A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics

Area of Science:

• Marine biology
• Proteomics
• Genomics

Background:

• Adipose tissue in marine mammals is key to understanding its evolution and function.
• Low nucleic acid and protein yields hinder molecular studies in lipid-rich tissues.
• Genomic data is often unavailable for these species.

Purpose of the Study:

• To develop and validate proteogenomic workflows for analyzing elephant seal blubber.
• To identify proteins in elephant seal blubber for functional studies.
• To improve protein identification sensitivity in challenging samples.

Main Methods:

• Proteomic analysis of elephant seal blubber using two different buffer types (Qiazol vs. sodium deoxycholate).
• Comparison of proteomics data analysis platforms, including *de novo* peptide sequencing.
• Integration of proteomic and transcriptomic data for proteogenomic analysis.

Main Results:

• Qiazol buffer yielded more subcellular proteins and RNA compared to detergent buffer.
• *De novo* peptide sequencing significantly improved protein identification sensitivity.
• A proteome of elephant seal blubber was generated, identifying 2678 proteins.

Conclusions:

• The developed proteogenomic workflow is effective for analyzing small, lipid-rich biopsies from marine mammals.
• This method facilitates molecular insights into adipose tissue function and evolution.
• The identified proteome provides a valuable resource for future research on marine mammal physiology.