It would be helpful to include an example of a MALDI spectrum you're referring to, but first thing that comes to mind is: desalting (via diafiltration) of the protein sample?
And is the aldolase A preparation you're looking at pure (>90%), or contaminated with other proteins/isoforms?
Since the performance of a protein spectra signal by MALDI-TOF analysis could be affected by different parameters, It would help you provide more information: Sample preparation used, matrix etc.
Nevertheless I send you our receipt in case it can be of help: desalt proteins with C4 Reverse Pahse ZipTips, and elute proteins from the resine usin Synapinic acid (10 mg/ml) in 70 ACN:30 0.1% TFA.
For MALDI it is very important crystallization, so be careful with salts, also you have to consider the sample concentration.
Sometimes it is helpful to control manually the laser power/position, increasing the quantity of spectra acquired, modifying the sets in the tof instrument method due they are several settings for large proteins instead peptides.