Sequencing of sulfonic acid derivatized peptides by electrospray mass spectrometry

We report the application of nanoeletrospray ionization tandem mass spectro metry (nES-MS/MS) and capillary LC/microelectrospray MS/MS (cLC/mu ES-MS/MS ) for sequencing sulfonic acid derivatized tryptic peptides, These derivati ves were specifically prepared to facilitate low-energy charge-site-initiat ed fragmentation of C-terminal arginine-containing peptides, and to enhance the selective detection of a single series of y-type fragment ions. Both s ingly and doubly protonated peptides were analyzed by MS/MS and the results were compared with those from their derivatized counterparts. Model peptid es and peptides from tryptic digests of gel-isolated proteins were analyzed . Derivatized singly protonated peptides fragment in the same way by nES-MS /MS as they do by post-source decay matrix-assisted laser desorption/ioniza tion mass spectrometry (PSD-MALDI-MS). They produce fragment ion spectra do minated by y-ions, and the simplified spectra are readily interpreted de no vo. Doubly protonated peptides fragment in much the same way as their non-d erivatized doubly protonated counterparts. The fragmentation of doubly prot onated derivatives is especially useful for sequencing peptides that posses s a proline residue near the N-terminus of the molecule. The singly protona ted forms of these proline-containing derivatives often show enhanced fragm entation on the N-terminal side of the proline and considerably reduced fra gmentation on the C-terminal side. In addition, sulfonic acid derivatizatio n increases the in-source fragmentation of arginine-containing peptides, Th is could be useful for sequence verification and sequence tagging far use i n single stage mass spectrometry, Copyright (C) 2000 John Wiley & Sons, Ltd .