PXD034386

PXD034386 is an original dataset announced via ProteomeXchange.

Title	Optimisation of a protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications
Description	The comprehension of the pathophysiological mechanisms, the identification of druggable targets, and putative biomarkers for aortic valve stenosis can be pursued through holistic approaches such as proteomics. However, tissue homogenisation and protein extraction are difficulted by tissue calcification. Reproducibility of proteome studies is key when minding clinical translation of the findings. Thus, we aimed to optimise a protocol for aortic valve homogenisation and protein extraction, and to develop a standard operating procedure (SOP), which can be used by researchers to maximise protein yield, while reducing inter-laboratory variability. We have compared the protein yield between conventional tissue grinding in nitrogen followed by homogenisation with a Potter apparatus, with a more advanced bead-beating system. Once confirmed the superiority of the latter, we further optimised it by testing the effect of beads size, the number of homogenisation cycles, tube capacity, lysis buffer/tissue mass ratio, and two different lysis buffers. Optimal protein extraction was achieved with 2.8 mm zirconium dioxide beads, in two homogenisation cycles, in the presence of 20 µL RIPA buffer/mg tissue, using 2-mL O-ring tubes. As a proof-of-concept of the usefulness of this SOP for proteomics, the AV proteome of men and women with aortic stenosis was characterised, resulting in the quantification of proteins across 6 orders of magnitude, and uncovering some putative proteins dysregulated by sex.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:28:59.906.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fábio Trindade
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	S-carboxamidoethyl-L-cysteine; dehydrated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; deamidated residue
Instrument	TripleTOF 6600

Revision	Datetime	Status	ChangeLog Entry
0	2022-06-06 07:38:19	ID requested
1	2022-10-13 11:11:37	announced
⏵ 2	2023-11-14 08:29:02	announced	2023-11-14: Updated project metadata.

Trindade F, Ferreira AF, Saraiva F, Martins D, Mendes VM, Sousa C, Gavina C, Leite-Moreira A, Manadas B, Falc, ã, o-Pires I, Vitorino R, Optimization of a Protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications: Development of a Standard Operating Procedure. Proteomes, 10(3):(2022) [pubmed]

submitter keyword: Human, SWATH-MS, Aortic Valve Stenosis, Aortic Valve

Fábio Trindade
contact affiliation	UnIC@RISE, Department of Surgery and Physiology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
contact email	fabiotrindade@ua.pt
lab head
Fábio Trindade
contact affiliation	iBiMED, University of Aveiro; UnIC, Faculty of Medicine, University of Porto
contact email	fabiotrindade@ua.pt
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/2022/10/PXD034386

PRIDE project URI

• PRIDE
  1. PXD034386
     1. Label: PRIDE project
     2. Name: Optimisation of a protocol for Protein Extraction from Calcified Aortic Valves for Proteomics Applications