PXD040947

PXD040947 is an original dataset announced via ProteomeXchange.

Title	Expanding the Characterization of Microbial Ecosystems using DIA-PASEF Metaproteomics
Description	Metaproteomics is gaining momentum in microbiome research due to the multi-dimensional information it provides. However, current approaches have reached their detection limits. We present a highly-sensitive metaproteomic workflow using the extra information captured by Parallel Accumulation-Serial Fragmentation (PASEF) technology. The comparison of different acquisition modes and data analysis software packages showed that DIA-PASEF and DIA-NN doubled protein identifications in the mouse gut microbiota and, importantly, also in the host proteome compared to DDA-PASEF. DIA-PASEF significantly improved peptide detection reproducibility and quantification accuracy, which resulted in more than twofold identified taxa, reaching depths comparable to metagenomic studies. Consequently, DIA-PASEF exhibited improved coverage of functional networks revealing 131 additional pathways compared to DDA-PASEF. We applied our optimized workflow to a pre-clinical mouse model of chronic pain, in which we deciphered novel host-microbiome interactions. In summary, we present here a metaproteomic approach that paves the way for increasing the functional characterization of microbiome ecosystems and is applicable to diverse fields of biological research.
HostingRepository	PRIDE
AnnounceDate	2023-05-04
AnnouncementXML	Submission_2023-05-04_01:51:42.605.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	FengXian
SpeciesList	scientific name: Microbiota; NCBI TaxID: 13613;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-17 09:22:41	ID requested
⏵ 1	2023-05-04 01:51:42	announced

Dataset with its publication pending

submitter keyword: Metaproteomics, DIA-PASEF, Mouse, Chronic pain, Gut microbiome

ManuelaSchmidt
contact affiliation	Division of Pharmacology & Toxicology, Department of Pharmaceutical Sciences, University of Vienna
contact email	manuela_schmidt@univie.ac.at
lab head
FengXian
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/2023/05/PXD040947

PRIDE project URI

• PRIDE
  1. PXD040947
     1. Label: PRIDE project
     2. Name: Expanding the Characterization of Microbial Ecosystems using DIA-PASEF Metaproteomics