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Assessing the Dark Field of Metaproteome
[Image: see text] 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 metaproteomi...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670033/ https://www.ncbi.nlm.nih.gov/pubmed/36327159 http://dx.doi.org/10.1021/acs.analchem.2c02452 |
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author | Duan, Haonan Cheng, Kai Ning, Zhibin Li, Leyuan Mayne, Janice Sun, Zhongzhi Figeys, Daniel |
author_facet | Duan, Haonan Cheng, Kai Ning, Zhibin Li, Leyuan Mayne, Janice Sun, Zhongzhi Figeys, Daniel |
author_sort | Duan, Haonan |
collection | PubMed |
description | [Image: see text] 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 (15)N-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 (15)N-labeled E. coli were linearly correlated with the spike-in levels even when (15)N-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 (15)N-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. |
format | Online Article Text |
id | pubmed-9670033 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-96700332022-11-18 Assessing the Dark Field of Metaproteome Duan, Haonan Cheng, Kai Ning, Zhibin Li, Leyuan Mayne, Janice Sun, Zhongzhi Figeys, Daniel Anal Chem [Image: see text] 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 (15)N-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 (15)N-labeled E. coli were linearly correlated with the spike-in levels even when (15)N-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 (15)N-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. American Chemical Society 2022-11-03 2022-11-15 /pmc/articles/PMC9670033/ /pubmed/36327159 http://dx.doi.org/10.1021/acs.analchem.2c02452 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Duan, Haonan Cheng, Kai Ning, Zhibin Li, Leyuan Mayne, Janice Sun, Zhongzhi Figeys, Daniel Assessing the Dark Field of Metaproteome |
title | Assessing the Dark Field of Metaproteome |
title_full | Assessing the Dark Field of Metaproteome |
title_fullStr | Assessing the Dark Field of Metaproteome |
title_full_unstemmed | Assessing the Dark Field of Metaproteome |
title_short | Assessing the Dark Field of Metaproteome |
title_sort | assessing the dark field of metaproteome |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670033/ https://www.ncbi.nlm.nih.gov/pubmed/36327159 http://dx.doi.org/10.1021/acs.analchem.2c02452 |
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