Automated Postprocessing of Electrospray LC/MS Data for Profiling Protein Expression in Bacteria

We describe an integrated approach for automating protein analysis of bacterial cell extracts. The method uses electrospray LC/MS to generate chromatographic profiles of proteins present in an extract, along with a software program that automates the data analysis. The software program, Retana, automates the sequential summing, centroiding, and deconvolution of multiply charged proteins present in consecutive scans of the LC/MS analysis. This procedure generates a concise, single spectrum of proteins present in the extract, along with their retention time and relative abundance. A comparison of the method with “whole cell” MALDI analysis demonstrates improved mass resolution and mass accuracy, along with the appearance of a greater number of proteins. Additionally, it is possible to compare protein expression among strains of bacteria by normalizing the relative abundance of similar proteins in each analysis.