A method for predicting the elution time of a peptide in chromatographic and electrophoretic separations by first providing a data set of known elution times of known peptides, then creating a plurality of vectors, each vector having a plurality of dimensions, and each dimension representing positional information about at least a portion of the amino acids present in the known peptides. A hypothetical vector is then created by assigning dimensional values for at least one hypothetical peptide, and a predicted elution time for the hypothetical vector is created by performing at least one multivariate regression fitting the hypothetical peptide to the plurality of vectors. Preferably, the multivariate regression is accomplished by the use of an artificial neural network and the elution times are first normalized using linear regression.
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
 This invention was made with Government support under Contract DE-AC0676RLO1830 awarded by the U.S. Department of Energy. The Government has certain rights in the invention.