providing one or more mass spectra for a query peptide, the query peptide being a protein cleavage product by one or more cleaving agents having defined cleavage specificity, wherein each spectrum comprises masses of members selected from immonium ions, modified immonium ions, fragmented immonium ions, dipeptide ions, fragmented dipeptide ions, tripeptide ions, and fragmented tripeptide ions;

obtaining a qualitative amino acid composition of the query peptide from said one or more mass spectra, wherein the qualitative amino acid composition indicates the presence or absence of specific amino acids in the peptide, irrespective of the total number of each type of amino acid present;

comparing the qualitative amino acid composition of the query peptide to a list of qualitative amino acid compositions of a plurality of predicted peptides in a predicted peptide database, the predicted peptides being predicted cleavage products of parent proteins assuming the parent proteins, whose amino acid sequences are known, are subjected to cleavage by said one or more cleaving agents, wherein the comparing step is performed by a computer;

correlating the query peptide to the parent protein of a predicted peptide whose qualitative amino acid composition is matched to the amino acid composition of the query peptide; and

outputting to a user the identity of the parent protein to which the query peptide has been correlated.