After conducting systematic and quantitative comparisons of different sample preparation techniques regarding their capability to efficiently and reproducibly recover proteins from biopsies, we present here our superior protocol for extracting proteins from low amounts of adipose tissue. Adipose tissue as a matrix in bottom-up proteomics is challenging due to the extremely high lipid content.
The lysis buffer utilized contains the detergent sodium deoxycholate, which does not impair the activity of trypsin and therefore enables direct digestion without detergent removal steps. The resulting workflow is time saving, cost efficient, easy to perform, and it can also be applied to other hydrophobic samples.
This is a preview of subscription content, log in to check access
Springer Nature is developing a new tool to find and evaluate Protocols. Learn more
We would like to thank Prof. Rolf Jorde, Sayda Colnoe, Allan Didriksen, and Jack-Ansgar Bruun. Our work was supported by a grant from the North Norway Regional Health Authorities.
Galic S, Oakhill JS, Steinberg GR (2010) Adipose tissue as an endocrine organ. Mol Cell Endocrinol 316(2):129–139CrossRefPubMedGoogle Scholar
Matsuzawa Y (2006) Therapy insight: adipocytokines in metabolic syndrome and related cardiovascular disease. Nat Clin Pract Cardiovasc Med 3(1):35–42CrossRefPubMedGoogle Scholar
Peral B, Camafeita E, Fernandez-Real JM et al (2009) Tackling the human adipose tissue proteome to gain insight into obesity and related pathologies. Expert Rev Proteomics 6(4):353–361CrossRefPubMedGoogle Scholar
Pasing Y, Colnoe S, Hansen T (2017) Proteomics of hydrophobic samples: fast, robust and low-cost workflows for clinical approaches. Proteomics 17(6)Google Scholar
Schniers A, Anderssen E, Fenton CG et al. The proteome of ulcerative colitis in colon biopsies from adults—optimized sample preparation and comparison with healthy controls. Proteomics Clin Appl. Epub ahead of print. Doi: https://doi.org/10.1002/prca.201700053
Zhou J, Zhou T, Cao R et al (2006) Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane. J Proteome Res 5(10):2547–2553CrossRefPubMedGoogle Scholar
Leon IR, Schwammle V, Jensen ON et al (2013) Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics 12(10):2992–3005CrossRefPubMedPubMedCentralGoogle Scholar
Lin Y, Wang K, Liu Z et al (2015) Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome. J Chromatogr B 1002:144–151CrossRefGoogle Scholar
Fu SL, Li JL, Chen J et al (2015) Extraction and identification of membrane proteins from black widow spider eggs. Zool Res 36(4):248–254PubMedPubMedCentralGoogle Scholar
Masuda T, Tomita M, Ishihama Y (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res 7(2):731–740CrossRefPubMedGoogle Scholar