The objective of a MALDI experiment is to determine the molecular masses of chemical components in a sample. MALDI generally produces molecular ions of the form (M+H)+ or (M-H)-; in other words, a proton (H+) is added to or taken away from the molecule to produce a molecular ion. MALDI is a versatile ionization method because it can generate these ions for molecules over a wide size range - from less than 500 amu to more than 100,000 amu. By using MALDI to measure the mass-to-charge ratios of molecular ions in a sample, the molecular masses of the corresponding chemical components can be determined. For example, it is possible to run a chemical reaction that breaks a large biomolecule such as a protein or DNA into smaller molecular units. These smaller molecular units are then analyzed by MALDI to determine the their molecular masses. The molecular masses allow the biomolecule to be identified and/or sequenced.

MALDI is performed by mixing the analyte solution with a matrix solution, spotting a microliter of the mixture on the probe (sample plate), and allowing the solvents to evaporate. The residue left behind contains analyte molecules imbedded within the (solid) matrix. The matrix enhances the desorption and ionization of sample molecules when the residue is irradiated with a pulsed laser beam at 337 nm.
 

In theory, once the probe (sample plate) is placed in the mass spectrometer, almost everything else can be controlled by a single user working on any single X display server. On the X desktop display, controls in one window are used to select the cell; controls in a second window provide fine motor control for moving the plate relative to the stationary laser and CCD camera. Other windows on the X desktop are used to control the laser and to display and manipulate a plot of the spectrum as it is acquired. The spectrum is saved and analyzed using a separate "xmass" program. The xmass window is generally iconified since that window nearly fills the screen. The investigator may alternate between use of the xmass window and the acquisition/control windows to improve the coverage or quality of the sampled spectrum.  In addition, the resulting data files are sometimes transferred to other systems for subsequent data analysis by the xmass program.

Although control of the instrument by an investigator at a remote X display server is theoretically possible, our experience was that not all X servers worked well with all of the X clients. For example, some of the clients depended on fonts that were not on every X server. Or, the data acquisition software's plotting client would not clear the plotting window on all X servers. All of the X clients did work well, however, when run locally on the attached Sun workstation.