Peptide fingerprints after partial acid hydrolysis: analysis by matrix-assisted laser desorption/ionization mass spectrometry.

A method is described by which a sequence-dependent peptide fingerprint can be rapidly obtained upon partial hydrolysis of peptides with hydrochloric acid and subsequent analysis by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). When synthetic peptides are treated with 3M HCI for 5 min at 110 degrees C, amino acids are released in turn from the C-terminus or, depending on the peptide, from the N-terminus. Sequence information can be deduced by identifying the amino acid whose mass corresponds to the difference in MW between the major hydrolysis products, beginning from the MW of the starting peptide. A similar pattern exclusively from the C-terminus has been obtained using pentafluoropropionic acid as a hydrolyzing agent (Tsugita et al. Eur. J. Biochem. 206, 691 (1992)), but required longer hydrolysis time and more handling prior to analysis. The technique we have developed could be used to obtain a sequence-dependent 'fingerprint' for a peptide cheaply and rapidly, starting with picomole amounts of peptide, because the hydrolysate can be directly analyzed by MALDI. This methodology might be especially useful for confirming the identity of peptides during peptide mapping.