최성우 (Korea Basic Science Institute (KBSI))

Nguyen Bao Tan (Korea Basic Science Institute (KBSI))

김진영 (Korea Basic Science Institute (KBSI))

최성우 (Korea Basic Science Institute (KBSI))

Nguyen Bao Tan (Korea Basic Science Institute (KBSI))

이수민 (Korea Basic Science Institute (KBSI))

방글 (Korea Basic Science Institute (KBSI))

정영애 (Korea Basic Science Institute (KBSI))

김진영 (Korea Basic Science Institute (KBSI))

Adipose tissue plays a key role in metabolism and immune regulation, therefore its proteomic characterization is essential for understanding diseases such as metabolic dysfunction-associated steatotic liver disease (MASLD). However, due to its high lipid content and low protein yield, adipose tissue poses significant technical challenges for in-depth proteomic analysis. To improve proteome coverage, we aimed to investigate a sample preparation method that maximizes lipid removal while minimizing protein loss by comparing two distinct strategies: removal of excess lipids (RELi) and a chloroform-based two-phase extraction (C2PE). Proteins obtained from each approach were identified and quantified using the TMT 16-plex labeling method to assess the strengths of each strategy and their suitability for analyzing lipid-rich tissues, murine adipocytes. A total of 5,686 proteins were identified across all samples, with notable differences depending on the sample preparation method. RELi-based processing enabled the detection of a greater number of proteins such as Pigu, Plaat3 and Lpcat1, which are associated with cellular metabolic process. In contrast, the C2PE-based processing was more effective in capturing proteins such as Col4a2, Fn1, and Cma1, which are involved in cellular component organization. Furthermore, a comparative analysis of retroperitoneal and mesenteric adipocytes revealed differentially expressed proteins related to metabolic processes and translational activity.

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