PXD073688

PXD073688 is an original dataset announced via ProteomeXchange.

Title	Systematic evaluation of PASEF acquisition strategies in complex metaproteomes
Description	Trapped ion mobility spectrometry coupled with parallel accumulation–serial fragmentation (PASEF) has enabled multiple acquisition strategies for proteomics, yet their comparative performance in complex metaproteomes remains unclear. Here we benchmark five modes—DDA-, DIA-, Slice-, Synchro- and midia-PASEF (PentaPASEF)—using human fecal samples spiked with defined bacterial references across three chromatographic gradients and input levels, comprising 540 LC–MS acquisitions. DIA-based strategies consistently delivered greater peptide and protein coverage than DDA-PASEF, particularly for low-abundance microbial features, and maintained stable performance under high-throughput conditions. Slice- and DIA-PASEF provided the lowest quantitative variability, minimal ratio compression and the most consistent species-level abundance scaling, while functional analysis revealed expanded dynamic range for DIA-based methods. Biological validation in a murine colonic epithelial injury model showed that DIA- and Slice-PASEF capture concordant host and microbial responses. This study establishes a unified reference for selecting PASEF acquisition strategies for sensitive and reproducible metaproteomics.
HostingRepository	PRIDE
AnnounceDate	2026-07-20
AnnouncementXML	Submission_2026-07-20_04:26:28.443.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Feng Xian
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: NEWT:10090;
ModificationList	acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	timsUltra AIP

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-27 20:16:02	ID requested
1	2026-07-03 01:28:07	announced
⏵ 2	2026-07-20 04:26:28	announced	2026-07-20: Updated project metadata.

10.1038/s41467-026-75845-5;

submitter keyword: PASEF, metaproteomics

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/2026/07/PXD073688

PRIDE project URI

• PRIDE
  1. PXD073688
     1. Label: PRIDE project
     2. Name: Systematic evaluation of PASEF acquisition strategies in complex metaproteomes