Probing SWATH-MS as a tool for proteome level quantification in a non-model fish.
Type
ArticleKAUST Department
Marine Science ProgramBiological and Environmental Sciences and Engineering (BESE) Division
Proteomics and Protein Expression
Date
2020-08-04Online Publication Date
2020-08-04Print Publication Date
2020-11Embargo End Date
2021-07-21Permanent link to this record
http://hdl.handle.net/10754/664351
Metadata
Show full item recordAbstract
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:10.1111/1755-0998.13229Publisher
WileyJournal
Molecular ecology resourcesPubMed ID
32687632Additional Links
https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13229ae974a485f413a2113503eed53cd6c53
10.1111/1755-0998.13229
Scopus Count
Related articles
- Reproducibility, Specificity and Accuracy of Relative Quantification Using Spectral Library-based Data-independent Acquisition.
- Authors: Barkovits K, Pacharra S, Pfeiffer K, Steinbach S, Eisenacher M, Marcus K, Uszkoreit J
- Issue date: 2020 Jan
- Development of a Gill Assay Library for Ecological Proteomics of Threespine Sticklebacks (Gasterosteus aculeatus).
- Authors: Li J, Levitan B, Gomez-Jimenez S, Kültz D
- Issue date: 2018 Nov
- SWATH mass spectrometry as a tool for quantitative profiling of the matrisome.
- Authors: Krasny L, Bland P, Kogata N, Wai P, Howard BA, Natrajan RC, Huang PH
- Issue date: 2018 Oct 30
- Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins.
- Authors: Blattmann P, Stutz V, Lizzo G, Richard J, Gut P, Aebersold R
- Issue date: 2019 Feb 12
- Arabidopsis proteome and the mass spectral assay library.
- Authors: Zhang H, Liu P, Guo T, Zhao H, Bensaddek D, Aebersold R, Xiong L
- Issue date: 2019 Nov 22