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SWATH mass spectrometry as a tool for quantitative profiling of the matrisome
Lukas Krasny1, Philip Bland2, Naoko Kogata2
1Division of Molecular Pathology, The Institute of Cancer Research, London, SW3 6JB, UK.
Journal of Proteomics
|March 5, 2018
Summary
Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) offers improved quantitative analysis of the matrisome, identifying more proteins with greater reproducibility than conventional methods. This technique simplifies workflows by eliminating the need for prior enrichment or fractionation.
Area of Science:
- Proteomics
- Biochemistry
- Mass Spectrometry
Background:
- The matrisome, comprising extracellular matrix (ECM) and associated proteins, is crucial for tissue structure and cellular regulation.
- Its inherent complexity and insolubility pose significant challenges for proteomic analysis.
- Current enrichment strategies can lead to the loss of soluble matrisome-associated proteins.
Purpose of the Study:
- To present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for quantitative matrisome analysis.
- To compare the performance and reproducibility of SWATH MS against data-dependent analysis mass spectrometry (DDA MS).
- To evaluate matrisome changes during ECM enrichment using SWATH MS.
Main Methods:
- Utilized SWATH MS for quantitative proteomic analysis of matrisomal proteins.
- Compared SWATH MS with DDA MS in unfractionated murine lung and liver tissues.
- Analyzed both non-enriched and ECM-enriched tissue samples.
- Employed a spectral library of 201 matrisomal proteins.
Main Results:
- SWATH MS increased reproducible peptide identification by 15-20% compared to DDA MS.
- SWATH MS identified 54% more matrisomal proteins in liver tissue than DDA MS.
- ECM enrichment systematically increased core matrisomal proteins but decreased matrisome-associated proteins like cathepsins and S100 family proteins.
Conclusions:
- SWATH MS is a versatile tool for in-depth matrisome characterization in unfractionated tissues.
- SWATH MS offers superior reproducibility and coverage of the matrisome compared to DDA MS.
- SWATH MS enables accurate quantification without prior enrichment, simplifying workflows and preserving associated proteins.
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