PXD063462-1

PXD063462 is an original dataset announced via ProteomeXchange.

Title	Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput
Description	Proteomic experiments, particularly those addressing dynamic proteome properties, time series, or genetic diversity, require the analysis of large sample numbers. Despite significant advancements in proteomic technologies in recent years, further improvements are needed to accelerate measurement and enhance proteome coverage and quantitative performance. Previously, we demonstrated that incorporating a scanning MS2 dimension into data-independent acquisition methods (Scanning SWATH, or more generally scanning DIA) but also ion trapping, improves analytical depth and quantitative performance, especially in proteomic methods using fast chromatography. Here, we evaluate the scanning DIA approach combined with ion trapping via the Zeno trap in a method termed ZT Scan DIA, using a ZenoTOF 7600+ instrument (SCIEX). Applying this method to established proteome standards across various analytical setups, enabling intermediate to high sample throughput, we observed a 30–40% increase in identified precursors. This enhancement extended to overall protein identification and precise quantification. Furthermore, ZT Scan DIA effectively eliminated quantitative bias, as demonstrated by its ability to deconvolute proteomes in multi-species mixtures. We propose that ZT Scan DIA can be used to broaden the application in proteomics, particularly in studies requiring high quantitative precision with low sample input, post-translational modification (PTM) analysis, and high-throughput workflows.
HostingRepository	PRIDE
AnnounceDate	2026-01-20
AnnouncementXML	Submission_2026-01-20_00:54:50.079.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ludwig Sinn
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: NEWT:4932; scientific name: Escherichia coli; NCBI TaxID: NEWT:562;
ModificationList	No PTMs are included in the dataset
Instrument	ZenoTOF 7600+

Revision	Datetime	Status	ChangeLog Entry
0	2025-04-29 12:37:58	ID requested
⏵ 1	2026-01-20 00:54:51	announced

10.1002/pmic.70093;

Sinn LR, Wang Z, Alvarez CP, Chelur A, Batruch I, Pribil P, Ludwig D, Tate S, Castro-Perez J, Messner CB, Demichev V, Ralser M, Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput. Proteomics, 26(1):68-81(2026) [pubmed]

submitter keyword: None

Markus Ralser
contact affiliation	Charité - Universitätsmedizin Berlin Research group Biochemistry and Systems Biology of the Metabolism Institute of Biochemistry Germany
contact email	markus.ralser@charite.de
lab head
Ludwig Sinn
contact affiliation	Charité – Universitätsmedizin Berlin
contact email	ludsinn@gmail.com
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/2026/01/PXD063462

PRIDE project URI

• PRIDE
  1. PXD063462
     1. Label: PRIDE project
     2. Name: Performance Characteristics of Zeno Trap Scanning DIA for Sensitive and Quantitative Proteomics at High Throughput