Instrumental parameters in the MALDI-TOF mass spectrometric analysis of quaternary protein structures

Several former studies have shown that MALDI-TOF-MS can be applied successfully to investigate the quaternary structure of proteins. Whereas most of these reports were focused on MALDI sample preparation, there is little information about the influence of instrumental parameters on the desorption/ionization and gas-phase behavior of protein subunit assemblies. Therefore, in addition of giving short examples of the quaternary structure analysis of a microheterogeneous glycoprotein, a metalloenzyme, and a heme-binding enzyme by MALDI-TOF-MS, we report a systematic study of the effect of some instrumental parameters on the analysis of chicken egg white avidin. From these tested parameters, only the laser pulse energy was found to influence the relative abundance of the intact assembly as well as the formation of nonspecific cluster ions significantly. This finding suggests that the disruption of the noncovalent interactions during the desorption/ionization process takes place at a very short time interval after the laser ablation, whereas those assemblies that survive this step are rather stable afterward in the gas phase. In addition, we present clear evidence that protein cluster ions are not preformed during sample preparation but originate from nonspecific assemblage during desorption/ionization.