It looks as though MSMS data may contain multiple peak lists for the same polypeptide. Would it be beneficial to combine the data of such suspected duplicates? I’ve noticed that sometimes there will be large gaps in regions of of a peak list; combining lists could fill these gaps and perhaps help our algorithms.

Of course, the great fear is that we would combine two peak lists which did not in fact come from the same polypeptide. Given the accuracy of our precursor mass, is there a substantial probability for this? Perhaps combined peak lists could simply be added to our gamut of spectra rather than than making the progenitors of the combined list redundant….

UPDATE: rather than simply using precursor mass, we could use the basic MSMSFit algorithm to compare to peak lists. Combination would then only occur if a MSMSFit score threshold is passed.