PXD034025

PXD034025 is an original dataset announced via ProteomeXchange.

Title	Analysis of proteotype, cell growth and metabolic changes induced by caspase-9 inhibition in chondrogenic cells
Description	Caspase-9 is the major apical caspase responsible for triggering the intrinsic apoptotic pathway. Our pilot study indicated that specific inhibition of caspase-9 caused microscopically evident alterations in appearance of the primary chondrogenic cultures which cannot be explained by decrease in apoptosis. In order to search for the complex molecular background of the effect, proteomics analysis after caspase-9 inhibition was performed. A selective fluoromethylketone inhibitor was applied to inhibit caspase-9 in the chondrogenic cultures. In this PRIDE project we present three LC-MS datasets: i) diaPASEF data obtained using timsTOF Pro LC-MS system; ii) iTRAQ-2DLC-MS3 dataset; and iii) conventional LC-DIA-MS dataset, both measured on Orbitrap Lumos. In this project we demonstrate superiority of the diaPASEF method offering better proteome coverage.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:44:35.458.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pavel Bouchal
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	methylthiolated residue
Instrument	timsTOF Pro; Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2022-05-23 03:29:54	ID requested
⏵ 1	2023-11-14 08:44:41	announced

Lapcik P, Vesela B, Potesil D, Dadakova K, Zapletalova M, Benes P, Bouchal P, Matalova E, DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspase-9 inhibition in chondrogenic cells. Proteomics, 23(11):e2200408(2023) [pubmed]

submitter keyword: metabolism, proteomics, MS3, DIA, chondrogenesis,diaPASEF, caspase-9, micromass cultures, iTRAQ

Pavel Bouchal
contact affiliation	Masaryk University, Faculty of Science, Department of Biochemistry
contact email	bouchal@chemi.muni.cz
lab head
Pavel Bouchal
contact affiliation	Masaryk University, Faculty of Science
contact email	bouchal@chemi.muni.cz
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/2023/04/PXD034025

PRIDE project URI

• PRIDE
  1. PXD034025
     1. Label: PRIDE project
     2. Name: Analysis of proteotype, cell growth and metabolic changes induced by caspase-9 inhibition in chondrogenic cells