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Structural Analysis of Glycosylated Peptides in Complex Mixtures with ,,, Ion Trap MSn

able to identify the 211 form of the T45 peptide (211-T45) at a retention time of 15.57 minutes. As would be expected from such a complex mixture, a number of co-eluting ions were observed. However, the triply-charged 211-T45 ion at m/z 1064 was easily identified. The base peak ion chromatogram and full-scan mass spectrum for the targeted glycopeptide are shown in Figure 4.

The signal intensities for the doubly- and triplycharged glycopeptides (m/z 1595 and m/z 1064, respectively) were less intense than those for co-eluting peptides because glycosylated peptides typically have lower ionization efficiencies than unmodified peptides. The use of Dynamic Exclusion allowed for automated analysis of these low-intensity glycopeptides. The LCQ Deca XP was operated in Data Dependent Ion Tree mode, where the most abundant ion in the MS2 spectrum was selected for MS3, and the most abundant MS3 product ion was chosen for MS4. Figure 6. MS3 on the 210-G, GlcN ion. The dominant ion in the spectrum, the T45 peptide +GlcN at m/z 1333, was selected for MS4.

Figure 7. MS4 on the T45 +GlcN ion at m/z 1333.
MS2 through MS4 spectra are presented in Figures 57. The MS2 and MS3 spectra generated a heterogeneous collection of glycosylated product ions. GlcN was not easily cleaved from the peptide, so it serves as a marker to identify the site of glycosylation. The CID energy was sufficient at the MS4 stage to begin fragmenting the T45 peptide and to confirm the peptide sequence.<
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