PMID: PMC4184449-1-7

 

    Legend: Gene, Sites

Title : Confident Site-Specific Glycan Profiling

Abstract :

1. We used theglycopeptides assignments to construct a site-specific glycosylationmap for HA and AGP (Figures 4 and S-3, respectively)
2. Glycan com positions wereclassified, based on the number of HexNAc units, as high-mannose (2HexNAc) , biantennary (3 or 4 HexNAc) , triantennary (5 HexNAc) , tetra-antennary(6 HexNAc) , and penta-antennary (7 HexNAc)
3. Only glycopeptides identifiedwith at least 40% peptide backbone coverage from tandem MS data wereincluded in the glycan profile maps
4. In some cases, particularly forHA, two putative glycosylation sites appeared on a single trypticpeptide
5. The peptide backbone fragment ions with an attached HexNAchelped resolve the ambiguity in such cases by helping to identifythe occupied site
6. Such site-specific glycan profile assignments werepossible only when using HILIC-C18-MS/MS, whereby at least 7 timesmore glycopeptides underwent tandem-MS, from evaluation of precursorsgenerating oxonium ions
7. It is evident from the data that the usefulnessof HILIC-C18-MS scales with the number of glycosylation sites andglycopeptides in the theoretical search space
8. For transferrin , wherethe glycopeptide and glycoform diversity is very limited, the C18and HILIC-C18 platforms yield similar results
9. However, with AGP andhemagglutinin , there is an obvious improvement in data quality withthe use of HILIC-C18 over C18
10. We made these assignments using assumptionsregarding the protein sequences , glycosylation sites , glycoform distributions,and post-translational modifications
11. It is, therefore, possible thatmodified peptides not included in our assumptions exist
12. Since thegoal of this study was to compare performances of the HILIC-C18 andC18 systems, our glycopeptide analyses sufficed to reach clear conclusionsdespite the absence of exhaustive discovery-mode proteomics data interpretation

Output (sent_index, trigger, protein, sugar, site):

• 1. theglycopeptides, , -, -, theglycopeptides
• 10. glycosylation, , -, -, sites
• 12. glycopeptide, , -, -, glycopeptide
• 3. glycopeptides, , -, -, glycopeptides
• 4. glycosylation, , -, -, sites
• 6. glycopeptides, , -, -, glycopeptides
• 7. andglycopeptides, , -, -, sites andglycopeptides
• 7. glycosylation, , -, -, sites andglycopeptides
• 8. glycopeptide, , -, -, glycopeptide

Output(Part-Of) (sent_index, protein, site):

*Output_Site_Fusion* (sent_index, protein, sugar, site):

 

Protein	NCBI ID	SENTENCE INDEX