PXD041421-2

PXD041421 is an original dataset announced via ProteomeXchange.

Title	DDA-PASEF and diaPASEF acquired A549/K562 proteomic datasets with deliberate batch effects
Description	We generated two comprehensive large-scale proteomics datasets with deliberate batch effects using the latest parallel accumulation-serial fragmentation in both Data-Dependent and Data-Indepentdent Acquisition modes. This dataset contain a balanced two-class design (cell lines: A549 vs K562), allowing for investigating mixed effects from class, batch and acquisition method. Investigators can also compare and integrate DDA and DIA platforms, delve into the various patterns and mechanisms of missing values, benchmark batch effects correction algorithms and assess confounding between different technical issues.
HostingRepository	PRIDE
AnnounceDate	2023-12-04
AnnouncementXML	Submission_2023-12-04_03:09:37.960.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	HE WANG
SpeciesList	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	2023-04-09 17:41:32	ID requested
1	2023-11-21 06:02:06	announced
⏵ 2	2023-12-04 03:09:38	announced	2023-12-04: Updated project metadata.

Wang H, Lim KP, Kong W, Gao H, Wong BJH, Phua SX, Guo T, Goh WWB, MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects. Sci Data, 10(1):858(2023) [pubmed]

10.1038/s41597-023-02779-8;

submitter keyword: DDA, PASEF, DIA, K562, A549, Batch Effects

Wilson Goh
contact affiliation	Lee Kong Chian School of Medicine, School of Biological Sciences, Nanyang Technological University, Singapore
contact email	wilsongoh@ntu.edu.sg
lab head
HE WANG
contact affiliation	Nanyang Technological University
contact email	HE009@e.ntu.edu.sg
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/2023/11/PXD041421

PRIDE project URI

• PRIDE
  1. PXD041421
     1. Label: PRIDE project
     2. Name: DDA-PASEF and diaPASEF acquired A549/K562 proteomic datasets with deliberate batch effects