PXD008651

PXD008651 is an original dataset announced via ProteomeXchange.

Title	SWATH mass spectrometry as a tool for quantitative profiling of the matrisome
Description	Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to its inherent complexity and insolubility. Here we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins in both non-enriched and ECM enriched tissue without the need for prior fractionation. Utilising a spectral library containing 201 matrisomal proteins, we compared the performance and reproducibility of SWATH MS over conventional data-dependent analysis mass spectrometry (DDA MS) in unfractionated murine lung and liver tissues. SWATH MS conferred a 15-20% increase in reproducible peptide identification across replicate experiments in both tissue types and identified 54% more matrisomal proteins in the liver over DDA MS. We further use SWATH MS to evaluate the quantitative changes in matrisome content that accompanies ECM enrichment. Our data shows that ECM enrichment led to a systematic increase in core matrisomal proteins that was accompanied by significant losses in specific matrisome-associated proteins including the cathepsins and proteins of the S100 family.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:07:50.402.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lukas Krasny
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-11 01:08:09	ID requested
1	2018-03-19 04:10:31	announced
⏵ 2	2024-10-22 04:07:51	announced	2024-10-22: Updated project metadata.

10.1016/j.jprot.2018.02.026;

Krasny L, Bland P, Kogata N, Wai P, Howard BA, Natrajan RC, Huang PH, SWATH mass spectrometry as a tool for quantitative profiling of the matrisome. J Proteomics, 189():11-22(2018) [pubmed]

ProteomeXchange project tag: deep learning, benchmarking, machine learning

curator keyword: Technical

submitter keyword: proteomics, mass spectrometry, DIA MS, Extracellular matrix,Matrisome, SWATH MS

Paul Huang
contact affiliation	The Institute of Cancer Research Division of Molecular Pathology 237 Fulham Road, London, SW3 6JB
contact email	Paul.Huang@icr.ac.uk
lab head
Lukas Krasny
contact affiliation	The Institute of Cancer Research
contact email	Lukas.Krasny@icr.ac.uk
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/2018/03/PXD008651

PRIDE project URI

• PRIDE
  1. PXD008651
     1. Label: PRIDE project
     2. Name: SWATH mass spectrometry as a tool for quantitative profiling of the matrisome