Dataset Information

SWATH mass spectrometry as a tool for quantitative profiling of the matrisome

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Lung, Liver

SUBMITTER: Lukas Krasny

LAB HEAD: Paul Huang

PROVIDER: PXD008651 | Pride | 2018-03-19

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20170927_Spec_lib_Liver1.group	Other
	20170927_Spec_lib_Liver1.mgf	Mgf
	20170927_Spec_lib_Liver1.zip	Other
	20171025_Spec_lib_Lung1.group	Other
	20171025_Spec_lib_Lung1.mgf	Mgf

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Publications

SWATH mass spectrometry as a tool for quantitative profiling of the matrisome.

Krasny Lukas L Bland Philip P Kogata Naoko N Wai Patty P Howard Beatrice A BA Natrajan Rachael C RC Huang Paul H PH

Journal of proteomics 20180301

Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to the inherent complexity and insolubility of these proteins. 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 co ...[more]

PMID: 29501709

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