PXD040205

PXD040205 is an original dataset announced via ProteomeXchange.

Title	Fast proteomics with dia-PASEF and analytical flow-rate chromatography
Description	The presented approach is a combination of analytical flow rate chromatography with ion mobility separation of peptide ions, data-independent acquisition, and raw data processing using the DIA-NN software suite, to conduct fast, low-cost proteomic experiments that only require moderate sample amounts. The present dataset contains a series of benchmarks. Specifically, a dilution series of a K562 digest standard acquired using 5-minute and 3-minute chromatographic gradients, as well as a mixed-species human–E.coli benchmark for quantitative performance. We further demonstrate the application of the proposed approach to the analysis of plasma proteomes of COVID-19 patients, using a 3-minute gradient acquisition on a dual-column liquid chromatography system at a throughput of 398 samples/day.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_09:02:00.499.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lukasz Szyrwiel
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-02-16 14:52:21	ID requested
1	2023-07-03 14:06:55	announced
⏵ 2	2023-11-14 09:02:08	announced	2023-11-14: Updated project metadata.

Szyrwiel L, Gille C, M, ü, lleder M, Demichev V, Ralser M, Fast proteomics with dia-PASEF and analytical flow-rate chromatography. Proteomics, 24(1-2):e2300100(2024) [pubmed]

submitter keyword: short gradient, dia-PASEF, TimsTOF, fast methods,Plasma proteomics, high-throughput, COVID-19

prof. Markus Ralser
contact affiliation	1)Department of Biochemistry, Charité – Universitätsmedizin Berlin, Berlin, Germany. 2)The Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK 3)Max Planck Institute for Molecular Genetics, Berlin, Germany
contact email	markus.ralser@charite.de
lab head
Lukasz Szyrwiel
contact affiliation	Charité - Universitätsmedizin Berlin Laboratory "Biochemistry und System biology of Metabolism"
contact email	l.szyrwiel@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/2023/07/PXD040205

PRIDE project URI

• PRIDE
  1. PXD040205
     1. Label: PRIDE project
     2. Name: Fast proteomics with dia-PASEF and analytical flow-rate chromatography