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.
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.