Toward a Clinical Molecular Scanner for Proteome Research:  Parallel Protein Chemical Processing before and during Western Blot

To increase the throughput of protein identification and characterization in proteome studies, we investigated three methods of performing protein digestion in parallel. The first, which we term “one-step digestion−transfer” (OSDT), is based on protein digestion during the transblotting process. It involves the use of membranes containing immobilized trypsin which are intercalated between the gel and a PVDF collecting membrane. During electrotransfer, some digestion of the transferred proteins occurs, although poorly for basic and/or high molecular weight proteins. The second method is based on “in-gel” digestion of all proteins in parallel and termed “parallel in-gel digestion” (PIGD) to denote this fact. The PIGD led to more efficient digestion of basic and high molecular weight proteins (>40 000) but suffered from a major drawback: loss of resolution for low molecular weight polypeptides (