It sounds like you've performed a MALDI-MS/MS experiment. Is this correct?
If it is a MALDI-MS/MS experiment, then summing MS/MS scans originating from the same precursor is appropriate. However, I would not combine MS/MS scans from different precursors. I'm fairly sure the vendor software has a way to do this automatically,
but you'll have check with them to find the appropriate option.
The side effect of leaving the scans separate is that you may have many peptide-spectrum matches (PSMs) for the same precursor (one for each scan), but each will likely be of lower quality than if the scans were summed. Summing MS/MS scans for the same precursor on a time-of-flight instrument results in a higher signal-to-noise ratio and a more confident PSM.