Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.
Article Details
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Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H
Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.
J Proteome Res. 2009 Feb;8(2):651-61. doi: 10.1021/pr8008012.
- PubMed ID
- 19159218 [ View in PubMed]
- Abstract
The study of protein glycosylation has lagged far behind the progress of current proteomics because of the enormous complexity, wide dynamic range distribution and low stoichiometric modification of glycoprotein. Solid phase extraction of tryptic N-glycopeptides by hydrazide chemistry is becoming a popular protocol for the analysis of N-glycoproteome. However, in silico digestion of proteins in human proteome database by trypsin indicates that a significant percentage of tryptic N-glycopeptides is not in the preferred detection mass range of shotgun proteomics approach, that is, from 800 to 3500 Da. And the quite big size of glycan groups may block trypsin to access the K, R residues near N-glycosites for digestion, which will result in generation of big glycopeptides. Thus many N-glycosites could not be localized if only trypsin was used to digest proteins. Herein, we describe a comprehensive way to analyze the N-glycoproteome of human liver tissue by combination of hydrazide chemistry method and multiple enzyme digestion. The lysate of human liver tissue was digested with three proteases, that is, trypsin, pepsin and thermolysin, with different specificities, separately. Use of trypsin alone resulted in identification of 622 N-glycosites, while using pepsin and thermolysin resulted in identification of 317 additional N-glycosites. Among the 317 additional N-glycosites, 98 (30.9%) could not be identified by trypsin in theory because the corresponding in silico tryptic peptides are either too small or too big to detect in mass spectrometer. This study clearly demonstrated that the coverage of N-glycosites could be significantly increased due to the adoption of multiple enzyme digestion. A total number of 939 N-glycosites were identified confidently, covering 523 noredundant glycoproteins from human liver tissue, which leads to the establishment of the largest data set of glycoproteome from human liver up to now.
DrugBank Data that Cites this Article
- Polypeptides
Name UniProt ID Insulin receptor P06213 Details Prothrombin P00734 Details Prolyl 4-hydroxylase subunit alpha-1 P13674 Details Carcinoembryonic antigen-related cell adhesion molecule 1 P13688 Details ATP-binding cassette sub-family A member 1 O95477 Details Scavenger receptor class B member 1 Q8WTV0 Details Corticosteroid-binding globulin P08185 Details Angiotensin-converting enzyme P12821 Details Antithrombin-III P01008 Details Corticosteroid 11-beta-dehydrogenase isozyme 1 P28845 Details GDH/6PGL endoplasmic bifunctional protein O95479 Details Alpha-N-acetylglucosaminidase P54802 Details Neutrophil elastase P08246 Details Vitamin K-dependent gamma-carboxylase P38435 Details Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 P22413 Details Low-density lipoprotein receptor P01130 Details Serotransferrin P02787 Details Aspartyl/asparaginyl beta-hydroxylase Q12797 Details Fibrinogen alpha chain P02671 Details Sex hormone-binding globulin P04278 Details Voltage-dependent calcium channel subunit alpha-2/delta-1 P54289 Details High affinity immunoglobulin gamma Fc receptor I P12314 Details Epidermal growth factor receptor P00533 Details Heparin cofactor 2 P05546 Details Ephrin type-A receptor 2 P29317 Details Dipeptidyl peptidase 4 P27487 Details Lysosomal alpha-glucosidase P10253 Details N-acetylgalactosamine-6-sulfatase P34059 Details Gamma-glutamyltranspeptidase 1 P19440 Details Alpha-2-macroglobulin P01023 Details Sialidase-1 Q99519 Details Alpha-1-acid glycoprotein 1 P02763 Details Complement decay-accelerating factor P08174 Details Serum paraoxonase/arylesterase 1 P27169 Details Cathepsin D P07339 Details Alpha-1-antitrypsin P01009 Details Thiamine transporter 2 Q9BZV2 Details Insulin-like growth factor-binding protein 3 P17936 Details Beta-glucuronidase P08236 Details Glucosylceramidase P04062 Details Angiotensin-converting enzyme 2 Q9BYF1 Details Lactotransferrin P02788 Details Membrane primary amine oxidase Q16853 Details Kininogen-1 P01042 Details Coagulation factor XI P03951 Details Basement membrane-specific heparan sulfate proteoglycan core protein P98160 Details Chymase P23946 Details Integrin beta-2 P05107 Details von Willebrand factor P04275 Details Proton-coupled folate transporter Q96NT5 Details Angiotensinogen P01019 Details Heparanase Q9Y251 Details Vitronectin P04004 Details Myeloperoxidase P05164 Details Aminopeptidase N P15144 Details Neutrophil gelatinase-associated lipocalin P80188 Details Intercellular adhesion molecule 1 P05362 Details 5'-nucleotidase P21589 Details CD44 antigen P16070 Details Ceruloplasmin P00450 Details Dipeptidase 1 P16444 Details Beta-hexosaminidase subunit beta P07686 Details Integrin beta-3 P05106 Details Endoplasmin P14625 Details Prosaposin P07602 Details Fibronectin P02751 Details Serum amyloid P-component P02743 Details ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 Q10588 Details Cathepsin F Q9UBX1 Details Complement C1s subcomponent P09871 Details Complement factor B P00751 Details Fibrinogen beta chain P02675 Details Fibrinogen gamma chain P02679 Details Complement C1r subcomponent P00736 Details Complement C1q subcomponent subunit A P02745 Details Laminin subunit alpha-5 O15230 Details Laminin subunit beta-1 P07942 Details Laminin subunit gamma-1 P11047 Details Laminin subunit alpha-1 P25391 Details Calreticulin P27797 Details Prolow-density lipoprotein receptor-related protein 1 Q07954 Details Asialoglycoprotein receptor 2 P07307 Details Serine protease hepsin P05981 Details Neuropilin-1 O14786 Details Cathepsin L1 P07711 Details Cholinesterase P06276 Details Choline transporter-like protein 2 Q8IWA5 Details Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 O00469 Details Prolyl 3-hydroxylase 1 Q32P28 Details Glutamyl aminopeptidase Q07075 Details Phosphatidylserine synthase 2 Q9BVG9 Details Disintegrin and metalloproteinase domain-containing protein 10 O14672 Details Alpha-galactosidase A P06280 Details Plasma kallikrein P03952 Details Epithelial cell adhesion molecule P16422 Details Plasma protease C1 inhibitor P05155 Details Ig gamma-1 chain C region P01857 Details Beta-2-glycoprotein 1 P02749 Details Zinc-alpha-2-glycoprotein P25311 Details Arylsulfatase A P15289 Details Scavenger receptor cysteine-rich type 1 protein M130 Q86VB7 Details Leptin receptor P48357 Details Angiopoietin-1 receptor Q02763 Details Carboxypeptidase B2 Q96IY4 Details Programmed cell death 1 ligand 1 Q9NZQ7 Details Complement C3 P01024 Details Transmembrane glycoprotein NMB Q14956 Details T-cell surface glycoprotein CD4 P01730 Details Endoglin P17813 Details Toll-like receptor 8 Q9NR97 Details Monocyte differentiation antigen CD14 P08571 Details UDP-glucuronosyltransferase 1-1 P22309 Details UDP-glucuronosyltransferase 1-4 P22310 Details Alkaline phosphatase, tissue-nonspecific isozyme P05186 Details Receptor-type tyrosine-protein phosphatase S Q13332 Details Integrin beta-1 P05556 Details Integrin alpha-V P06756 Details Cation-independent mannose-6-phosphate receptor P11717 Details Solute carrier family 22 member 7 Q9Y694 Details Alpha-1-acid glycoprotein 2 P19652 Details UDP-glucuronosyltransferase 1-3 P35503 Details UDP-glucuronosyltransferase 2B7 P16662 Details UDP-glucuronosyltransferase 2B4 P06133 Details UDP-glucuronosyltransferase 1-8 Q9HAW9 Details Tryptase alpha/beta-1 Q15661 Details Endothelin-converting enzyme 1 P42892 Details Ig gamma-2 chain C region P01859 Details Pro-cathepsin H P09668 Details HLA class I histocompatibility antigen, B-27 alpha chain P01889 Details Carcinoembryonic antigen-related cell adhesion molecule 5 P06731 Details Apolipoprotein M O95445 Details Poliovirus receptor P15151 Details Cation-dependent mannose-6-phosphate receptor P20645 Details Decorin P07585 Details Inositol 1,4,5-trisphosphate receptor type 1 Q14643 Details Palmitoyl-protein thioesterase 1 P50897 Details L-amino-acid oxidase Q96RQ9 Details Carboxypeptidase D O75976 Details N-acetylmuramoyl-L-alanine amidase Q96PD5 Details Alpha-N-acetylgalactosaminidase P17050 Details Carboxypeptidase Q Q9Y646 Details Complement C4-A P0C0L4 Details UDP-glucuronosyltransferase 2B15 P54855 Details Cocaine esterase O00748 Details Transferrin receptor protein 1 P02786 Details Transferrin receptor protein 2 Q9UP52 Details Cytochrome b-245 heavy chain P04839 Details Stabilin-2 Q8WWQ8 Details Sodium/potassium-transporting ATPase subunit beta-1 P05026 Details Sodium/potassium-transporting ATPase subunit beta-2 P14415 Details Apolipoprotein D P05090 Details Ig gamma-4 chain C region P01861 Details Ig mu chain C region P01871 Details ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 P28907 Details Selenoprotein P P49908 Details P2X purinoceptor 4 Q99571 Details Lysosomal protective protein P10619 Details Solute carrier family 13 member 5 Q86YT5 Details Fibrillin-2 P35556 Details Afamin P43652 Details Integrin alpha-5 P08648 Details Neural cell adhesion molecule L1 P32004 Details Macrophage receptor MARCO Q9UEW3 Details Minor histocompatibility antigen H13 Q8TCT9 Details Nodal modulator 1 Q15155 Details Splicing factor 3A subunit 3 Q12874 Details Alpha-2-HS-glycoprotein P02765 Details C4b-binding protein alpha chain P04003 Details Complement component C8 beta chain P07358 Details Complement component C9 P02748 Details Complement factor H P08603 Details Complement factor I P05156 Details Clusterin P10909 Details Insulin-like growth factor-binding protein complex acid labile subunit P35858 Details Inter-alpha-trypsin inhibitor heavy chain H2 P19823 Details Lumican P51884 Details Pigment epithelium-derived factor P36955 Details C4b-binding protein beta chain P20851 Details Complement component C8 alpha chain P07357 Details Coagulation factor XIII B chain P05160 Details Ficolin-3 O75636 Details Inter-alpha-trypsin inhibitor heavy chain H1 P19827 Details Inter-alpha-trypsin inhibitor heavy chain H4 Q14624 Details Immunoglobulin J chain P01591 Details Pregnancy zone protein P20742 Details Alpha-1-antichymotrypsin P01011 Details N-acylethanolamine-hydrolyzing acid amidase Q02083 Details Iduronate 2-sulfatase P22304 Details Alpha-L-iduronidase P35475 Details Arylsulfatase B P15848 Details UDP-glucuronosyltransferase 2B10 P36537 Details Phospholipid transfer protein P55058 Details HLA class II histocompatibility antigen, DR alpha chain P01903 Details HLA class II histocompatibility antigen, DR beta 5 chain Q30154 Details N-sulphoglucosamine sulphohydrolase P51688 Details Ectonucleoside triphosphate diphosphohydrolase 5 O75356 Details Prostaglandin-H2 D-isomerase P41222 Details Zinc transporter ZIP14 Q15043 Details Apolipoprotein B-100 P04114 Details Hemopexin P02790 Details Histidine-rich glycoprotein P04196 Details Haptoglobin P00738 Details Serum paraoxonase/arylesterase 2 Q15165 Details V-type proton ATPase subunit S1 Q15904 Details Integrin alpha-X P20702 Details Beta-galactosidase P16278 Details Interleukin-6 receptor subunit beta P40189 Details Immunoglobulin heavy constant gamma 3 P01860 Details Angiopoietin-related protein 3 Q9Y5C1 Details Lymphatic vessel endothelial hyaluronic acid receptor 1 Q9Y5Y7 Details Extracellular superoxide dismutase [Cu-Zn] P08294 Details HLA class I histocompatibility antigen, C alpha chain P10321 Details Arylacetamide deacetylase P22760 Details CD276 antigen Q5ZPR3 Details Asialoglycoprotein receptor 1 P07306 Details