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

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When all of the glycosylated peptides were identified and combined with the unmodified peptides, the sequence coverage obtained in the experiment was increased to greater than 90%. Figure 8. MSn on the LCQ ion trap mass spectrometer confirms predicted sequence, linkage site and glycostructure of an rt-PA peptide. The precursor ion in glycostructure 211 was determined using MS/MS. To determine oligosaccharide structure, glycostructure 210 was selected for further fragmentation using MS3. To further confirm the linked peptide sequence and the site of attachment, ion m/z = 1333 was trapped and fragmented further (MS4).
Conclusions The Thermo Finnigan LCQ Deca XP ion trap mass spectrometer coupled with TurboSEQUEST protein identification software is an extremely powerful tool for the elucidation of post-translational modifications of proteins. In this case, the combination of Data Dependent MSn and Dynamic Exclusion have been used to quickly generate results which are more comprehensive than those provided by traditional approaches to glycoprotein analysis. While MS/MS can give limited oligosaccharide structure information, MSn can unambiguously confirm complete structure and the sites of attachment. This is yet another example of why the LCQ is an essential tool for every proteomics laboratory.
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