Differential proteomic analysis (comparative quantitative proteomics) is a robust quantitative technique used to detect and identify the proteome of selected tissues. The expression levels (upregulated vs. downregulated) of proteins in tissue samples that differ by experimental design or anatomic location are determined by a series of assays including (1) 2D difference gel electrophoresis (2D-DiGE), (2) protein spot picking based on a priori thresholds, (3) Mass Spectrometry, and (4) follow-up Western Blot for antibody validation (Chen et al., Mol Cell Proteomics 14:2466–2478, 2015). Differential proteomic analysis is a perfect method for analyzing a heterogeneous tissue such as adipose tissue with a composition spectrum consisting of white to brown adipocytes along with a stromal vascular fraction dependent on anatomical location and inflammation. The adipose tissue proteomic protocol outlined here was successful in identifying differentially expressed proteins both significantly upregulated and downregulated between the experimental and control groups (Shields et al., Pulm Circ 6:586–596, 2016).
Adipose tissue Mass spectrometry Proteomics Western blotting
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