteomics. We observed that the number of identified peptides and peptide intensity from 15N-labeled E. coli were linearly correlated with the spike-in levels even when 15N-labeled E. coli was down to 0.5% of the biomass. Below that level, it was not detected. Interestingly, the match-between-run strategy significantly increased the number of quantified peptides even when 15N-labeled E. coli peptides were at low abundance. This is indicative that in metaproteomics of complex gut microbiomes many peptides from low abundant species are likely observable in MS1 but are not selected for MS2 by standard shotgun strategies.

Item Type:	Article
Additional Information:	D.F. acknowledges a Distinguished Research Chair from the University of Ottawa. H.D. was supported by the NSERC-CREATE TECHNOMISE program. The art image used in the paper is from https://smart.servier.com/ . Servier Medical Art by Servier is licensed under a Creative Commons Attribution 3.0 Unported License ( https://creativecommons.org/licenses/by/3.0/ ). The line charts and bar graphs in Figure 2a, Figure 2c, Figure S1, Figure S2a, Figure S2c, Figure S3 and Figure S8 were performed using GraphPad Prism version 8.0.0 for Windows, GraphPad Software, San Diego, California USA, www.graphpad.com.
Uncontrolled Keywords:	analytical chemistry ,/dk/atira/pure/subjectarea/asjc/1600/1602
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:	06 Mar 2026 15:30
Last Modified:	09 Mar 2026 16:31
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102244
DOI:	10.1021/acs.analchem.2c02452

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