Label-free comparative analysis of proteomics mixtures using chromatographic alignment of high-resolution μLC-MS data

Label-free relative quantitative proteornics is a powerful tool for the survey of protein level changes between two biological samples. We have developed and applied an algorithm using chromatographic alignment of mu LC-MS runs to improve the detection of differences between complex protein mixtures. We demonstrate the performance of our software by finding differences in E. coli protein abundance upon induction of the lac operon genes using isopropyl P-D-thiogalactopyranoside. The use of our alignment gave a 4-fold decrease in mean relative retention time error and a 6-fold increase in the number of statistically significant differences between samples. Using a conservative threshold, we have identified 5290 total mu LC-MS regions that have a different abundance between these samples. Of the detected difference regions, only 23% were mapped to MS/MS peptide identifications. We detected 74 proteins that had a greater relative abundance in the induced sample and 21 with a greater abundance in the uninduced sample. We have developed an effective tool for the label-free detection of differences between samples and demonstrate an increased sensitivity following chromatographic alignment.