A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics
Abstract
Animals with large adipose stores, such as marine mammals, may provide insights into evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can be rapidly obtained by proteomics and transcriptomics, but their application to adipose tissue is hindered by low nucleic acid and protein yields. We sequenced and compared proteomes isolated from blubber of four elephant seals using phenol and guanidine thiocyanate (Qiazol) or detergent (sodium deoxycholate) buffer. Qiazol recovered more subcellular proteins such as metabolic enzymes, in addition to extracting RNA, facilitating proteogenomic analyses of small lipid-rich tissue biopsies. We also compared proteomics data analysis platforms and found that de novo peptide sequencing improved protein identification sensitivity compared to database search alone. We report sample preparation and data analysis workflows for proteogenomics and a proteome of elephant seal blubber containing 2,678 proteins, including many of interest for further functional studies.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jan 01, 2018
- Source ID
- 10.1242/bio.036731
Entities
People
- Cory D Champagne
- Daniel E Crocker
- Jane Khudyakov
- Jared S. Deyarmin
- Laura Pujade Busqueta
- Melony J. Mody
- Rasool Maan
- Reeti Banerjee
- Ryan M. Hekman
Organizations
- National Marine Mammal Foundation
- Office of Naval Research
- Sonoma State University
- University of the Pacific