Abstract
Reporter ion quantification techniques utilizing reagents such as TMT and iTRAQ allow proteomics studies to multiplex up to 11 different samples within a single LC-MS/MS experimental run. In these experiments, peptides derived from different samples are labeled with chemical tags possessing identical mass but differing distributions of heavy isotopes through their structure. Peptides from all samples may then be physically combined prior to LC-MS/MS. Relative quantification of the peptides from each sample is obtained from the liberation of low mass reporter ions alone, as these are the only discernible factor between peptides in the entire LC-MS/MS workflow. When coeluting ions of similar mass to charge ratios are fragmented along with the ions of interest, it is not possible to determine the source of the reporter fragments and quantification is skewed, most often resulting in ratio suppression. One technique for combatting ratio suppression is the selection of MS2 fragment ions that are likely to retain the intact mass tag region by synchronous precursor selection (SPS) and the liberation of the reporter ions from this combination of ions in MS/MS/MS (MS3). In this study we utilize a new post processing tool that can directly assess the accuracy of the SPS system for picking ions for quantification that are truly derived from the peptide of interest. We then apply this tool to the re-analysis of 3 public proteomics datasets. Directly assessing SPS accuracy allows a new measurement of confidence in the quantification values obtained from these reporter ion quantification experiments.
