Atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry of sulfonic acid derivatized tryptic peptides

Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) and ion trap mass spectrometry have been used to study the fragmentation b ehavior of native peptides and peptide derivatives prepared for de novo seq uencing applications. Sulfonic acid derivatized peptides were observed to f ragment more extensively and up to 28 times more efficiently than the corre sponding native peptides. Tandem mass spectra of native peptides containing aspartic or glutamic acids are dominated by cleavage on the C-terminal sid e of the acidic residues. This significantly limits the amount of sequence information that can be derived from those compounds. The MS/MS spectra of native Cryptic peptides containing oxidized Met residues show extensive los s of CH3SOH and little sequence-specific fragmentation. On the other hand, the tandem mass spectra of derivatized peptides containing Asp, Glu and oxi dized Met show much more uniform fragmentation along the peptide backbone. The AP-MALDI tandem mass spectra of some derivatized peptides were shown to be qualitatively very similar to the corresponding vacuum MALDI postsource decay mass spectra, which were obtained on a reflector time-of-flight inst rument. However, the ion trap mass spectrometer offers several advantages f or peptide sequencing relative to current reflector time-of-flight instrume nts including improved product ion mass measurement accuracy, improved prec ursor ion selection and MSn. These latter capabilities were demonstrated wi th solution digests of model proteins and with in-gel digests of 2D-gel sep arated proteins. Copyright (C) 2001 John Wiley & Sons, Ltd.