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; aligning the spectra of each spectra in the spectral pair to identify signal peaks and noise peaks, wherein aligning the spectra further comprises: generating a spectral product matrix by mapping the two spectra onto respective x and y axes of a scatter graph; identifying matching peaks between the two spectra where vertical and horizontal lines extending from the peaks of each of the two spectra intersect; connecting pairs of adjacent matching peaks with at least one jump to form an optimal path from an origin of the scatter graph, wherein the optimal path is a longest sequence of valid jumps on the spectral product matrix; and identifying the matching peaks in the optimal path as signal peaks and the peaks outside the optimal path as noise peaks; removing the noise peaks; generating a de novo sequence reconstruction by combining the signal peaks for the spectral pairs; conducting a sequence database search with a computer comprising a processor and a memory using the de novo sequence; and generating an output comprising results of the sequence database search.