ArticleCell systems2018
ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Foundation model enables interpretable open and error-tolerant searching for mass spectrometry-based proteomics.Bioinformatics (Oxford, England) · 2026Article
- End-to-end deep attention-based multitask pipeline for predicting uncertainty-quantified peptide properties from mass spectrometry data.Scientific reports · 2026Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- metaExpertPro: A Computational Workflow for Metaproteomics Spectral Library Construction and Data-Independent Acquisition Mass Spectrometry Data Analysis.Molecular & cellular proteomics : MCP · 2024Article
- Article
- Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.Journal of the American Society for Mass Spectrometry · 2024Article
- MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall.Journal of computational biology : a journal of computational molecular cell biology · 2024Article
- Bioinformatic Workflows for Metaproteomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
- GPU-acceleration of the distributed-memory database peptide search of mass spectrometry data.Scientific reports · 2023Article
- Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics.Computational and structural biotechnology journal · 2022Review
- High Performance Computing Framework for Tera-Scale Database Search of Mass Spectrometry Data.Nature computational science · 2021Article
- Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data.Microbiome · 2021Article
- A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis.Microbiome · 2021Article
- Metagenomics for taxonomy profiling: tools and approaches.Bioengineered · 2020Article
- A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.Nature protocols · 2020Article
- A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation.Molecular & cellular proteomics : MCP · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Shotgun metaproteomics has the potential to reveal the functional landscape of microbial communities but lacks appropriate methods for complex samples with unknown compositions. In the absence of prior taxonomic information, tandem mass spectra would be searched against large pan-microbial databases, which requires heavy computational workload and reduces sensitivity. We present ProteoStorm, an efficient database search framework for large-scale metaproteomics studies, which identifies high-confidence peptide-spectrum matches (PSMs) while achieving a two-to-three orders-of-magnitude speedup over popular tools. A reanalysis of a urinary tract infection (UTI) dataset of 110 individuals revealed a complex pattern of polymicrobial expression, including sub-types of UTIs, cases of bacterial vaginosis, and evidence of no underlying disease. Importantly, compared to the initial UTI study that restricted the search database to a manually curated list of 20 genera, ProteoStorm identified additional genera that were previously unreported, including a case of infection with the rare pathogen Propionimicrobium.
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Registered trials
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