A Novel Protein Digestion Workflow for the Analysis of Surrogate Peptides by LC-MS/MS

Pellet digestion is an extremely effective protocol, yet requires centrifugation and wash steps prior to analysis of the resulting peptides by LC-MS/MS. These steps are time-consuming, labor intensive, and difficult to automate procedures. Described here is a novel workflow to streamline the pellet digestion protocol using Control Flow Plate (CFP)1, Narrow Bore Extraction Plate (NBE)1, and SMART Digest Kit2. Including a newly developed specially designed Flow Control Tube format which eliminates the centrifugation step and allows the protein denaturation and digestion steps to be performed seamlessly in a single tube. If the sample matrix requires additional cleanup after protein digestion, NBE (with sorbent) can be used to further purify the samples before LC-MS/MS analysis. The new workflows provide reproducible quality results with minimal manual steps and are amendable to automation.