ArticleNPJ biofilms and microbiomes2023
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota.
Article in NPJ biofilms and microbiomes, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Metaproteomic portrait of the healthy human gut microbiota.NPJ biofilms and microbiomes · 2024Pooled it
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- Gut microbiota and pancreatic cancer: tumorigenesis, progression, and clinical applications.Cancer biology & medicine · 2026Review
- Review
- Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.Journal of proteomics · 2026Article
- Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.PloS one · 2026Article
- Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis.PloS one · 2026Article
- Rewiring the proteome of the Euscelidius variegatus holobiont in response to Flavescence dorée phytoplasma.Scientific reports · 2025Article
- Multi-Metaomics Unveils the Development Process of Microbial Communities During the Fermentation of Baobaoqu.Foods (Basel, Switzerland) · 2025Article
- Article
- Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome.NPJ biofilms and microbiomes · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome.Proteomics · 2025Article
- Evaluation of imputation and imputation-free strategies for differential abundance analysis in metaproteomics data.Briefings in bioinformatics · 2025Article
- Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.Microbiology spectrum · 2025Article
- Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- Software-aided efficient identification of the components of compound formulae and their metabolites in rats by UHPLC/IM-QTOF-MS and an in-house high-definition MSJournal of pharmaceutical analysis · 2024Article
- Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping.Molecular & cellular proteomics : MCP · 2024Article
- STAVER: a standardized benchmark dataset-based algorithm for effective variation reduction in large-scale DIA-MS data.Briefings in bioinformatics · 2024Article
- Engineering of a Substrate Affinity Reduced S-Adenosyl-methionine Synthetase as a Novel Biosensor for Growth-Coupling Selection of L-Methionine Overproducers.Applied biochemistry and biotechnology · 2024Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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