ArticleISME communications2022
Introducing untargeted data-independent acquisition for metaproteomics of complex microbial samples.
Article in ISME communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Area under the curve quantification outperforms spectral counting in metaproteomics, but matching between runs is detrimental.bioRxiv : the preprint server for biology · 2026Article
- The Peptonizer2000: Bringing Confidence to Metaproteomics.Journal of proteome research · 2026Article
- Complete Data Analysis Workflow for Quantitative DIA Mass Spectrometry Using Nextflow.Journal of proteome research · 2026Article
- Taxonomic-Level Protein Quantification in Metaproteomics Using a Biomass-Constrained Expectation-Maximization Approach.Journal of the American Society for Mass Spectrometry · 2026Article
- Mono-mix strategy enables comparative proteomics of a cross-kingdom microbial symbiosis.PloS one · 2026Article
- From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.Journal of proteome research · 2025Review
- Multi-Metaomics Unveils the Development Process of Microbial Communities During the Fermentation of Baobaoqu.Foods (Basel, Switzerland) · 2025Article
- Biological Function Assignment across Taxonomic Levels in Mass-Spectrometry-Based Metaproteomics via a Modified Expectation Maximization Algorithm.Journal of proteome research · 2025Article
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.Scientific reports · 2025Article
- metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis.Molecular & cellular proteomics : MCP · 2024Article
- Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics.mSystems · 2024Article
- [Microbial metaproteomics--From sample processing to data acquisition and analysis].Se pu = Chinese journal of chromatography · 2024Review
- Article
- Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry.Microbiome research reports · 2024Article
- Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota.NPJ biofilms and microbiomes · 2023Article
- Metaproteomics profiling of the microbial communities in fermentation starters (Frontiers in nutrition · 2023Article
- Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics.Computational and structural biotechnology journal · 2023Review
- Assessing the Dark Field of Metaproteome.Analytical chemistry · 2022Article
- Quantitative metaproteomics reveals composition and metabolism characteristics of microbial communities in Chinese liquor fermentation starters.Frontiers in microbiology · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Mass spectrometry-based metaproteomics is a relatively new field of research that enables the characterization of the functionality of microbiota. Recently, we demonstrated the applicability of data-independent acquisition (DIA) mass spectrometry to the analysis of complex metaproteomic samples. This allowed us to circumvent many of the drawbacks of the previously used data-dependent acquisition (DDA) mass spectrometry, mainly the limited reproducibility when analyzing samples with complex microbial composition. However, the DDA-assisted DIA approach still required additional DDA data on the samples to assist the analysis. Here, we introduce, for the first time, an untargeted DIA metaproteomics tool that does not require any DDA data, but instead generates a pseudospectral library directly from the DIA data. This reduces the amount of required mass spectrometry data to a single DIA run per sample. The new DIA-only metaproteomics approach is implemented as a new open-source software package named glaDIAtor, including a modern web-based graphical user interface to facilitate wide use of the tool by the community.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.