Improved isobaric tandem mass tag quantification by ion mobility mass spectrometry

RATIONALE Isobaric tandem mass tags are an attractive alternative to mass difference tags and label-free approaches for quantitative proteomics due to the high degree of multiplexing that can be performed with their implementation. A drawback of tandem mass tags are that the co-isolation and co-fragmentation of labeled peptide precursors can result in chimeric tandem mass (MS/MS) spectra that can underestimate the fold-change expression of each peptide. Ion mobility (IM) separations coupled to quadrupole time-of-flight (Q-TOF) instruments have the potential to mitigate MS/MS spectra chimeracy since IM-MS has the ability to separate ions based on charge, m/z, and collision cross section (CCS). METHODS Two complex protein mixtures, labeled with DiLeu isobaric tandem mass tags in opposite ratios, were mixed together and analyzed by data-dependent LC/IM-MS/MS. The accuracy of reporters from interfering pairs was compared with and without IM separation. RESULTS IM separation was able to mitigate isobaric interference from differentially charged interfering ion pairs, as well as pairs of the same charge. Of the eight example precursors shown, only one had reporters that remained compressed below the significance threshold after IM separation. CONCLUSIONS The results of this investigation demonstrate proof-of-principle that IM separation of tagged precursors prior to MS/MS fragmentation can help mitigate quantitative inaccuracies caused by isobaric interference. Future improvements of the method would include software for automated correction and use of higher resolution IM instrumentations. Copyright (c) 2014 John Wiley & Sons, Ltd.