Methods, systems and computer readable media for identifying peaks in a three-dimensional mass spectrometry/elution time dataset. The dataset is represented as a matrix of intensity values with column and row positions corresponding to specific elution time and m/z value, respectively. Peaks may be detected using a watershed image segmentation technique. Further provided are methods, systems and recordable media for creating a mask matrix to be overlaid on a large three-dimensional dataset represented as an image matrix, to identify a much smaller portion of the three dimensional dataset of interest, and to greatly reduce the amount of subsequent processing required for processing data of interest. The mask matrix has the same dimension as the image matrix and includes areas corresponding to one or more peaks identified by the watershed segmentation technique.

In an RF ion trap mass spectrometer, selected parent ions are fragmented by collisions or electrons and a spectrum of the ion fragments is measured. The measured fragment ion spectrum is then analyzed for the presence of a dominant ion species and, when a dominant ion species is present, selected parent ions are fragmented and a spectrum of the ion fragments is again measured, but with an additional collision excitation of the dominant ion species. The resulting daughter ion spectrum is qualitatively improved.

A mass spectrometer having an ionization source, a ion trap mass analyzer, an ion guide and gating apparatus between the ion guide and the ion trap. The gating apparatus includes sealing apparatus. A stream of ions from the ion source are guided to through the gating apparatus in pulses to the ion trap. The number of ions in each pulse are controlled by the scaling apparatus.