Table 2 Summary of the published glycomics studies on biomarker discovery

Human serum

N-glycome

DNA sequencer

3 upregulated, 1 downregulated glycans identified. Log ratio of two features used as diagnostic test (GlycoCirrhoTest)

Area under ROC curve: 0.87 for liver cirrhosis

Not done

Sequencing by exoglycosidase treatment

N-glycome was released from serum using PNGase F, followed by APTS labeling and separation on DNA sequencer

[18]

Human serum

N-glycome

DNA sequencer

1 upregulated, 1 downregulated glycans identified. Log ratio of two features specifically and significantly increased in HCC, and used as diagnostic test (GlycoHCCTest)

Area under ROC curve: 0.81 for HCC

Not done

Sequencing by exoglycosidase treatment

N-glycome was released from serum using PNGase F, followed by APTS labeling and separation on DNA sequencer

[63]

Rat serum

N-glycome

DNA sequencer

1 upregulated, 2 downregulated glycans identified. Mean values of all glycomic peaks correlated with liver fibrosis stages and interferon-γ treatment

Not evaluated

Not done

Not done

N-glycome was released from serum using PNGase F, followed by APTS labeling and separation on DNA sequencer

[62]

Human serum

N-glycome

MALDI-TOF MS

10 upregulated, 7 downregulated glycans identified. Linear regression of 4 features used as diagnostic test (FibroGlyco Index)

Area under ROC curve: 0.91 for liver fibrosis; 0.91 for liver cirrhosis

Not done

Not done

N-glycome was released from serum using PNGase F, followed by hydrophilic purification and MALDI-TOF MS analysis

[19]

Human serum

N-glycome

MALDI-TOF MS

Unique N-glycan profile observed for 1 patient compared with another 2 patients

Not evaluated

Permethylation followed by GC-MS analysis.

Characterization by exoglycosidase sequencing and ESI-MS/MS

N-glycan was released from serum using PNGase F, followed by graphitized carbon purification, esterification or removal of sialic acid, GC-MS and MALDI-TOF MS analysis

[64]

Human serum

N-glycome

MALDI-TOF MS

Several ratio of N-glycan abundance shown significant difference between normal and HCC. Combination of 3 of these ratio used as diagnostic test

100% accuracy in differentiating normal and HCC.

Not done

Not done

N-glycome was released from trypsinized serum using PNGase F, followed by immobilization on beads. Purification, methyl esterification of sialic acid and labeling was carried out on beads. Glycans were eluted for MALDI-TOF MS analysis

[65]

Human serum

N-glycome

MALDI-TOF MS

Abnormal N-glycan profile identified for CDG-IIx patients; decrease in total N-glycan for CDG-I patients; different combinations of N-glycans differentate CDG-I, CDG-Ia and CDG-Ib patients; PCA of total N-glycan profile distinguish CDG from normal and between different types of CDG

Clear segregation between normal and CDG and between different CDG by using PCA of total N-glycan profile in the pilot study. Biomarker is to be validated by using more samples

Not done

Not done

N-glycome was released from trypsinized serum using PNGase F, followed by immobilization on beads. Purification, methyl esterification of sialic acid and labeling was carried out on beads. Glycans were eluted for MALDI-TOF MS analysis

[65]

Human prostate cancer PC-3 cells and normal human prostate epithelial PrEC cells

N-glycome

MALDI-TOF MS

Unique N-glycan profile observed for each cell line

Not evaluated

Not done

Not done

N-glycome was released from trypsinized serum using PNGase F, followed by immobilization on beads. Purification, methyl esterification of sialic acid and labeling was carried out on beads. Glycans were eluted for MALDI-TOF MS analysis

[65]

Conditioned media from Caov-3, OVCAR-3, ES-2 and SK-OV3 cell lines; human patients serum

Shed glycome obtained by β-elimination

MALDI-FTICR MS

16 unique glycan features identified in serum of ovarian cancer patients, giving a unique glycomic pattern

Not evaluated

Not done

Fragmentation analysis by infrared Multiphoton Dissociation (IRMPD)

Total glycan was released by β-elimination, followed by graphitized carbon purification and MALDI-FTICR MS analysis

[65]

Conditioned media from MCF-10A cell lines; breast tumor transplanted mouse serum and human patient serum

Shed glycome obtained by β-elimination

MALDI-FTICR MS

4 upregulated glycans identified in mouse serum; differential human serum O-glycan profile observed between normal and breast cancer subject. PCA of serum O-glycan profile used as biomarker

Clear segregation between normal and breast cancer sample by using PCA of total O-glycan profile. Correct assignment of normal and breast cancer sample by using principal component regression (PCR). Biomarker is to be validated by using more samples

Not done

Fragmentation analysis by infrared Multiphoton Dissociation (IRMPD)

Total glycan was released by β-elimination, followed by graphitized carbon purification and MALDI-FTICR MS analysis

[67]