MS/MS of protonated polyproline peptides: the influence of N-terminal protonation on dissociation.

A unique collision-induced dissociation pattern was observed for protonated polyproline peptides of length n in which y(n-2) and/or y(n-4) ions were formed in much higher abundance than any other product ions. Cleavage occurs only at every other amide bond, such that product ions are formed only from the losses of even numbers of proline residues. Exclusive losses of even numbers of proline residues were not observed from sodiated peptides. Further study of the tandem mass spectrometry (MS/MS) patterns of protonated proline-rich peptides showed that the substitution of alanine in the second position of polyproline peptides did not prevent the dominant formation of y(n-2) and y(n-4) ions. The loss of ProAla to form the y(8) ion from (ProAlaPro(8)NH(2)+H)(+) was as abundant as the loss of ProPro from (Pro(10)NH(2)+H)(+). However, modification of the peptides that presumably affected the location of the proton on the peptide did alter the MS/MS spectra. Pro(10) and Pro(5) with blocked N-termini or with arginine substituted for the first proline residue did not form abundant y(n-2) or y(n-4) ions. MS(3) and double resonance experiments showed that dissociation of intermediate y(n) product ions can produce y(n-2) ions, but are not necessary dissociation pathway intermediates. This analysis suggests that the ionizing proton must be located at the N-terminus for the peptide ion to dissociate in this manner.

Note: A simple dual polarity dual nanoelectrospray ionization source for ion/ion reactions.

A continuously operated dual polarity dual nanoelectrospray ionization source has been constructed and tested. A commercial quadrupole ion trap mass spectrometer was modified to accumulate and trap ions of opposite charge. All changes to the commercial three-dimensional quadrupole ion trap have been made external to the instrument outside of the vacuum system. Few hardware modifications were required because the two emitters send ion beams through the same transmission guides. Computer controlled source voltage polarities are switched quickly and efficiently to transmit one of two continuously generated ion beams. With customized software, this design has proved simple to implement and to operate.