How to interpret a MALDI mass spectrum?
Please see the wiki articles for the general method:


http://en.wikipedia.org/wiki/Mass_spectrum
http://en.wikipedia.org/wiki/Matrix-assisted_laser_desorption/ionization
http://en.wikipedia.org/wiki/Time-of-flight_mass_spectrometry


Then let's start with question 2: yes, you can and you should. The spectrometer measures in arbitrary units, therefore you can speak only about relative abundances.

And question 1: it depends how easily is the given molecule ionized. So if the fragment A is rich in polar aminoacids, whereas fragment B is mostly hydrophobic and difficult to ionize, than you should expect this big difference in signal intensities.