Figure 3. Many negative Δmass peptides are generated via in-source dissociation.

A) In-source dissociation is observed as the co-elution of two related ions, one being the precursor ion and the second being the same precursor with a mass loss due to fragmentation. These two related ions once fragmented and recorded in MS2 spectra share fragment ion masses. B) MS/MS spectrum for the intact precursor from Panel A. C) MS/MS spectrum for the in-source fragmented peptide. This peptide is only matched in the Open search. In-source dissociation events are observed in 500-Da searches as amino acid losses from one terminus of the peptide. In this example, all b-type ions (shown with an asterisk) were not matched in the 500-Da search, but nearly all y-type ions were, identifying the peptide. D) With accurate mass measurements in the MS2 scans, the fragment ions were measured at low part-per-million accuracy.