PXD059171-1

PXD059171 is an original dataset announced via ProteomeXchange.

Title	Comparative proteomic analysis of the composition of decellularized extracellular matrix (dECM) and dECM-based inks as compared to the native tissue
Description	Regenerative medicine and tissue engineering approaches based on the use of 3D-bioprinted decellularized extracellular matrix (dECM) present the advantage of a relatively biomolecule-rich matrix, which directs cell growth and differentiation in a tissue-specific manner. However, little is known about the composition changes that occur with standard processing of dECM-based inks. To characterize this process, six porcine tissues/tissue layers (artery, breast, dermis, epidermis, muscle and nerve) were independently decellularized via chemical, mechanical and enzymatic processes and the resulting dECMs formulated into biocompatible inks, to serve as source biomaterials for 3D printing. A comparative liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomic analysis was carried out for native tissue, decellularized and formulated ECMs, and the resulting complexity of the matrisome analyzed. A core matrisome was found to overlap in all decellularized tissues, as well as tissue-specific components that correlated with predicted functional (gene ontology-based) definitions. The proportion of collagens (mostly the α1 chains of collagen type I and III) increased in the final processing step (inks) as compared to the native ECM and dECM stages. Overall, a median of 55 matrisomal proteins (range 45-126) was detected in the dECM-derived inks. This complexity is far superior in terms of mimicking the composition of native tissue to non-dECM-based inks. Our results support the use of dECM-based inks and biomaterials in mimicking native tissue ECM complexity.
HostingRepository	PRIDE
AnnounceDate	2025-05-15
AnnouncementXML	Submission_2025-05-15_03:56:11.271.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Paula Vazquez
SpeciesList	scientific name: Sus scrofa domesticus (domestic pig); NCBI TaxID: 9825;
ModificationList	No PTMs are included in the dataset
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2024-12-22 22:34:49	ID requested
⏵ 1	2025-05-15 03:56:11	announced

Dataset with its publication pending

submitter keyword: ECM,3D bioprinting, ink composition, decellularization, LC–MS/MS

Ander Izeta Permisán
contact affiliation	BioGipuzkoa Health Research Institute, Stem Cells & Aging Group, Donostia-San Sebastián, 20014, Spain; Donostia University Hospital, Advanced Therapies Unit, Donostia-San Sebastián, 20014, Spain.
contact email	ander.izetapermisan@osakidetza.eus
lab head
Paula Vazquez
contact affiliation	CIC biomaGUNE
contact email	pvazquez@cicbiomagune.es
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/2025/05/PXD059171

PRIDE project URI

• PRIDE
  1. PXD059171
     1. Label: PRIDE project
     2. Name: Comparative proteomic analysis of the composition of decellularized extracellular matrix (dECM) and dECM-based inks as compared to the native tissue