PMID: PMC6243375-1-2

 

    Legend: Gene, Sites

Title : Large‐scale and precision mapping of the O‐linked glycoproteome in human kidney tissues, T cells, and serum sample

Abstract :
  1. EXoO was benchmarked using human kidney tissue, T cells, and serum to determine performance of the method in samples with differing levels of protein complexity
  2. To do this, O‐linked glycopeptides were extracted using EXoO and fractionated into 24 fractions and then subjected to LC‐MS/MS analysis (Fig 2A)
  3. To study kidney tissue, paired tumor and normal tissues were collected from three patients
  4. The extracted proteins from these tissues were separately pooled to generate two samples, that is, tumor and normal
  5. After analysis with 1% false discovery rate (FDR) at PSM level, 35,848 PSMs were assigned to 2,804 O‐linked glycopeptides containing 1,781 O‐linked glycosylation sites from 592 glycoproteins (Dataset EV2)
  6. A number of 112 spectra with different sequences , charge, peptide length, scores, and glycan com positions were annotated (Appendix Fig S2)
  7. When the EXoO approach was applied to the analysis of T cells, 4,623 PSMs were assigned to contain 1,295 O‐linked glycosylation sites from 1,982 O‐linked glycopeptides and 590 glycoproteins (Dataset EV3)
  8. Finally, we studied human serum that contains a number of highly glycosylated proteins and has been previously subjected to detailed mapping of N‐linked glycosylation sites and N‐linked glycans but for which there has been little success in mapping of O‐linked glycosylation sites and O‐linked glycans (Zhang et al, 2005; Stumpo & Reinhold, 2010; Yabu et al, 2014; Darula et al, 2016; Hoffmann et al, 2016)
  9. With 1% FDR, 6,157 PSMs were assigned to 1,060 O‐linked glycopeptides with 732 O‐linked glycosylation sites from 306 glycoproteins being identified (Dataset EV4)
  10. This analysis of human tissue, T cells, and serum demonstrated that EXoO is a highly effective tool for accessing the O‐linked glycoproteome in different types of samples
Output (sent_index, trigger, protein, sugar, site):
  • 2. glycopeptides, , -, -, glycopeptides
  • 5. glycopeptides, , -, -, glycopeptides
  • 5. glycoproteins, , glycoproteins, -, -
  • 5. glycosylation, , -, -, sites
  • 7. glycopeptides, , -, -, glycopeptides
  • 7. glycoproteins, , glycoproteins, -, -
  • 7. glycosylation, , -, -, sites
  • 8. glycosylated, , proteins, -, -
  • 8. glycosylation, , -, -, sites
  • 9. glycopeptides, , -, -, glycopeptides
  • 9. glycoproteins, , glycoproteins, -, -
  • 9. glycosylation, , -, -, sites
Output(Part-Of) (sent_index, protein, site):
  • 7. glycoproteins, sites
  • 9. glycoproteins, sites
*Output_Site_Fusion* (sent_index, protein, sugar, site):

 

 

Protein NCBI ID SENTENCE INDEX