Hi,

What mass spectrometer are you using?

It's a XevoG2-XS Q-TOF

It is presumable you should be using argon or helium to do your CID fragmentation, aren´t you? You may also try a MALDI-TOF/TOF equipment, if available.

Yes we are using argon but how does it justify non- formation of b1 ions.

I copied this answer from http://what-when-how.com/proteomics/interpreting-tandem-mass-spectra-of-peptides-proteomics/. A figure of the oxazolane structure can be found here: http://www.weddslist.com/ms/tandem.html

I can also recommend the referenced Lehmann article for further reading.

For the sake of simplicity, Figure 1a depicts b-type ions as acylium cations. However, it is currently thought that a more likely reaction mechanism involves nucleophilic attack of the protonated carbonyl carbon by the adjacent carbonyl oxygen located N-terminal to the cleavage site (Arnott et al., 1994; Schlosser and Lehmann, 2000). This would result in a five-member oxazolone ring structure on the C-terminal end of b-type ions. Such a fragmentation mechanism is appealing in that it accounts for certain well-known observations. First, one does not observe b1 ions (b-type ions comprised only of the N-terminal amino acid in the peptide) for peptides with free N-termini, since there is no carbonyl group to induce cleavage. In contrast, if a carbonyl is added to the N-terminal amino group, either by acylation or carbamylation, such modified peptides can fragment to produce b1 ions. Second, fragmentation on the C-terminal side of proline residues is much reduced, since the side chain ring structure constrains the attack of the carbonyl.