Quantitative Analysis of mTRAQ-Labeled Proteome Using Full MS Scans

Proteomic techniques are mostly used these days to identify proteins in a biological sample. Quantification of the differences between two or more physiological conditions, such as disease or no disease, has become an increasingly challenging task in proteomics. Mass tags introducing stable isotopes into peptides or proteins provide means for quantification in mass spectrometry. The mass tags are recognized by mass spectrometry and at the same time provide quantitative information. In the current study, we introduce mTRAQ for the purpose of quantification by full MS scans. Although mTRAQ reagent was initially designed for multiple reaction monitoring, we verified the utility of mTRAQ for MS1-based relative quantification using standard protein mixtures and blood plasma samples. mTRAQ-labeled peptides showed better quality MS2 spectra with increased XCorr values in a SEQUEST search output than corresponding unlabeled peptides. The improved spectral quality was due mostly to the enhanced matching of b-type ions. By combining mTRAQ with ICAT and applying them to colon cancer tissues, we identified and quantified a total of 3,320 proteins. mTRAQ covered a wider range of the proteome than did ICAT, and only 1053 proteins were shared by the two independent methods. Our results suggest the usefulness of mTRAQ, alone or in combination with ICAT, as a comparative profiling method in quantitative proteomics.