PXD017703

PXD017703 is an original dataset announced via ProteomeXchange.

Title	Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)
Description	Data independent acquisition modes isolate and concurrently fragment populations of different precursors by cycling through segments of a predefined precursor m/z range. Although these selection windows collectively cover the entire m/z range, overall only a few percent of all incoming ions in each window are sampled. Making use of the correlation of molecular weight and ion mobility in a trapped ion mobility device (timsTOF Pro), we here devise a novel scan mode that samples up to 100% of the peptide precursor ion current in m/z and mobility windows. We extend an established targeted data extraction workflow by including the ion mobility dimension for both signal extraction and scoring, thereby increasing the specificity for precursor identification. Data acquired from whole proteome digests and mixed organism samples demonstrate deep proteome coverage and a very high degree of reproducibility as well as quantitative accuracy, even from 10 ng sample amounts.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:16:54.205.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	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	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-24 06:08:48	ID requested
1	2020-09-22 02:08:40	announced
2	2020-12-06 23:32:28	announced	2020-12-07: Updated publication reference for PubMed record(s): 33257825.
⏵ 3	2024-10-22 05:16:55	announced	2024-10-22: Updated project metadata.

10.1038/s41592-020-00998-0;

Meier F, Brunner AD, Frank M, Ha A, Bludau I, Voytik E, Kaspar-Schoenefeld S, Lubeck M, Raether O, Bache N, Aebersold R, Collins BC, R, ö, st HL, Mann M, diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition. Nat Methods, 17(12):1229-1236(2020) [pubmed]

ProteomeXchange project tag: deep learning, benchmarking, ion mobility, machine learning

submitter keyword: TIMS, PASEF, DIA,technical, ion mobility

Matthias Mann
contact affiliation	Proteomics and Signal Transduction Max Planck Institute of Biochemistry Germany
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.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/2020/12/PXD017703

PRIDE project URI

• PRIDE
  1. PXD017703
     1. Label: PRIDE project
     2. Name: Parallel accumulation – serial fragmentation combined with data-independent acquisition (diaPASEF)