Mass spectrometry is a very powerful tool in the identification of chemical modifications of proteins and peptides. Often these modifications cannot be determined by conventional techniques. This report describes the combined use of electrospray ionization mass spectrometry and fast atom bombardment mass spectrometry to complete the primary structure of proteins and peptides. Examples illustrate how mass spectrometry is used to locate sites of phosphorylation, methylation and acetylation, and identify blocking groups and unexpected side reactions such as deamidation or alkylation.