Methods like MALDI and SELDI TOF-MS ionize proteins and then measure their time of flight in an electric field. This gives a spectrum of the m/z values where m is mass and z is charge. But will a given protein always be ionized in an equal amount? (always completely ionized or always only one electron lost) If not, should I assume that a protein that makes a peak at the m/z value of 400 Da (Or 400 Da/e) , also would make it at 200 and 133 Da? (For respectively 1, 2, and 3 lost electrons)

STOP !!!

Proteins are not ionized by losses of electrons in MALDI ! Radical cations of proteins would be very unstable and frament immediately.

The ionization occurs by protonation of the protein on basic residues, as in electrospray.

MALDI usually yields preferentially singly protonated species [M+H]+, together with a few multiply protonated ions [M+nH]n+.