Fig. 1.

Systematic determination of the optimal drift bin specific collision energy ramp. (A) A series of HDMSe runs were acquired with a fixed high energy collision value for fragmentation in the transfer cell. Ions were detected using a time-of-flight (TOF) mass spectrometer. For each subsequent run, the collision energy was increased. When a peptide was identified at multiple collision energies, the collision energy producing the highest scoring match was retained. (B) Peptides were binned by the (M + H) of the precursor, and within each bin, the average best collision energy for those peptides was determined. Error bars represent one standard deviation. (C) For precursor ions, there is a linear dependence observed between drift time and mass-to-charge. (D–E) The distribution of collision energies used to generate product ions at a particular drift bin window is shown. Black bars represent the average collision energy for that drift bin window. (F) The average collision energies for peptides eluting from all drift bin windows are plotted as black circles. The intensities of the red circles are proportional to the number of individual peptide identifications. Error bars represent one standard deviation. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)