A program known as MacProMass has been written for Macintosh computers to assist in the analysis of mass spectral data of peptides and proteins. The program employs a user friendly, graphical interface and accommodates a variety of protein structures including cyclic peptides and multiple chain proteins. In addition to molecular mass calculations for positive and negative molecular ions, MacProMass also calculates elemental composition, amino acid composition, isoelectric point, surface free energy, and high-performance liquid chromatography index values for whole structures and peptide fragments resulting from enzymatic or chemical degradation. Users can program their own amino acid residues and terminal groups. In addition to search routines for both mass and sequence, theoretical fragment ions for peptide mass spectra can be calculated. Analysis of variant proteins is facilitated with a subroutine that systematically catalogs single amino acid substitutions that correspond to mass differences between observed and expected molecular ions. Interchain and intrachain disulfide bonds and other types of linkages are maintained throughout the chemical and enzymatic degradation operations.