PXD036566-1

PXD036566 is an original dataset announced via ProteomeXchange.

Title	Comparative analysis of DDA- and DIA-PASEF methods for proteomics analysis of human valve interstitial cells and osteoblasts during osteogenic differentiation
Description	Shotgun proteomics is one of the key "omics" methods, the methodology of which is rapidly developing. Mass spectrometers of the TimsToF series (Bruker) with ion mobility are one of the young technological platforms for shotgun proteomics in which both data dependent (DDA) and data independent acquisition (DIA) proteomics methods might be performed. However, only a few comparisons of the effectiveness of DDA and DIA proteomics on TimsToF have been published, carried out mainly on the test samples. From the other hand, peculiarities of osteogenic differentiation of human valve interstitial cells (VICs) are fruitful therapeutic target for calcific aortic valve disease (CAVD) treatment. Still, there is no data whether pathological osteogenic differentiation of VICs similar to normal ossification. Combining this technical and biological tasks we performed comparative proteomics analysis of osteogenic differentiation of human VICs and osteoblasts by DIA- and DDA-PASEF proteomics on TimsToF Pro.
HostingRepository	PRIDE
AnnounceDate	2024-11-12
AnnouncementXML	Submission_2024-11-12_11:15:52.469.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Arseniy Lobov
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2022-09-08 06:44:47	ID requested
⏵ 1	2024-11-12 11:15:52	announced

Dataset with its publication pending

submitter keyword: data independent acquisition, PASEF, shotgun proteomics,homo sapiens, TimsToF Pro, calcific aortic valve disease

Anna B. Malashicheva
contact affiliation	Leading scientist, head of Laboratory of Regenerative Biomedicine, Institute of Cytology, Russian Academy of Sciences
contact email	amalashicheva@gmail.com
lab head
Arseniy Lobov
contact affiliation	Yifat Merbl Lab, Dept. of Systems Immunology, Weizmann Institute of Science
contact email	arseniylobov@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/2024/11/PXD036566

PRIDE project URI

• PRIDE
  1. PXD036566
     1. Label: PRIDE project
     2. Name: Comparative analysis of DDA- and DIA-PASEF methods for proteomics analysis of human valve interstitial cells and osteoblasts during osteogenic differentiation