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Summary form only given. Automatic de novo peptide identification from collision-induced dissociation tandem mass spectrometry data is made difficult by large plateaus in the fitness landscapes of scoring functions and the fuzzy nature of the constraints that is due to noise in the data. A framework is presented for combining different peptide identification methods within a parallel genetic algorithm. The distinctive feature of our approach, based on Pareto ranking, is that it can accommodate constraints and possibly conflicting scoring functions. We have also shown how population structure can significantly improve the wall clock time of a parallel peptide identification genetic algorithm while at the same time maintaining some exchange of information across local populations.