Colorectal Cancer Cell Line
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
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.
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.
| 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 |
|
|
2 | 2 | 1 | 0 | 0.14 | 0.15 | 0.77 | 0.6 | 0.38 | 0.38 | 0.14 | 0.21 | 0.41 | 1.56 |  |
|
|
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 | |
- 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.
- 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