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

Molecular Ecology Resources
Alison A MonroeTimothy Ravasi

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 analysing 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 nonmodel 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...Continue Reading

References

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Citations

Jun 3, 2021·Cancers·Miao SuEdouard C Nice

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Datasets Mentioned

BETA
PXD017605

Methods Mentioned

BETA
dissection
protein assay
environmental stress

Software Mentioned

Spectronaut Pulsar X
DIA
SWATH
Perseus
Biognosys
Spectronaut
DDA
MS

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