PXD050877-2

PXD050877 is an original dataset announced via ProteomeXchange.

Title	Targeted proteomic approach for quantification of Collagen type I and type III in formalin-fixed paraffin-embedded tissue
Description	Collagen is the most abundant protein in mammals and a major structural component of the extracellular matrix (ECM). Changes to ECM composition occur as a result of numerous physiological and pathophysiological causes, and a common means to evaluate these changes is the collagen 3 (Col3) to collagen 1 (Col1) ratio. Current methods to measure the Col3/1 ratio suffer from a lack of specificity and often under- or over-estimate collagen composition and quantity. This manuscript presents a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) method for quantification of Col3 and Col1 in FFPE tissues. Using surrogate peptides to generate calibration curves, Col3 and Col1 are readily quantified in FFPE tissue sections with high accuracy and precision. The method is applied to several tissue types from both human and reindeer tissues, demonstrating its generalizability. In addition, the targeted LC-MS/MS method permits quantitation of the hydroxyprolinated form of Col3, which has significant implications for understanding not only the quantity of Col3 in tissue, but also understanding of the pathophysiology underlying many causes of ECM changes. This manuscript presents a straight forward, accurate, precise and generalizable method for quantifying the Col3/1 ratio in a variety of tissue types and organisms.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:34:56.284.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Luiz Gustavo de Almeida
SpeciesList	scientific name: Rangifer tarandus (Reindeer) (Cervus tarandus); NCBI TaxID: 9870;
ModificationList	4-hydroxy-L-proline; acetylated residue; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-21 16:44:37	ID requested
1	2024-04-01 10:47:42	announced
⏵ 2	2024-10-22 06:34:56	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: LC-MSMS, ECM,Collagen

Antoine Dufour
contact affiliation	Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada; Department of Physiology and Pharmacology, University of Calgary, Alberta, Canada; The Hotchkiss Brain Institute, University of Calgary, Alberta, Canada; McCaig Institute for Bone and Joint Health, University of Calgary, Alberta, Canada
contact email	antoine.dufour@ucalgary.ca
lab head
Luiz Gustavo de Almeida
contact affiliation	University of Calgary
contact email	luizgustavo.biotec@hotmail.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/2024/04/PXD050877

PRIDE project URI

• PRIDE
  1. PXD050877
     1. Label: PRIDE project
     2. Name: Targeted proteomic approach for quantification of Collagen type I and type III in formalin-fixed paraffin-embedded tissue