Proteomic analysis of E. coli using 2D HPLC and MALDI-TOF mass spectrometry

Abstract

In this post-genomic era, researchers are striving to find new ways to use the enormous amounts of data that have been collected. One obvious way is with proteomics, the large-scale identification of expressed proteins. We have developed a novel method for identifying proteins using two dimensions of non-denaturing high performance liquid chromatography (HPLC) and matrix assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry. The first dimension of separation uses an anion exchange column and each of those fractions is run through the second dimension, a hydrophobic interaction column. The proteins were then dialyzed, denatured, and digested with trypsin before being subjected to mass spectrometry. Identifications were made based on the peptide masses. Using this method we have made 2012 protein identifications, 310 of which are unique. These numbers are comparable to other forms of proteomics such as 2-D gels.