PXD006428

PXD006428 is an original dataset announced via ProteomeXchange.

Title	Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization
Description	The extracellular matrix (ECM) is readily enriched by decellularizing tissues with non-denaturing detergents to solubilize and deplete the vast majority of cellular components. This approach has been used extensively to generate ECM scaffolds for regenerative medicine technologies and in 3D cell culture to model how the ECM contributes to disease progression. A highly-enriched ECM fraction can then be generated using a strong chaotrope buffer that is compatible with downstream bottom-up proteomic analysis or 3D cell culture experiments after extensive dialysis. With most tissues, an insoluble pellet remains that is rich in structural ECM components. Previously we showed that this understudied fraction represented approximately 80 percent of total fibrillar collagen from the lung and other ECM fiber components that are known to be covalently cross-linked. Here we present a hydroxylamine digestion approach for post-chaotrope insoluble ECM analysis with comparison to an established CNBr method for matrisome characterization. Because ECM characteristics vary widely among tissues, we chose five tissues that represent unique and diverse ECM abundances, composition and biomechanical properties. Hydroxylamine digestion is compatible with downstream proteomic workflows, yields high levels of ECM peptides from the insoluble ECM fraction and reduces analytical variability when compared to CNBr digestion.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:37:13.286.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD006428
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Alexander Barrett
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	Oxidation; Acetyl; Carbamidomethyl; Gln->pyro-Glu
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-02 06:34:29	ID requested
1	2017-10-20 08:19:17	announced
⏵ 2	2024-10-22 04:37:21	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.7b00527;

10.6019/PXD006428;

Barrett AS, Wither MJ, Hill RC, Dzieciatkowska M, D'Alessandro A, Reisz JA, Hansen KC, Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization. J Proteome Res, 16(11):4177-4184(2017) [pubmed]

curator keyword: Technical

submitter keyword: proteomics, mass spectrometry, LC-SRM, matrisome,tissue extraction, collagen, chemical digestion, extracellular matrix

Kirk C Hansen
contact affiliation	University of Colordao Denver - Anschutz Medical Campus
contact email	kirk.hansen@ucdenver.edu
lab head
Alexander Barrett
contact affiliation	University of Colorado Denver
contact email	alexander.barrett@ucdenver.edu
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/2017/10/PXD006428

PRIDE project URI

• PRIDE
  1. PXD006428
     1. Label: PRIDE project
     2. Name: Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization