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
.