The synthesis of defined arrays of polypeptide analogues in conjunction with a simple self-encoded chemical readout system provides a powerful method for the systematic investigation of the relationship between polypeptide molecular structure and function. A novel solid-phase synthesis procedure was used to prepare arrays of polypeptide analogues in which a specific modification was systematically incorporated into a unique position in a peptide sequence; The synthesis was carried out in such a way that the resulting arrays contained a defined family of modified peptides, with each peptide molecule containing only a single specific modification. The array of polypeptide analogues was self-encoded in a positional fashion by incorporating a selectively cleavable bond into the analogue structure. Following cleavage of the polypeptide analogue array, analysis of the resulting peptide fragments by MALDI mass spectrometry defined, in a single step, the presence and identity of each peptide analogue in the mixture. The feasibility of this approach was demonstrated by the synthesis and mass spectrometric readout of an array of nine analogues of the 58-residue polypeptide chain of the cCrk N-terminal SH3 domain, before and after folding and affinity selection.