Use of the PROTEAN i12 IEF System for In-Gel Peptide Fractionation Prior to LC-MS and Comparison with Off-Gel Fractionation

The separation of proteolytically digested samples by LC-MS is a powerful and widely used technique for proteomic analysis. In this application note, off-gel and in-gel methods for peptide separation using IPG strips are compared. The PROTEAN® i12™ IEF System, from Bio-Rad Laboratories Inc., used for in-gel fractionations provided a greater yield of peptide identifications compared to off-gel methods used. Other benefits of in-gel fractionation are also described.