Comprehensive glycomics comparison between colon cancer cell cultures and tumours: implications for biomarker studies

Chik JH, Zhou J, Moh ES, Christopherson R, Clarke SJ, Molloy MP, Packer NH

PubMed Entry: 24840470

Percentage Abundance
Structure Hex HexNAc Fuc NeuNAc SW1116 (Sample A) SW1116 (Sample B) SW620 (Sample A) SW620 (Sample B) SW837 (Sample A) SW837 (Sample B) SW480 (Sample A) SW480 (Sample B) Tissue 1 Tissue 2 UniCarb-DB
3 2 0 0 0.28 0.33 0.51 0.62 0.4 0.32 0.26 0.41 0.0 0.55
3 2 1 0 1.18 0.97 1.67 1.36 0.78 0.84 0.68 0.73 0.38 0.95
5 2 0 0 0.86 0.87 0.58 0.4 0.73 0.48 1.06 1.51 1.95 0.87
6 2 0 0 4.59 4.89 4.32 3.28 6.2 6.91 2.36 3.04 3.1 3.57
6 2 0 0 0.41 0.28 0.35 0.34 0.61 0.41 0.0 0.0 0.71 0.25
4 3 1 0 0.11 0.07 0.21 0.17 0.07 0.1 0.0 0.0 0.0 0.0
5 3 0 0 0.23 0.23 0.16 0.21 0.0 0.0 0.0 0.0 0.0 0.0
3 4 1 0 0.05 0.03 0.05 0.05 0.0 0.0 0.0 0.0 0.0 0.0
3 4 1 0 0.16 0.12 0.46 0.54 0.0 0.0 0.1 0.14 0.0 0.0
3 4 1 0 0.12 0.11 0.34 0.31 0.29 0.24 0.0 0.0 0.6 0.92

    Data Processing

    • Each glycan structure was quantified relative to the total content by integration of the extracted ion chromatogram peak area (EIC).
    • For comparison of glycan abundances the area-under-the-curves (AUCs) of each glycan structure were normalised to the total AUC (for all glycan structures in a sample summed) and expressed as a percentage.

    Additonal Notes

    • Glycoproteins immobilized on PVDF membranes before N-glycans released by PNGase F, isolated and reduced
    • O-glycans are chemically released from the same protein spot by reductive β-elimination
    • Porous graphitised carbon liquid chromatography tandem mass spectrometry
    • Negative ion mode
    • Agilent LCD/MSD Trap XCT Ultra or Bruker HCT Ultra
    • MS scans were between m/z 100–2200