A strategy for precise and large scale identification of core fucosylated glycoproteins.

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Jia W, Lu Z, Fu Y, Wang HP, Wang LH, Chi H, Yuan ZF, Zheng ZB, Song LN, Han HH, Liang YM, Wang JL, Cai Y, Zhang YK, Deng YL, Ying WT, He SM, Qian XH

A strategy for precise and large scale identification of core fucosylated glycoproteins.

Mol Cell Proteomics. 2009 May;8(5):913-23. doi: 10.1074/mcp.M800504-MCP200. Epub 2009 Jan 12.

PubMed ID
19139490 [ View in PubMed
]
Abstract

Core fucosylation (CF) patterns of some glycoproteins are more sensitive and specific than evaluation of their total respective protein levels for diagnosis of many diseases, such as cancers. Global profiling and quantitative characterization of CF glycoproteins may reveal potent biomarkers for clinical applications. However, current techniques are unable to reveal CF glycoproteins precisely on a large scale. Here we developed a robust strategy that integrates molecular weight cutoff, neutral loss-dependent MS(3), database-independent candidate spectrum filtering, and optimization to effectively identify CF glycoproteins. The rationale for spectrum treatment was innovatively based on computation of the mass distribution in spectra of CF glycopeptides. The efficacy of this strategy was demonstrated by implementation for plasma from healthy subjects and subjects with hepatocellular carcinoma. Over 100 CF glycoproteins and CF sites were identified, and over 10,000 mass spectra of CF glycopeptide were found. The scale of identification results indicates great progress for finding biomarkers with a particular and attractive prospect, and the candidate spectra will be a useful resource for the improvement of database searching methods for glycopeptides.

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Polypeptides
NameUniProt ID
ProthrombinP00734Details
Type-1 angiotensin II receptorP30556Details
Dopamine beta-hydroxylaseP09172Details
Potassium voltage-gated channel subfamily H member 6Q9H252Details
SerotransferrinP02787Details
Heparin cofactor 2P05546Details
Glutaminase kidney isoform, mitochondrialO94925Details
Alpha-2-macroglobulinP01023Details
Alpha-1-antitrypsinP01009Details
Insulin-like growth factor-binding protein 3P17936Details
Membrane primary amine oxidaseQ16853Details
E3 ubiquitin-protein ligase Mdm2Q00987Details
Kininogen-1P01042Details
von Willebrand factorP04275Details
VitronectinP04004Details
Intercellular adhesion molecule 1P05362Details
CeruloplasminP00450Details
FibronectinP02751Details
Fibrinogen gamma chainP02679Details
Prolow-density lipoprotein receptor-related protein 1Q07954Details
CholinesteraseP06276Details
Plasma protease C1 inhibitorP05155Details
Ig gamma-1 chain C regionP01857Details
Beta-2-glycoprotein 1P02749Details
Zinc-alpha-2-glycoproteinP25311Details
Scavenger receptor cysteine-rich type 1 protein M130Q86VB7Details
Cadherin-5P33151Details
Cholesteryl ester transfer proteinP11597Details
Ig gamma-2 chain C regionP01859Details
Proteasome subunit beta type-4P28070Details
Ig alpha-2 chain C regionP01877Details
Complement C4-AP0C0L4Details
Apolipoprotein DP05090Details
Ig gamma-4 chain C regionP01861Details
Ig alpha-1 chain C regionP01876Details
Ig mu chain C regionP01871Details
Selenoprotein PP49908Details
AfaminP43652Details
Alpha-2-HS-glycoproteinP02765Details
Complement component C9P02748Details
Complement factor HP08603Details
Complement factor IP05156Details
ClusterinP10909Details
Leucine-rich alpha-2-glycoproteinP02750Details
KallistatinP29622Details
Pigment epithelium-derived factorP36955Details
Ficolin-3O75636Details
Inter-alpha-trypsin inhibitor heavy chain H1P19827Details
Immunoglobulin J chainP01591Details
A disintegrin and metalloproteinase with thrombospondin motifs 13Q76LX8Details
Phospholipid transfer proteinP55058Details
Prostaglandin-H2 D-isomeraseP41222Details
HemopexinP02790Details
HaptoglobinP00738Details
Interleukin-6 receptor subunit betaP40189Details
Hyaluronidase-4Q2M3T9Details