PMID: PMC4739677-2-7

 

    Legend: Gene, Sites

Title : Glycopeptide Identification

Abstract :
  1. Low-energy CID- MS2 fragmentation of glycopeptides , as employed in the present work, almost exclusively generates fragment ions corresponding to the fragmentation of the glycan moiety, while leaving the peptide backbone mainly intact
  2. Thus, this type of fragmentation does usually not provide any information on the sequence of the peptide backbone nor on the occupied glycosylation site
  3. To identify the peptide we have employed manual CID-MS3 fragmentation on the putative peptide mass, which has been inferred from the annotation of the corresponding CID- MS2 spectra before
  4. In a few of cases the signal of the putative peptide mass was too low to yield sufficient fragment ions
  5. Consequently, the putative peptide\+HexNAc ion was subjected to CID-MS3 fragmentation instead
  6. We did not employ an automated CID-MS3 fragmentation procedure, e.g. fragmentation of the three most intense precursor ions in the CID- MS2 spectrum, because we wanted to generate and sum up as many fragment spectra as possible from the selected putative peptide mass, in order to increase spectra quality and therefore the chance of successful peptide identification
  7. By searching the acquired CID-MS3 fragment spectra against the human subset of the UniProtKB/Swiss- Prot protein database , a total of 60 peptides (of 88 detected O-glycopeptides ) could be identified unambiguously
  8. Notably, in a few cases also peptide fragment ions present in CID- MS2 spectra allowed for an unambiguous peptide identification (supplemental Fig
  9. S4, 267AVPPVVDPDAPPSPPL283, m/z 872.733+)
  10. Overall, the identified peptides belong to 22 different proteins —primarily acute phase proteins
  11. This constantly growing group of blood plasma proteins fulfills essential functions during inflammation (e.g. coagulation, anti-inflammatory and anti-pathogenic activity), and, accordingly, their expression is known to be either significantly up- or downregulated (positive and negative acute phase proteins ) in this context
  12. As a result, this group of proteins attracted a lot of attention as potential cancer biomarkers in recent years (5)
  13. Noteworthy, the identified proteins span a concentration range of 5 orders of magnitude
  14. Therefore, the applied approach seems to be suitable to also detect lower abundant proteins or peptides
  15. A group of O-glycosylated proteins that have frequently been identified in other large-scale glycoproteomic studies are Coagulation factors (30, 58, 60, 77)
  16. In our study there is an indication for the presence of an O-glycosylated peptide derived from Coagulation factor V (HILIC fraction #15, m/z 761.782+, 1453QIPPPDL1460\+HexNAc1Hex1NeuAc1 Table II, supplemental Fig
  17. S5)
  18. Interestingly, the detected Coagulation factor V O-glycosylation site ( Ser1455 ) has not been described so far
  19. Unfortunately, our data do not allow an unambiguous identification of this protein
Output (sent_index, trigger, protein, sugar, site):
  • 1. glycopeptides, , -, -, glycopeptides
  • 15. O-glycosylated, , proteins, -, -
  • 16. O-glycosylated, , -, -, peptide
  • 18. O-glycosylation, , -, -, Ser1455
  • 18. O-glycosylation, , -, -, site
  • 2. glycosylation, , -, -, site
  • 7. O-glycopeptides, , -, -, O-glycopeptides
Output(Part-Of) (sent_index, protein, site):
  • 18. Coagulation factor V O-glycosylation, Ser1455
  • 18. Coagulation factor V O-glycosylation, site
*Output_Site_Fusion* (sent_index, protein, sugar, site):
  • 18. Coagulation factor V O-glycosylation, -, Ser1455

 

 

Protein NCBI ID SENTENCE INDEX