Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota
Abstract Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional prote...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-01-01
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| Series: | npj Biofilms and Microbiomes |
| Online Access: | https://doi.org/10.1038/s41522-023-00373-9 |
| _version_ | 1811175924571308032 |
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| author | Jinzhi Zhao Yi Yang Hua Xu Jianxujie Zheng Chengpin Shen Tian Chen Tao Wang Bing Wang Jia Yi Dan Zhao Enhui Wu Qin Qin Li Xia Liang Qiao |
| author_facet | Jinzhi Zhao Yi Yang Hua Xu Jianxujie Zheng Chengpin Shen Tian Chen Tao Wang Bing Wang Jia Yi Dan Zhao Enhui Wu Qin Qin Li Xia Liang Qiao |
| author_sort | Jinzhi Zhao |
| collection | DOAJ |
| description | Abstract Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis. |
| first_indexed | 2024-04-10T19:44:56Z |
| format | Article |
| id | doaj.art-20127814c0ca45458908710ec92b3a9b |
| institution | Directory Open Access Journal |
| issn | 2055-5008 |
| language | English |
| last_indexed | 2024-04-10T19:44:56Z |
| publishDate | 2023-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Biofilms and Microbiomes |
| spelling | doaj.art-20127814c0ca45458908710ec92b3a9b2023-01-29T12:05:45ZengNature Portfolionpj Biofilms and Microbiomes2055-50082023-01-019111410.1038/s41522-023-00373-9Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiotaJinzhi Zhao0Yi Yang1Hua Xu2Jianxujie Zheng3Chengpin Shen4Tian Chen5Tao Wang6Bing Wang7Jia Yi8Dan Zhao9Enhui Wu10Qin Qin11Li Xia12Liang Qiao13Department of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityDepartment of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityDepartment of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of MedicineDepartment of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityShanghai Omicsolution Co., LtdChanghai Hospital, The Naval Military Medical UniversityDepartment of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of MedicineCollege of Food Science and Technology, Shanghai Ocean UniversityDepartment of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityDepartment of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityDepartment of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityChanghai Hospital, The Naval Military Medical UniversityDepartment of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of MedicineDepartment of Chemistry, Shanghai Stomatological Hospital, Fudan UniversityAbstract Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.https://doi.org/10.1038/s41522-023-00373-9 |
| spellingShingle | Jinzhi Zhao Yi Yang Hua Xu Jianxujie Zheng Chengpin Shen Tian Chen Tao Wang Bing Wang Jia Yi Dan Zhao Enhui Wu Qin Qin Li Xia Liang Qiao Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota npj Biofilms and Microbiomes |
| title | Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota |
| title_full | Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota |
| title_fullStr | Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota |
| title_full_unstemmed | Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota |
| title_short | Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota |
| title_sort | data independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota |
| url | https://doi.org/10.1038/s41522-023-00373-9 |
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