PXD008442

PXD008442 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
Description	Remodeling of the extracellular matrix (ECM) is a common feature in lung diseases such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Here, we applied a sequential tissue extraction strategy to describe disease-specific remodeling of human lung tissue in disease, using end-stages of COPD and IPF. Our strategy was based on quantitative comparison of the disease proteomes, with specific focus on the matrisome, using data-independent acquisition and targeted data analysis (SWATH-MS). Our work provides an in-depth proteomic characterization of human lung tissue during impaired tissue remodeling. In addition, we show important quantitative and qualitative effects of the solubility of matrisome proteins. COPD was characterized by a disease-specific increase in ECM regulators, metalloproteinase inhibitor 3 (TIMP3) and matrix metalloproteinase 28 (MMP-28), whereas for IPF, impairment in cell adhesion proteins, such as collagen VI and laminins, was most prominent. For both diseases, we identified increased levels of proteins involved in the regulation of endopeptidase activity, with several proteins belonging to the serpin family. The established human lung quantitative proteome inventory and the construction of a tissue-specific protein assay library provides a resource for future quantitative proteomic analyses of human lung tissues.
HostingRepository	PRIDE
AnnounceDate	2018-04-05
AnnouncementXML	Submission_2018-04-05_03:41:56.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emma Åhrman
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-12-14 01:07:20	ID requested
⏵ 1	2018-04-05 03:41:58	announced

Å, hrman E, Hallgren O, Malmstr, ö, m L, Hedstr, ö, m U, Malmstr, ö, m A, Bjermer L, Zhou XH, Westergren-Thorsson G, Malmstr, ö, m J, Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. J Proteomics, 189():23-33(2018) [pubmed]

curator keyword: Biomedical

submitter keyword: Human, Lung, SWATH-MS, COPD, IPF

Johan Malmström
contact affiliation	Infection medicine proteomics BMC D13 Klinikgatan 28 22241 Lund Sweden
contact email	johan.malmstrom@med.lu.se
lab head
Emma Åhrman
contact affiliation	Lund University
contact email	emma.ahrman@med.lu.se
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/2018/04/PXD008442

PRIDE project URI

• PRIDE
  1. PXD008442
     1. Label: PRIDE project
     2. Name: Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis