Comparison of protein characterization using In solution and S-Trap digestion methods for proteomics

Abstract

Protein extraction and digestion are important analytical steps in the study of proteomics. The use of sodium dodecyl sulfate (SDS) buffer makes it possible to effectively analyze various proteins. Its use was evaluated using the S-Trap digestion method and compared to the traditional In solution digestion method. Differences in protein composition were examined for each protein preparation method. S-Trap digestion followed by SDS buffer extraction clearly increased the number of identified proteins, including more mitochondrial and membrane-related proteins. The S-Trap digestion method with 5% SDS buffer was applied to the pellet remaining from the removal of RIPA buffer-soluble proteins, which identified more extracellular space proteins than the conventional S-Trap digestion method. S-Trap digestion of the pellet was particularly advantageous for identifying proteins located inside multilayer membranes.

Keywords: Pellet S-Trap digestion; S-Trap digestion; Shotgun proteomics; Sodium dodecyl sulfate.