Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.

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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
NameUniProt ID
Insulin receptorP06213Details
ProthrombinP00734Details
Prolyl 4-hydroxylase subunit alpha-1P13674Details
Carcinoembryonic antigen-related cell adhesion molecule 1P13688Details
ATP-binding cassette sub-family A member 1O95477Details
Scavenger receptor class B member 1Q8WTV0Details
Corticosteroid-binding globulinP08185Details
Angiotensin-converting enzymeP12821Details
Antithrombin-IIIP01008Details
Corticosteroid 11-beta-dehydrogenase isozyme 1P28845Details
GDH/6PGL endoplasmic bifunctional proteinO95479Details
Alpha-N-acetylglucosaminidaseP54802Details
Neutrophil elastaseP08246Details
Vitamin K-dependent gamma-carboxylaseP38435Details
Ectonucleotide pyrophosphatase/phosphodiesterase family member 1P22413Details
Low-density lipoprotein receptorP01130Details
SerotransferrinP02787Details
Aspartyl/asparaginyl beta-hydroxylaseQ12797Details
Fibrinogen alpha chainP02671Details
Sex hormone-binding globulinP04278Details
Voltage-dependent calcium channel subunit alpha-2/delta-1P54289Details
High affinity immunoglobulin gamma Fc receptor IP12314Details
Epidermal growth factor receptorP00533Details
Heparin cofactor 2P05546Details
Ephrin type-A receptor 2P29317Details
Dipeptidyl peptidase 4P27487Details
Lysosomal alpha-glucosidaseP10253Details
N-acetylgalactosamine-6-sulfataseP34059Details
Gamma-glutamyltranspeptidase 1P19440Details
Alpha-2-macroglobulinP01023Details
Sialidase-1Q99519Details
Alpha-1-acid glycoprotein 1P02763Details
Complement decay-accelerating factorP08174Details
Serum paraoxonase/arylesterase 1P27169Details
Cathepsin DP07339Details
Alpha-1-antitrypsinP01009Details
Thiamine transporter 2Q9BZV2Details
Insulin-like growth factor-binding protein 3P17936Details
Beta-glucuronidaseP08236Details
GlucosylceramidaseP04062Details
Angiotensin-converting enzyme 2Q9BYF1Details
LactotransferrinP02788Details
Membrane primary amine oxidaseQ16853Details
Kininogen-1P01042Details
Coagulation factor XIP03951Details
Basement membrane-specific heparan sulfate proteoglycan core proteinP98160Details
ChymaseP23946Details
Integrin beta-2P05107Details
von Willebrand factorP04275Details
Proton-coupled folate transporterQ96NT5Details
AngiotensinogenP01019Details
HeparanaseQ9Y251Details
VitronectinP04004Details
MyeloperoxidaseP05164Details
Aminopeptidase NP15144Details
Neutrophil gelatinase-associated lipocalinP80188Details
Intercellular adhesion molecule 1P05362Details
5'-nucleotidaseP21589Details
CD44 antigenP16070Details
CeruloplasminP00450Details
Dipeptidase 1P16444Details
Beta-hexosaminidase subunit betaP07686Details
Integrin beta-3P05106Details
EndoplasminP14625Details
ProsaposinP07602Details
FibronectinP02751Details
Serum amyloid P-componentP02743Details
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2Q10588Details
Cathepsin FQ9UBX1Details
Complement C1s subcomponentP09871Details
Complement factor BP00751Details
Fibrinogen beta chainP02675Details
Fibrinogen gamma chainP02679Details
Complement C1r subcomponentP00736Details
Complement C1q subcomponent subunit AP02745Details
Laminin subunit alpha-5O15230Details
Laminin subunit beta-1P07942Details
Laminin subunit gamma-1P11047Details
Laminin subunit alpha-1P25391Details
CalreticulinP27797Details
Prolow-density lipoprotein receptor-related protein 1Q07954Details
Asialoglycoprotein receptor 2P07307Details
Serine protease hepsinP05981Details
Neuropilin-1O14786Details
Cathepsin L1P07711Details
CholinesteraseP06276Details
Choline transporter-like protein 2Q8IWA5Details
Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2O00469Details
Prolyl 3-hydroxylase 1Q32P28Details
Glutamyl aminopeptidaseQ07075Details
Phosphatidylserine synthase 2Q9BVG9Details
Disintegrin and metalloproteinase domain-containing protein 10O14672Details
Alpha-galactosidase AP06280Details
Plasma kallikreinP03952Details
Epithelial cell adhesion moleculeP16422Details
Plasma protease C1 inhibitorP05155Details
Ig gamma-1 chain C regionP01857Details
Beta-2-glycoprotein 1P02749Details
Zinc-alpha-2-glycoproteinP25311Details
Arylsulfatase AP15289Details
Scavenger receptor cysteine-rich type 1 protein M130Q86VB7Details
Leptin receptorP48357Details
Angiopoietin-1 receptorQ02763Details
Carboxypeptidase B2Q96IY4Details
Programmed cell death 1 ligand 1Q9NZQ7Details
Complement C3P01024Details
Transmembrane glycoprotein NMBQ14956Details
T-cell surface glycoprotein CD4P01730Details
EndoglinP17813Details
Toll-like receptor 8Q9NR97Details
Monocyte differentiation antigen CD14P08571Details
UDP-glucuronosyltransferase 1-1P22309Details
UDP-glucuronosyltransferase 1-4P22310Details
Alkaline phosphatase, tissue-nonspecific isozymeP05186Details
Receptor-type tyrosine-protein phosphatase SQ13332Details
Integrin beta-1P05556Details
Integrin alpha-VP06756Details
Cation-independent mannose-6-phosphate receptorP11717Details
Solute carrier family 22 member 7Q9Y694Details
Alpha-1-acid glycoprotein 2P19652Details
UDP-glucuronosyltransferase 1-3P35503Details
UDP-glucuronosyltransferase 2B7P16662Details
UDP-glucuronosyltransferase 2B4P06133Details
UDP-glucuronosyltransferase 1-8Q9HAW9Details
Tryptase alpha/beta-1Q15661Details
Endothelin-converting enzyme 1P42892Details
Ig gamma-2 chain C regionP01859Details
Pro-cathepsin HP09668Details
HLA class I histocompatibility antigen, B-27 alpha chainP01889Details
Carcinoembryonic antigen-related cell adhesion molecule 5P06731Details
Apolipoprotein MO95445Details
Poliovirus receptorP15151Details
Cation-dependent mannose-6-phosphate receptorP20645Details
DecorinP07585Details
Inositol 1,4,5-trisphosphate receptor type 1Q14643Details
Palmitoyl-protein thioesterase 1P50897Details
L-amino-acid oxidaseQ96RQ9Details
Carboxypeptidase DO75976Details
N-acetylmuramoyl-L-alanine amidaseQ96PD5Details
Alpha-N-acetylgalactosaminidaseP17050Details
Carboxypeptidase QQ9Y646Details
Complement C4-AP0C0L4Details
UDP-glucuronosyltransferase 2B15P54855Details
Cocaine esteraseO00748Details
Transferrin receptor protein 1P02786Details
Transferrin receptor protein 2Q9UP52Details
Cytochrome b-245 heavy chainP04839Details
Stabilin-2Q8WWQ8Details
Sodium/potassium-transporting ATPase subunit beta-1P05026Details
Sodium/potassium-transporting ATPase subunit beta-2P14415Details
Apolipoprotein DP05090Details
Ig gamma-4 chain C regionP01861Details
Ig mu chain C regionP01871Details
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1P28907Details
Selenoprotein PP49908Details
P2X purinoceptor 4Q99571Details
Lysosomal protective proteinP10619Details
Solute carrier family 13 member 5Q86YT5Details
Fibrillin-2P35556Details
AfaminP43652Details
Integrin alpha-5P08648Details
Neural cell adhesion molecule L1P32004Details
Macrophage receptor MARCOQ9UEW3Details
Minor histocompatibility antigen H13Q8TCT9Details
Nodal modulator 1Q15155Details
Splicing factor 3A subunit 3Q12874Details
Alpha-2-HS-glycoproteinP02765Details
C4b-binding protein alpha chainP04003Details
Complement component C8 beta chainP07358Details
Complement component C9P02748Details
Complement factor HP08603Details
Complement factor IP05156Details
ClusterinP10909Details
Insulin-like growth factor-binding protein complex acid labile subunitP35858Details
Inter-alpha-trypsin inhibitor heavy chain H2P19823Details
LumicanP51884Details
Pigment epithelium-derived factorP36955Details
C4b-binding protein beta chainP20851Details
Complement component C8 alpha chainP07357Details
Coagulation factor XIII B chainP05160Details
Ficolin-3O75636Details
Inter-alpha-trypsin inhibitor heavy chain H1P19827Details
Inter-alpha-trypsin inhibitor heavy chain H4Q14624Details
Immunoglobulin J chainP01591Details
Pregnancy zone proteinP20742Details
Alpha-1-antichymotrypsinP01011Details
N-acylethanolamine-hydrolyzing acid amidaseQ02083Details
Iduronate 2-sulfataseP22304Details
Alpha-L-iduronidaseP35475Details
Arylsulfatase BP15848Details
UDP-glucuronosyltransferase 2B10P36537Details
Phospholipid transfer proteinP55058Details
HLA class II histocompatibility antigen, DR alpha chainP01903Details
HLA class II histocompatibility antigen, DR beta 5 chainQ30154Details
N-sulphoglucosamine sulphohydrolaseP51688Details
Ectonucleoside triphosphate diphosphohydrolase 5O75356Details
Prostaglandin-H2 D-isomeraseP41222Details
Zinc transporter ZIP14Q15043Details
Apolipoprotein B-100P04114Details
HemopexinP02790Details
Histidine-rich glycoproteinP04196Details
HaptoglobinP00738Details
Serum paraoxonase/arylesterase 2Q15165Details
V-type proton ATPase subunit S1Q15904Details
Integrin alpha-XP20702Details
Beta-galactosidaseP16278Details
Interleukin-6 receptor subunit betaP40189Details
Immunoglobulin heavy constant gamma 3P01860Details
Angiopoietin-related protein 3Q9Y5C1Details
Lymphatic vessel endothelial hyaluronic acid receptor 1Q9Y5Y7Details
Extracellular superoxide dismutase [Cu-Zn]P08294Details
HLA class I histocompatibility antigen, C alpha chainP10321Details
Arylacetamide deacetylaseP22760Details
CD276 antigenQ5ZPR3Details
Asialoglycoprotein receptor 1P07306Details