Title : Pinpointing of O-glycosylation Sites
Abstract :
- Pinpointing the correct O-glycosylation sites is a crucial but very challenging task
- Proteinase K , in this regard, proved to be beneficial as it can generate short glycopeptides , which exhibit only one potential O-glycosylation site
- In case the occupied O-glycosylation site could not be inferred directly, we have employed ETD- MS2 fragmentation
- In first attempts database-assisted peptide identification via MASCOT was tested on the acquired ETD glycopeptide spectra, but turned out to be not successful
- 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)
- A possible solution for this is the (manual) removal of these additional m/z-values from the ETD-spectra before running the search algorithm
- In the present study, however, this procedure did not improve the database-assisted peptide identification
- For these reasons we relied on manual spectra annotation and interpretation using DataAnalysis, Biotools as well as public repositories (UniProtKB and UniCarbKB)
- Furthermore, NetOGlyc 4.0 was employed to predict O-glycosylation sites and to support experimental findings
- 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
- A general shortcoming of glycopeptide enrichment methods is that they are biased toward glycosylated peptides , while underrepresenting potential corresponding aglyosylated counterparts
- 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):