1. A method of calibrating an ion source, the ion source including a sample control system including a sample holder for supporting a sample plate in a sample plane and a laser source having a focal point representing a point at which a beam generated by the laser source intersects the sample plane, the method comprising: mounting a sample plate in the sample holder, the sample plate including one or more target regions; determining a relationship between a coordinate system of the sample plate and a coordinate system of the sample control system, the relationship being determined at least in part by aligning one or more fiducials relative to a reference point of the sample control system, the fiducials defining reference points of the sample plate coordinate system; and using the determined relationship to align a target region of the sample plate with ion optics of a mass spectrometer for a mass spectrometric analysis.