Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation.

Analysis of a database containing over 20,000 high-resolution collision-activation mass spectra of tryptic peptide dications was employed to study the relative specificity of neutral losses from backbone fragments. The high resolution of the FTMS instrument allowed for the first time the first isotope of the water loss and the monoisotope of the ammonia loss to be distinguished. Contrary to a popular belief, water losses from y' ions are not specific enough to rely upon for detecting the presence of amino acids with oxygen in the side chains. At the same time, ammonia loss from b ions is sufficiently specific (>95%) to detect the presence of amino acids Gln, Asn, His, Lys, and Arg. This feature will be useful for de novo algorithms for high-resolution MS data. Clear trends were observed when the effect of amino acids proximate to the cleavage site on the rate of loss formation was studied. These trends turned out to be different for losses from b and y ions.