Data processing workflow. The data obtained from the FTICR-ion trap cluster was processed using the workflow illustrated here. First, the LC-MS/MS datasets from the ion trap were searched against the Escherichia coli protein sequence database using Mascot. Each individual result was aligned to a single master LC-MS dataset and then merged into one file with aligned retention times. Each separate FTICR LC-MS dataset was aligned against the merged LC-MS/MS data (and hence the master FTICR dataset). Intensities of the identified peptides were then extracted from each FTICR LC-MS dataset by taking the maximum signal in a window of defined m/z and retention time relative to the identified peptide. The resulting list contained the protein name, peptide sequence, maximum observed ion score, and absolute intensities for each peptide. This information from each sample could then easily be collapsed into a single, uniform sample/data matrix with the total absolute intensities for all identified proteins and samples.