The present invention provides a method of generating ions from a sample, the method comprising the steps of (1) designating a plurality of sample target sites, and (2) for each of said plurality of sample target sites, generating ions from a plurality of locations associated with the sample target site, wherein said plurality of locations are selected automatically with reference to the said sample target site. Each of the plurality of sample target sites is associated with a discrete sample region, wherein the sample is part of a MALDI ion source and the plurality of discrete sample regions comprise regions of matrix, suitably formed by chemical inkjet printing. The plurality of locations can be at least 5 and preferably at least 10 locations, each of which can be selected randomly or in accordance with a predetermined pattern. Ions generated from the plurality of locations associated with each of the sample target sites are assigned only a single set of sample position coordinates, which coordinates correspond to those of the sample target site. This averaging technique leads to improved data reliability.