Improving peptide fragment ion detection using travelling wave ion mobility spectrometry with signal enhancement MSE (seMSE)

Recently, a solution to inherent poor ion beam sampling of time-of-flight (TOF) mass analyzers was proposed by restricting detection to ions expected at specific arrival times after being separated in a travelling wave ion mobility spectrometry (TWIMS) cell. Here, we show that this approach can be applied to data independent acquisition (DIA) using a so-called signal enhancement MSE (seMSE) experiment, which was compared to two different TWIMS-DDA and three different TWIMS-MSE methods with respect to the number of peptide identifications, the spectral quality of supporting peptide spec-tra matches, and, more importantly, fragment ion sensitivity. Comparison of fragment ion summed areas showed that seM-SE showed 6.8 to 11.5-fold improvement in fragment ion detection when compared to other MSE methods and although co-fragmentation of co-eluting peptides limited the seMSE peptide identifications it was possible to consistently detect peptides of interest by integrating DDA and MSE results within Skyline.