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For MALDI-TOF instrument running peptide and protein, you'd need a 
trasient recorder that, at minimum, can:
1) sample the analo signal every 5-10 ns, or 100-200 MHz
2) record 48K data points from a single transient
3) digitize the signal at 8 bit (256 steps) vertical (amplitude) resolution.
An ideal data acquisition system should have:
1) sampling rate of 500ps/sample (2 GHz) or higher
2) record 48K or more data points
3) 12 bit vertical (amplitude) resolution
4) good analog circuit with minimum ringing or impedence mismatch
5) high data transfer rate from digitizer to host computer (better than 3 Hz)
As far as I know, no commercial vendor can supply so called 
"ideal" data acquisition system. Let me kown if you find otherwise.
Wen Yu
Genetics Institute
wyu@genetics.com
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I recently found an article by C.J. Robinson in an old Analytical
Chemistry pub.(Vol. 43, No. 11, Sept. 1971) titled Low-Resolution Mass
Spectrometric Determination of Aromatics and Saturates in Petroleum
Fractions.  Robinson was one of the leaders in this area.  I would like to
contact him (hopefully he is still alive), or someone familiar with this
method since the article is missing a few of the details necessary to
implement his algorithm.  I would also be appreciative if anyone out there
has a listing of the FORTRAN program he wrote, since this would clarify
the calculations discussed.  Please e-mail or you are welcome to call me
collect.
Bill Geiger (713) 920-1696