I have to admit up front that I'm not the world's biggest MALDI expert. I have only used the ABI 4800 at the Virginia Tech Mass Spectrometry Incubator. I have, however, kept up with a lot of MALDI technology and papers, particularly the innovative drug discovery work of the Dorrestein lab at UC San Diego.
And of course, I'm probably kind of biased. 1) There isn't much question that I love the Orbitrap series of instruments. I did when I got my first XL as a postdoc and that has only been amplified by the rest of the Orbi family (I have, at this point, finally operated every instrument with an Orbitrap except for the 'Classic').
Despite these obvious flaws in my background and impartiality, believe me when I say: I do not understand how anyone could possibly justify purchasing a MALDI-TOF instrument. Ever. The MALDI-Orbitrap produced by Thermo is an Orbitrap XL with the upgraded HCD cell. 100,000 unit maximum resolution (has a TOF ever exceeded 30,000? and the sensitivity of an Orbitrap. I was watching signal intensity being generated at 3E6 with <5 laser pulses. The MALDI seamlessly switches from plates to imaging mass spectrometry --- again, with the resolution and sensitivity of an Orbitrap.
If this wasn't bad enough for the MALDI-TOF field, it doesn't end at the Orbitrap XL. Although Thermo has decided to not push the development of MALDI sources on the newer systems, a company in Maryland, called Mass Tech has developed an atmospheric pressure MALDI source that can be fitted to just about anything -- including the Q Exactive and the high field Orbitrap Elite. Anyone want to do MALDI at even higher sensitivity with 240,000 resolution?