PXD036786

PXD036786 is an original dataset announced via ProteomeXchange.

Title	High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA
Description	The ability to conduct high-quality proteomic experiments in high throughput has opened new avenues in clinical research, drug discovery, and systems biology. Next to an increase in quantitative precision, recent developments in high-throughput proteomics have also gained proteomic depth, to the extent that earlier gaps between classic and high-throughput experiments have significantly narrowed. Here we introduce and benchmark Zeno SWATH, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) in order to increase proteomic depth and dynamic range in proteomic experiments. Combined with the high acquisition speed, these gains in sensitivity are particularly attractive for conducting high-throughput proteomics experiments with high chromatographic flow rates and fast gradients. We demonstrate that when combined with either micro-flow- or analytical-flow-rate chromatography, Zeno SWATH increases protein identification in complex samples 5- to 10-fold when compared to current SWATH acquisition methods on the same instrument. Using 20-min micro-flow chromatography, Zeno SWATH identified > 6,000 proteins from a 62.5 ng load of human cell lysate with more than 5,000 proteins consistently quantified in triplicate injections with a median CV of 6%. Using 5-min analytical-flow-rate chromatography (800 µl/min), Zeno SWATH identified 4,907 proteins from a triplicate injection of 2 µg of a human cell lysate; or more than 3,000 proteins from 250 ng tryptic digest. Zeno SWATH hence facilitates precise proteomic experiments with small sample amounts using a fast and robust high flow-rate chromatographic method, broadening the application space that requires precise proteomic experiments on a large scale.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:59:05.183.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ziyue Wang
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Cicer arietinum (Chickpea) (Garbanzo); NCBI TaxID: 3827; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	iodoacetamide derivatized residue
Instrument	SCIEX software; TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-17 02:42:08	ID requested
1	2022-12-01 00:28:22	announced
⏵ 2	2023-11-14 08:59:05	announced	2023-11-14: Updated project metadata.

Dataset with its publication pending

submitter keyword: DIA,Zeno SWATH

Markus Ralser
contact affiliation	Department of Biochemistry, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Berlin, Germany
contact email	markus.ralser@charite.de
lab head
Ziyue Wang
contact affiliation	Charité – Universitätsmedizin Berlin
contact email	ziyue.wang@charite.de
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/2022/12/PXD036786

PRIDE project URI

• PRIDE
  1. PXD036786
     1. Label: PRIDE project
     2. Name: High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA