Cone-voltage fragmentation has been widely used to fragment ions in the spraying region of API sources to generate structurally significant information. The limiting factor of this technique is the loss of certainty of the molecular mass information, and the increased complexity of the data generated as more than one species may be present in the sample being analysed.
We have found that by using alternating scans of low and high cone voltage during data acquisition we can generate both molecular mass and structurally significant fragment ion mass information in two separate data sets from as single experiment. If this mass spectrometric approach is used in conjunction with chromatographic separation, the ambiguity in the analysis of a mixture is considerably reduced. We have used alternating cone-voltage fragmentation LC-MS routinely for several months and found that the additional information provided has considerably reduced the demand for follow-up experiments and simplified the analysis of the impurities and by-products present in the reaction mixtures. This additional information has been obtained without loss of chromatographic resolution or sensitivity.
We will present data from some typical experiments that highlight the routine use of this technique in the synthetic pharmaceutical environment.