1. A method for interpreting peptide sequences via combination of spectra from different peptides comprising: providing a sample comprising a plurality of proteins; defining a plurality of peptide pairs wherein one peptide of the pair differs from the other peptide by a modification or mutation; obtaining a spectrum for each peptide of each peptide pair to form a spectral pair; generating a spectral product from the spectral pair and comparing the spectra of the spectral pair to separate signal and noise peaks within the spectra; removing the noise peaks; generating a de novo sequence reconstruction by combining the separated signal peaks for the spectral pairs; conducting a sequence database search using the de novo sequence; and generating an output comprising results of the sequence database search.