Observation of sequence‐specific peptide fragmentation using extended tandem mass spectrometry experiments

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Abstract
Reaction‐intermediate spectra are reported for peptide mixtures using a hybrid BEQQ and a pentaquadrupole mass spectrometer. In this extended tandem mass spectrometry scan, the protonated molecule and a terminal fragment ion are selected with the first and third mass analyzers, respectively. A subsequent linked scan at constant B/E (hybrid instrument) or a scan of the middle quadrupole (pentaquadrupole instrument) produces the reaction‐intermediate spectrum. The resulting spectra are simpler than conventional tandem mass spectrometry daughter‐ion spectra and display only sequence ions of one group, viz. A, B and C or X, Y and Z. This information facilitates structural elucidation and is obtainable on nanomole amounts of peptide.