Disclosed are methods for identifying one or more amino acid molecules and nucleic acid molecules encoding such amino acid molecules of at least two proteomes that are conserved, unique or express at higher or lower levels in at least one of the proteomes. Expression libraries are used that produce the proteome, and in one embodiment, may produce the proteome from at least one cDNA expression library in one to five reactions. Anti-proteome antibodies are prepared that selectively bind to one of the proteomes and binding with at least one second proteome compared.