PXD063632

PXD063632 is an original dataset announced via ProteomeXchange.

Title	MetaDIA: A Novel Database Reduction Strategy for DIA Human Gut Metaproteomics
Description	Microbiomes, especially within the gut, are complex and may comprise hundreds of species. The identification of peptides in metaproteomics presents a significant challenge, as it involves matching peptides to mass spectra within an enormous search space for complex and unknown samples. This poses difficulties for both the accuracy and the speed of identification. Specifically, analysis of data-independent acquisition (DIA) datasets has relied on libraries constructed from prior data-dependent acquisition (DDA) results. However, this method is resource-intensive, consumes samples, and limits identification to peptides previously identified. These limitations restrict the application of DIA in metaproteomics research. We introduced a novel strategy to reduce the search space by utilizing species abundance and functional abundance information from the microbiome to score each peptide and prioritize those most likely to be detected. Using this strategy, we have developed and optimized a workflow called MetaDIA for the analysis of microbiome data generated by DIA, which operates independently of DDA assistance. Our approach successfully created a smaller, yet sufficient database for DIA data search in metaproteomics. The results demonstrated strong consistency with the traditional DDA-based library approach at both protein and functional levels. MetaDIA is readily accessible as an open-source project hosted on GitHub (https://github.com/northomics/MetaDIA).
HostingRepository	PRIDE
AnnounceDate	2026-03-06
AnnouncementXML	Submission_2026-03-06_04:14:20.452.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Haonan Duan
SpeciesList	scientific name: Bacteria; NCBI TaxID: NCBITaxon:2; scientific name: human gut metagenome; NCBI TaxID: NEWT:408170;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2025-05-06 02:57:33	ID requested
⏵ 1	2026-03-06 04:14:20	announced

Dataset with its publication pending

submitter keyword: Human gut microbiome,Metaproteomics, Data Independent Acquisition, diaPASEF, Data Dependent Acquisition-free

Daniel Figeys
contact affiliation	Faculty of Medicine, University of Ottawa, Ottawa, Canada Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK
contact email	dfigeys@uottawa.ca
lab head
Haonan Duan
contact affiliation	School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
contact email	hduan084@uottawa.ca
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/03/PXD063632

PRIDE project URI

• PRIDE
  1. PXD063632
     1. Label: PRIDE project
     2. Name: MetaDIA: A Novel Database Reduction Strategy for DIA Human Gut Metaproteomics