In one aspect of the present invention, the less "useful" spectral data is disregarded from the spectral data resulting from the fragmentation by ETD and candidate charge states for the "useful" data assigned. Knowledge of the first order ion product charge state reduces the subset of comparison data hence aiding in the eventual identification of the precursor ion, and thus aiding in peptide sequence database searching capabilities. Such capabilities include, but are not limited to, computational requirements for database search and data storage, CPU time, the volume taken up on the hard disk to store results, visualization and dissemination of data, and overall improvement in the confidence in the precursor identification. Thus determination of the peptide sequence can be resolved in less time, costing less money, and requiring less computer power.