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    Probing SWATH-MS as a tool for proteome level quantification in a non-model fish.

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    Type
    Article
    Authors
    Monroe, Alison cc
    Zhang, Huoming cc
    Schunter, Celia Marei cc
    Ravasi, Timothy cc
    KAUST Department
    Marine Science Program
    Biological and Environmental Sciences and Engineering (BESE) Division
    Proteomics and Protein Expression
    Date
    2020-08-04
    Online Publication Date
    2020-08-04
    Print Publication Date
    2020-11
    Embargo End Date
    2021-07-21
    Permanent link to this record
    http://hdl.handle.net/10754/664351
    
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    Abstract
    Quantitative 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.
    Citation
    Monroe, 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
    Publisher
    Wiley
    Journal
    Molecular ecology resources
    DOI
    10.1111/1755-0998.13229
    10.1101/2020.02.23.946913
    PubMed ID
    32687632
    Additional Links
    https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13229
    ae974a485f413a2113503eed53cd6c53
    10.1111/1755-0998.13229
    Scopus Count
    Collections
    Articles; Biological and Environmental Science and Engineering (BESE) Division; Marine Science Program

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