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Glycobiology Advance Access published online on March 6, 2009
Glycobiology, doi:10.1093/glycob/cwp034
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© The Author 2009. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

De novo glycan structure search with CID MS/MS spectra of native N-glycopeptides

Hannu Peltoniemi1,2, Sakari Joenväärä1,3 and Risto Renkonen1,4,*

1 Transplantation Laboratory & Infection Biology Research Program, Haartman Institute, University of Helsinki
2 Applied Numerics Oy, Ltd, Helsinki
3 Medicel Oy, Ltd, Espoo
4 HUSLAB, Helsinki University Central Hospital, Helsinki, Finland

Received on January 14, 2009; accepted on February 27, 2009

The aim of our study is to automatically analyze the glycan and peptide structures of N-glycopeptides without a need to release glycans from the glycopeptides. Our wet laboratory raw data represents a series of MS/MS mass spectra obtained from a reverse phase liquid chromatography run of size-exclusion enriched tryptic digested glycopeptides from glycoproteins. The MS/MS spectra are first analyzed in order to identify glycosylated peptides and N-glycan monosaccharide compositions present on each glycopeptide. We further developed a Branch-and-Bound algorithm to search de novo N-glycan structures, i. e., monosaccharide compositions and their ordered sequences from native glycopeptides. Our de novo algorithm is based on iterative growth and selection of a population of glycan structures and it does not use databases of known glycan structures. We validate the algorithm with (i) in silico generated spectra, with or without deteriorating deletions, (ii) with a purified glycoprotein transferrin and (iii) with a complex mixture of N-glycopeptides enriched from human plasma. Our Branch-and-Bound algorithm depicted glycan structures from all the above mentioned three input data types. Due to the large diversity of glycan structures, the results typically contained several proposed structures matching almost equally well to the spectra. In conclusion, this algorithm automatically identifies glycopeptides and their structures from MS/MS spectra and thus greatly reduces the number of possible glycan structures from the vast amount of potential ones.


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