Systematic delineation of scan modes in multidimensional mass spectrometry.

A logical analysis of mass spectrometric scan modes is performed that reveals the full set of experiments available in multidimensional mass spectrometry. The analysis utilizes a symbolism that helps provide an organizational scheme for the representation and classification of the wide variety of experiments that exist. In general, for an n-stage experiment, there is a closed set of experimental modes producing spectral types that vary in mass dimensionality from 0 to n. There is a total of 2n experiments that have 1 or 0 mass dimensions, along with an increasing number of experiments of higher mass dimensionality. There also exists a set of 2n fundamental scan modes, viz., experiments in which only mass-to-charge ratios of individual ions, but not their interrelationships, are specified. Scans in which functional relationships between ion masses are defined (e.g., neutral loss scans) introduce complexity into the total number of scan types available in an MSn experiment, giving a total of 1, 2, 5, 15, 52, and 203 experiments of 0 through 5th order, respectively. It is shown that combinations of data from lower order experiments can be used to construct higher order spectra. Extraction of data of lower mass dimensionality from data of higher dimensionality is also demonstrated. A different method of reducing dimensionality, projection of dispersed data back into a smaller number of mass dimensions, is also introduced and characterized. The analysis reveals several new types of scan modes including an MS/MS/MS scan having unit mass dimensionality, referred to as the selective neutral-loss scan, and several new MS/MS/MS scans that are two-dimensional in mass. Examples of these new experiments are provided, and their potential value is discussed.