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

Abstract

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Anemonefishes: A model system for evolutionary genomics

“…Yet, technologies for quantifying the proteome are still lagging behind other "omics" fields. 6 Until recently, only a couple of studies have measured changes in protein expression of a closely related species to anemonefish, exposed to elevated CO 2. 6,97,109 Proteomics can then be a powerful tool for identifying specific proteins and pathways that are crucial to stress responses, but more general for studying the evolution, biodiversity, and physiological adaptations of fish living in extreme environments.…”

“…6 Until recently, only a couple of studies have measured changes in protein expression of a closely related species to anemonefish, exposed to elevated CO 2. 6,97,109 Proteomics can then be a powerful tool for identifying specific proteins and pathways that are crucial to stress responses, but more general for studying the evolution, biodiversity, and physiological adaptations of fish living in extreme environments. 110 Conventional methods in proteomics first focused on isolating specific proteins to study their structure and function, 107 which led to a very small number of intensely studied proteins over the past decades.…”

“…A recent study laid the groundwork for using this approach on a non-model fish species. 6 It evaluated the performance of SWATH-MS in detecting significant proteomic expression differences in a complex experimental design of fish exposed to multiple climate change stressors. Most of all, the authors provided a guide on the efficiency, cost-effectiveness and applicability of this method in creating future proteomics references in non-model organisms aiming to identify genome-wide and ecologically relevant differential protein expression.…”

“…Most of all, the authors provided a guide on the efficiency, cost-effectiveness and applicability of this method in creating future proteomics references in non-model organisms aiming to identify genome-wide and ecologically relevant differential protein expression. 6 Certainly, the advancement of new techniques allows for the broad application of proteomics to study many aspects of anemonefishes. A few studies have investigated the proteomic responses of the spiny chromis damselfish Acanthochromis polyacanthus to ocean acidification, 6,97,109 and one provided the proteomic profile of a sea anemone species from temperate seas.…”

“…Though not specifically for anemonefish, a growing number of studies are applying proteomics in coral reef fish (see Section 2.4). Monroe and colleagues (2020) used a mass spectrometry data-independent acquisition method for proteome quantification in a non-model fish species for the first time, 6 a stepping stone for the application of proteomics to study many anemonefish. ).…”