Sequence analysis by automated Edman degradation has been one of the most powerful tools for the characterization of peptides for many years. Its sensitivity allows experiments in the low picomole range, and its results provide complete information about the primary structure of proteins and peptides. A new method in protein and peptide sequencing has been developed which allows for the direct application of automated Edman degradation to the analysis of peptide mixtures. With the aid of multiple sequence analysis, first, sequence motifs of isolated, naturally processed peptides binding to MHC molecules have been defined. Second, the method proved to be a valuable and reliable tool for the characterization of synthetic peptide libraries, and third, the specificity of proteases has been determined in a fast and efficient way.