PXD051792-1

PXD051792 is an original dataset announced via ProteomeXchange.

Title	Ultra-sensitive metaproteomics (uMetaP) redefines the “dark” metaproteome, enables single-bacterium resolution, and discovers hidden functions in the gut microbiome
Description	Metaproteomics uniquely characterizes host-microbiome interactions. However, most species detected by metagenomics remain hidden to metaproteomics due to sensitivity limits. We present a novel ultra-sensitive metaproteomic solution (uMetaP) that, for the first time, reaches full-length 16S rRNA taxonomic depth and can simultaneously decipher functional features. Querying the mouse gut microbiome, uMetaP achieved unprecedented performance in key metrics like protein groups (47925) alongside taxonomic (220 species) and functional annotations (223 KEGG pathways) - all within 30-min analysis time and with high reproducibility, sensitivity, and quantitative precision. uMetaP revealed previously unidentified proteins of unknown functions, small proteins, and potentially new natural antibiotics. Leveraging the extreme sensitivity of uMetaP and SILAC-labelled bacteria, we revealed the true limit of detection and quantification for the “dark” metaproteome of the mouse gut. Moreover, using a two-bacteria proteome mix, we demonstrated single-bacterium resolution (500 femtogram) with exceptional quantification precision and accuracy. From deciphering the interplay of billions of microorganisms with the host to exploring microbial heterogeneity, uMetaP represents a quantum leap in metaproteomics. Taken together, uMetaP will open new avenues for our understanding of the microbial world and its connection to health and disease.
HostingRepository	PRIDE
AnnounceDate	2025-06-25
AnnouncementXML	Submission_2025-06-25_12:49:11.782.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Feng Xian
SpeciesList	scientific name: Salinibacter ruber DSM 13855; NCBI TaxID: 309807; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Ligilactobacillus murinus DSM 20452 = NBRC 14221; NCBI TaxID: 1423772;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro; timsTOF Ultra

Revision	Datetime	Status	ChangeLog Entry
0	2024-04-27 05:02:20	ID requested
⏵ 1	2025-06-25 12:49:12	announced

Dataset with its publication pending

submitter keyword: LC-MS, Metaproteomics, Sensitivity,Microbiome

Manuela Schmidt
contact affiliation	Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna
contact email	manuela_schmidt@univie.ac.at
lab head
Feng Xian
contact affiliation	Division of Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Vienna
contact email	feng.xian@univie.ac.at
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/2025/06/PXD051792

PRIDE project URI

• PRIDE
  1. PXD051792
     1. Label: PRIDE project
     2. Name: Ultra-sensitive metaproteomics (uMetaP) redefines the “dark” metaproteome, enables single-bacterium resolution, and discovers hidden functions in the gut microbiome