PXD006428 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
Publication List
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] |
Keyword List
curator keyword: Technical |
submitter keyword: proteomics, mass spectrometry, LC-SRM, matrisome,tissue extraction, collagen, chemical digestion, extracellular matrix |
Contact List
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 | |
Full Dataset Link List
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 |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD006428
- Label: PRIDE project
- Name: Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization