Is Multidimensional High Performance Liquid Chromatography (HPLC) an Alternative in Protein Analysis to 2D Gel Electrophoresis?

Abstract

The interactive modes of High Performance Liquid Chromatography (HPLC) of proteins provide a platform for the construction of a multidimensional HPLC system coupled to mass spectrometry. We present a system composed of both anion and cation exchanger columns, in the first dimension, and n-octadecyl bonded 1.5 μm nonporous silica columns in the second dimension. Both columns are operated under gradient conditions. A system suitability test with standard proteins showed that the total analysis can be performed within about 20 minutes. The fractions taken from the ion exchanger column are directly analyzed within one minute on the reversed phase column at a high flow rate. Two reversed phase columns are applied and operated alternatively: while the first column performs the separation within one minute, the analytes leaving the first dimension are enriched in an on-column focusing mode on top of the second column. The sample clean-up and enrichment is performed on a novel type of restricted access cation exchanger column with internal sulfonic acid groups and external diol groups. The columns exhibit a molecular weight exclusion limit for globular proteins of about 15 kDa. Our next studies will be directed towards the analysis of proteins and peptides from extracts of fibroblasts.