1. A method for preparing peptide spectra for identification, the method comprising: a) constructing a symmetric distance matrix from a plurality of peptide spectra, wherein a cluster of at least one of said spectra is represented in a row of said matrix, and wherein said cluster is also represented in a column of said matrix; b) finding the minimum of each of said clusters in said matrix; c) constructing a vector from said minima 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.