1. A method of analysing ions comprising: performing an initial multidimensional survey scan comprising separating parent ions according to a first physico-chemical property and separating said parent ions according to a second physico-chemical property; producing a two-dimensional data set comprising data corresponding to said first physico-chemical property and data corresponding to said second physico-chemical property; identifying one or more target ion species of interest; and determining a mode of operation of a mass spectrometer for said target ion species of interest using data relating to said target ion species of interest in said two-dimensional data set, wherein said mode of operation comprises the location of fragmentation of said target ions of interest.