Impact of Surfactants on Cumulative Trypsin Activity for Bottom-up Proteome Analysis

Detergents are often employed in bottom-up proteome workflows to maximize total proteome recovery, especially in the interest of membrane proteins. Conventionally, they are depleted prior to digestion, but recent works report enhanced proteolysis of membrane proteins by including denaturants across the whole bottom-up workflow. The present work evaluates initial and cumulative trypsin activity in the presence of denaturants by spectroscopic acitivity assays, followed by a quantitative bottom-up LC-MS assessment of a whole proteome digested in the presence of sodium deoxycholate and sodium dodecyl sulfate. It is shown that the presence of detergents (although important for solubilization) significantly impede digestion efficiency and consequentially, proteome coverage.