In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics

We assessed two physical disruption methods to homogenize cells —sonication and BeatBox—alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based, and SDC (Sodium deoxycholate)-based in-solution digestion, and two are commercially available kits: the EasyPep kit from Thermo Fisher Scientific and S-Trap from Protifi. Each method's efficacy was evaluated based on protein recovery, peptide yield, and number of unique proteins identified through LC-MS analysis.