PXD036451

PXD036451 is an original dataset announced via ProteomeXchange.

Title	Increasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics
Description	The combination of short liquid chromatography (LC) gradients and data independent acquisition (DIA) by mass spectrometry (MS) has proven its huge potential for high-throughput proteomics. However, the optimization of isolation window schemes resulting in a certain number of data points per peak (DPPP) is understudied, although it is one of the most important parameters for the outcome of this methodology. In this study, we show that substantially reducing the number of data points per peak (DPPP) for short gradient DIA massively increases protein identifications while maintaining quantitative precision. This is due to a large increase in the number of precursors identified, which keeps the number of data points per protein almost constant even at long cycle times. When proteins are inferred from its precursors, quantitative precision is maintained at low DPPP while greatly increasing proteomic depth. This strategy enabled us quantifying 6018 HeLa proteins (> 80,000 precursor identifications) with coefficients of variation below 20% in 30 min using a Q Exactive HF, which corresponds to a throughput of 29 samples per day. This indicates that the potential of high-throughput DIA-MS has not been fully exploited yet.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:47:49.929.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Joerg Doellinger
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-02 04:56:26	ID requested
1	2023-05-10 15:26:17	announced
⏵ 2	2023-11-14 08:47:57	announced	2023-11-14: Updated project metadata.

Doellinger J, Blumenscheit C, Schneider A, Lasch P, Increasing Proteome Depth While Maintaining Quantitative Precision in Short-Gradient Data-Independent Acquisition Proteomics. J Proteome Res, 22(6):2131-2140(2023) [pubmed]

submitter keyword: Isolation Windows,DIA, Multi-species, short-gradient

Peter Lasch
contact affiliation	ZBS6, Proteomics and Spectroscopy, Robert Koch-Institute
contact email	LaschP@rki.de
lab head
Joerg Doellinger
contact affiliation	Proteomics and Spectroscopy (ZBS6), Robert Koch-Institute
contact email	Doellingerj@rki.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/2023/05/PXD036451

PRIDE project URI

• PRIDE
  1. PXD036451
     1. Label: PRIDE project
     2. Name: Increasing proteome depth while maintaining quantitative precision in short gradient data-independent acquisition proteomics