PMID: PMC4739677-2-9

 

    Legend: Gene, Sites

Title : Pinpointing of O-glycosylation Sites

Abstract :
  1. Pinpointing the correct O-glycosylation sites is a crucial but very challenging task
  2. Proteinase K , in this regard, proved to be beneficial as it can generate short glycopeptides , which exhibit only one potential O-glycosylation site
  3. In case the occupied O-glycosylation site could not be inferred directly, we have employed ETD- MS2 fragmentation
  4. In first attempts database-assisted peptide identification via MASCOT was tested on the acquired ETD glycopeptide spectra, but turned out to be not successful
  5. One reason for this is the presence of intense signals in the ETD- MS2 spectrum, which do not correspond to peptide fragment ions (e.g. unfragmented precursor ions, glycan fragment ions), and which thus compromise automated peptide identification (85)
  6. A possible solution for this is the (manual) removal of these additional m/z-values from the ETD-spectra before running the search algorithm
  7. In the present study, however, this procedure did not improve the database-assisted peptide identification
  8. For these reasons we relied on manual spectra annotation and interpretation using DataAnalysis, Biotools as well as public repositories (UniProtKB and UniCarbKB)
  9. Furthermore, NetOGlyc 4.0 was employed to predict O-glycosylation sites and to support experimental findings
  10. Predicted and experimentally determined O-glycosylation sites were mostly in good agreement for already known O-glycosylation sites—however , support for potentially novel sites could only be found in a few cases
  11. A general shortcoming of glycopeptide enrichment methods is that they are biased toward glycosylated peptides , while underrepresenting potential corresponding aglyosylated counterparts
  12. Hence, in the present study no conclusions with respect to the macro-heterogeneity of the glycoproteins ( site-occupancy ) can be drawn
Output (sent_index, trigger, protein, sugar, site):
  • 1. O-glycosylation, , -, -, sites
  • 10. O-glycosylation, , -, -, sites
  • 11. glycopeptide, , -, -, glycopeptide
  • 11. glycosylated, , -, -, peptides
  • 12. glycoproteins, , glycoproteins, -, site-occupancy
  • 12. macro-heterogeneity, , glycoproteins, -, site-occupancy
  • 2. O-glycosylation, , -, -, site
  • 2. glycopeptides, , -, -, glycopeptides
  • 3. O-glycosylation, , -, -, site
  • 4. glycopeptide, , -, -, glycopeptide
  • 9. O-glycosylation, , -, -, sites
Output(Part-Of) (sent_index, protein, site):
*Output_Site_Fusion* (sent_index, protein, sugar, site):

 

 

Protein NCBI ID SENTENCE INDEX