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.
Williams
Tracie L
TL
Instrumentation and Biophysics Branch, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland 20740, USA.
Leopold
Peter
P
Musser
Steven
S
D001331:Automation; D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000737:chemistry*; D002851:Chromatography, High Pressure Liquid; D003627:Data Interpretation, Statistical; D011499:Protein Processing, Post-Translational; D021241:Spectrometry, Mass, Electrospray Ionization; D014736:Vibrio parahaemolyticus / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins