PXD066357-1

PXD066357 is an original dataset announced via ProteomeXchange.

Title	COLLAGEN POST-TRANSLATIONAL MODIFICATIONS ARE ALTERED IN IPF INCLUDING WITHIN ECM RECEPTOR BINDING MOTIFS
Description	Idiopathic pulmonary fibrosis (IPF) is a fatal chronic lung disease with a median survival of 3.8 years, a prevalence of 10 to 60 cases per 100,000 in the United States, and rising incidence and mortality rates. Currently approved antifibrotic agents can slow disease progression but are insufficient to significantly improve long-term outcomes. Tissue remodeling in IPF is driven by fibroblast activation and excessive deposition of fibrillar collagen and other extracellular matrix (ECM) components. An increasing body of evidence suggests that the ECM instructs resolution or progression of fibrotic disease. To date, ECM-targeting therapies including e.g. ECM crosslinking inhibitors, and drugs targeting ECM receptors like integrins have shown promise in preclinical animal models of organ fibrosis but were ineffective or associated with unfavorable safety profiles in clinical trials. Targeting collagen biosynthesis is a promising antifibrotic therapeutic avenue and imaging with collagen-binding peptides emerges as a non-invasive biomarker for diagnosis and disease progression. But collagen measurements in preclinical models and patient samples typically rely on methods that do not differentiate between collagen types or chains, as e.g. the hydroxyproline assay. Also, collagen post-translational modifications (PTMs), which have important biological functions, are not assessed in chain- and site-specific detail. A deeper understanding of fibrotic ECM is critical for advancing ECM-targeted diagnostics and therapies, but many molecular specifics of pathological collagen including PTMs remain elusive. Here, we fractionated protein from control lung and IPF tissue and quantified insoluble ECM components and soluble protein using iBAQ quantification in the MaxQuant software, as well as collagen PTMs in site-specific detail using our established bioinformatic pipeline (Merl-Pham et al 2029 Matrix Biology Plus).
HostingRepository	PRIDE
AnnounceDate	2025-08-25
AnnouncementXML	Submission_2025-08-25_02:03:51.615.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Juliane Merl-Pham
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2025-07-21 03:59:54	ID requested
⏵ 1	2025-08-25 02:03:52	announced

10.1164/RCCM.202505-1276RL;

submitter keyword: LC-MSMS, collagen,IPF

Claudia A. Staab-Weijnitz
contact affiliation	Institute of Lung Health and Immunity, and Comprehensive Pneumology Center with the CPC-M bioArchive, Ludwig-Maximilians-Universität München and Helmholtz Zentrum München, Munich, Germany, Member of the German Center for Lung Research (DZL); 8Department of Pediatrics, and Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
contact email	claudia.staab-weijnitz@cuanschutz.edu
lab head
Juliane Merl-Pham
contact affiliation	Metabolomics and Proteomics Core, Helmholtz Munich
contact email	juliane.merl@helmholtz-muenchen.de
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/2025/08/PXD066357

PRIDE project URI

• PRIDE
  1. PXD066357
     1. Label: PRIDE project
     2. Name: COLLAGEN POST-TRANSLATIONAL MODIFICATIONS ARE ALTERED IN IPF INCLUDING WITHIN ECM RECEPTOR BINDING MOTIFS