1. A method for preparing peptide spectra for identification, the method comprising: a) populating a matrix with a plurality of clusters of a plurality of peptide spectra, wherein each of said clusters is represented in both a different row of said matrix and a different column of said matrix, thereby resulting in a symmetric matrix; b) finding the minimum of each of said clusters in said matrix; c) populating a vector with said minima of said clusters wherein each element in said vector corresponds to one of said clusters; d) finding the global minimum of said matrix as being the minimum of said vector; e) merging two of said clusters identified by said global minimum into a merged cluster; and f) providing said merged cluster for identification of at least one peptide associated with said merged cluster.