Journal
EUROPEAN JOURNAL OF MASS SPECTROMETRY
Volume 16, Issue 3, Pages 421-428Publisher
SAGE PUBLICATIONS LTD
DOI: 10.1255/ejms.1028
Keywords
O-glycosylation; glycopeptides; CID; ETD; site-assignment; database search
Funding
- NATIONAL CENTER FOR RESEARCH RESOURCES [P41RR001614, S10RR019934] Funding Source: NIH RePORTER
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [P41GM103481] Funding Source: NIH RePORTER
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Complex mixtures containing O-linked glycopeptides bearing SA(1-0)GalGalNAc structures, or single GalNAc units were subjected to collision-induced dissociation (CID) and electron transfer dissociation (ETD) analysis on a linear ion trap-Orbitrap mass spectrometer and the resulting data was analyzed using the Protein Prospector software. An overview of the structural information provided by the different fragmentation techniques, as well as their limitations, is presented. We illustrate the importance of the complementary information in the mass spectrometry survey scans as well as the different tandem mass spectrometry techniques. We also present some unique features offered by Protein Prospector that are advantageous in glycopeptide analysis: Id considering a modification that will produce a neutral loss, without labeling the original modification site; (ii) merging CID and ETD search results; (iii) permitting the comparison of different modification site-assignments. Although these data were obtained from secreted glycopeptides, the observations and conclusions are also valid for the intracellular regulatory O-GlcNAc modification.
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