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

Area of Science:

• Proteomics and Mass Spectrometry
• Marine Biology and Ecotoxicology
• Molecular Biology and Genomics

Background:

• Quantitative proteomics using mass spectrometry offers insights into biological systems.
• Data-independent acquisition (DIA-MS) is a sensitive method for whole proteome analysis, requiring comprehensive spectral libraries.
• Developing species-specific spectral libraries is crucial for advancing proteomic research in various organisms.

Purpose of the Study:

• To compare spectral library construction methods for nonmodel organisms using coral reef fish.
• To demonstrate the feasibility and value of building spectral libraries for nonmodel species.
• To validate the application of these libraries in identifying environmentally responsive proteins.

Main Methods:

• Construction of a large spectral library (12,553 protein groups) from liver and brain tissues of a coral reef fish.
• Utilizing data-independent acquisition (DIA-MS) and data-dependent acquisition (DDA) methods for library creation and proteomic analysis.
• Exposing fish to elevated pCO2 and temperature to identify differentially expressed proteins.

Main Results:

• A comprehensive spectral library was successfully created for a nonmodel organism.
• Identification of differentially expressed proteins under simulated ocean warming and acidification conditions.
• Validation of heat shock protein upregulation in response to combined environmental stressors.

Conclusions:

• This study presents the first reference spectral library for a nonmodel organism, specifically a coral reef fish.
• The developed spectral library is effective for identifying ecologically relevant proteomic changes in response to environmental stressors.
• This work provides a valuable framework for constructing spectral libraries for other nonmodel organisms, advancing ecological and evolutionary proteomic studies.