Probing SWATH-MS as a tool for proteome level quantification in a non-model fish.
KAUST DepartmentMarine Science Program
Biological and Environmental Sciences and Engineering (BESE) Division
Proteomics and Protein Expression
Online Publication Date2020-08-04
Print Publication Date2020-11
Embargo End Date2021-07-21
Permanent link to this recordhttp://hdl.handle.net/10754/664351
MetadataShow full item record
AbstractQuantitative proteomics via mass spectrometry can provide valuable insight into molecular and phenotypic characteristics of a living system. Recent mass spectrometry developments include data-independent acquisition (SWATH/DIA-MS), an accurate, sensitive, and reproducible method for analyzing the whole proteome. The main requirement for this method is the creation of a comprehensive spectral library. New technologies have emerged producing larger and more accurate species-specific libraries leading to a progressive collection of proteome references for multiple molecular model species. Here, for the first time, we set out to compare different spectral library constructions using multiple tissues from a coral reef fish to demonstrate its value and feasibility for non-model organisms. We created a large spectral library composed of 12,553 protein groups from liver and brain tissues. Via identification of differentially expressed proteins under fish exposure to elevated pCO2 and temperature, we validated the application and usefulness of these different spectral libraries. Successful identification of significant differentially expressed proteins from different environmental exposures occurred using the library with a combination of data-independent and data-dependent acquisition methods as well as both tissue types. Further analysis revealed expected patterns of significantly up-regulated heat shock proteins in a dual condition of ocean warming and acidification indicating the biological accuracy and relevance of the method. This study provides the first reference spectral library for a non-model organism. It represents a useful guide for future building of accurate spectral library references in non-model organisms allowing the discovery of ecologically relevant changes in the proteome.
CitationMonroe, A. A., Zhang, H., Schunter, C., & Ravasi, T. (2020). Probing SWATH-MS as a tool for proteome level quantification in a non-model fish. Molecular Ecology Resources. doi:10.1111/1755-0998.13229
JournalMolecular ecology resources
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