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Site-specific glycan-Peptide analysis for determination of N-glycoproteome heterogeneity

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Authors:
  • Parker, Benjamin L ;
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    Department of Biochemistry and Molecular Biology, Faculty of Science, SDU
  • Thaysen-Andersen, Morten ;
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    Department of Biochemistry and Molecular Biology, Faculty of Science, SDU
  • Solis, Nestor ;
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    unknown
  • Scott, Nichollas E ;
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    unknown
  • Larsen, Martin Røssel ;
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    Department of Biochemistry and Molecular Biology, Faculty of Science, SDU
  • Graham, Mark E ;
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    unknown
  • Packer, Nicolle H ;
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    unknown
  • Cordwell, Stuart J
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    Department of Biochemistry and Molecular Biology, Faculty of Science, SDU
DOI:
10.1021/pr400783j
Abstract:
A combined glycomics and glycoproteomics strategy was developed for the site-specific analysis of N-linked glycosylation heterogeneity from a complex mammalian protein mixture. Initially, global characterization of the N-glycome was performed using porous graphitized carbon liquid chromatography-tandem mass spectrometry (PGC-LC-MS/MS) and the data used to create an N-glycan modification database. In the next step, tryptic glycopeptides were enriched using zwitterionic hydrophilic interaction liquid chromatography (Zic-HILIC) and fractionated by reversed-phase liquid chromatography (RPLC; pH 7.9). The resulting fractions were each separated into two equal aliquots. The first set of aliquots were treated with peptide-N-glycosidase F (PNGase F) to remove N-glycans and the former N-glycopeptides analyzed by nano-RPLC-MS/MS (pH 2.7) and identified by Mascot database search. This enabled the creation of a glycopeptide-centric concatenated database for each fraction. The second set of aliquots was analyzed directly by nanoRPLC-MS/MS (pH 2.7), employing fragmentation by CID and HCD. The assignment of glycan compositions to peptide sequences was achieved by searching the N-glycopeptide HCD MS/MS spectra against the glycopeptide-centric concatenated databases employing the N-glycan modification database. CID spectra were used to assign glycan structures identified in the glycomic analysis to peptide sequences. This multidimensional approach allowed confident identification of 863 unique intact N-linked glycopeptides from 161 rat brain glycoproteins.
Type:
Journal article
Language:
English
Published in:
Journal of Proteome Research, 2013, Vol 12, Issue 12, p. 5791-5800
Main Research Area:
Science/technology
Publication Status:
Published
Review type:
Peer Review
Submission year:
2013
Scientific Level:
Scientific
ID:
247936572

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