Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.
Article Details
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Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD
Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.
J Proteome Res. 2005 Nov-Dec;4(6):2070-80.
- PubMed ID
- 16335952 [ View in PubMed]
- Abstract
The enormous complexity, wide dynamic range of relative protein abundances of interest (over 10 orders of magnitude), and tremendous heterogeneity (due to post-translational modifications, such as glycosylation) of the human blood plasma proteome severely challenge the capabilities of existing analytical methodologies. Here, we describe an approach for broad analysis of human plasma N-glycoproteins using a combination of immunoaffinity subtraction and glycoprotein capture to reduce both the protein concentration range and the overall sample complexity. Six high-abundance plasma proteins were simultaneously removed using a pre-packed, immobilized antibody column. N-linked glycoproteins were then captured from the depleted plasma using hydrazide resin and enzymatically digested, and the bound N-linked glycopeptides were released using peptide-N-glycosidase F (PNGase F). Following strong cation exchange (SCX) fractionation, the deglycosylated peptides were analyzed by reversed-phase capillary liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). Using stringent criteria, a total of 2053 different N-glycopeptides were confidently identified, covering 303 nonredundant N-glycoproteins. This enrichment strategy significantly improved detection and enabled identification of a number of low-abundance proteins, exemplified by interleukin-1 receptor antagonist protein (approximately 200 pg/mL), cathepsin L (approximately 1 ng/mL), and transforming growth factor beta 1 (approximately 2 ng/mL). A total of 639 N-glycosylation sites were identified, and the overall high accuracy of these glycosylation site assignments as assessed by accurate mass measurement using high-resolution liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) is initially demonstrated.
DrugBank Data that Cites this Article
- Polypeptides
Name UniProt ID Coagulation factor XIII A chain P00488 Details Coagulation factor VIII P00451 Details Vascular endothelial growth factor receptor 3 P35916 Details Coagulation factor V P12259 Details Prothrombin P00734 Details Carcinoembryonic antigen-related cell adhesion molecule 1 P13688 Details Dopamine beta-hydroxylase P09172 Details Corticosteroid-binding globulin P08185 Details Angiotensin-converting enzyme P12821 Details Transcobalamin-1 P20061 Details Antithrombin-III P01008 Details Transthyretin P02766 Details Vitamin K-dependent protein C P04070 Details Integrin alpha-IIb P08514 Details Mast/stem cell growth factor receptor Kit P10721 Details Low-density lipoprotein receptor P01130 Details Serotransferrin P02787 Details Thyroxine-binding globulin P05543 Details Fibrinogen alpha chain P02671 Details Sex hormone-binding globulin P04278 Details Voltage-dependent calcium channel subunit alpha-2/delta-1 P54289 Details Heparin cofactor 2 P05546 Details Macrophage colony-stimulating factor 1 receptor P07333 Details Dipeptidyl peptidase 4 P27487 Details Complement C5 P01031 Details Lysosomal alpha-glucosidase P10253 Details Alpha-2-macroglobulin P01023 Details Alpha-1-acid glycoprotein 1 P02763 Details Serum paraoxonase/arylesterase 1 P27169 Details Cathepsin D P07339 Details Vitamin K-dependent protein S P07225 Details Alpha-1-antitrypsin P01009 Details Tissue factor pathway inhibitor P10646 Details Insulin-like growth factor-binding protein 3 P17936 Details Beta-glucuronidase P08236 Details Transforming growth factor beta-1 proprotein P01137 Details Amine oxidase [copper-containing] 3 Q16853 Details Kininogen-1 P01042 Details Coagulation factor XI P03951 Details Basement membrane-specific heparan sulfate proteoglycan core protein P98160 Details Integrin beta-2 P05107 Details Angiotensinogen P01019 Details Vitronectin P04004 Details Myeloperoxidase P05164 Details Aminopeptidase N P15144 Details Neutrophil gelatinase-associated lipocalin P80188 Details Intercellular adhesion molecule 1 P05362 Details CD44 antigen P16070 Details Vascular cell adhesion protein 1 P19320 Details Alpha-2-antiplasmin P08697 Details Ceruloplasmin P00450 Details Integrin beta-3 P05106 Details Fibronectin P02751 Details Serum amyloid P-component P02743 Details ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 Q10588 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 beta-1 P07942 Details Laminin subunit gamma-1 P11047 Details Prolow-density lipoprotein receptor-related protein 1 Q07954 Details Plasma serine protease inhibitor P05154 Details Asialoglycoprotein receptor 2 P07307 Details Neuropilin-1 O14786 Details Fibroblast growth factor receptor 1 P11362 Details Procathepsin L P07711 Details Cholinesterase P06276 Details Glutamyl aminopeptidase Q07075 Details Plasma kallikrein P03952 Details Plasma protease C1 inhibitor P05155 Details Beta-2-glycoprotein 1 P02749 Details Zinc-alpha-2-glycoprotein P25311 Details Integrin beta-4 P16144 Details Scavenger receptor cysteine-rich type 1 protein M130 Q86VB7 Details Leptin receptor P48357 Details Amyloid-beta precursor protein P05067 Details Cadherin-5 P33151 Details Carboxypeptidase B2 Q96IY4 Details Complement C3 P01024 Details Carboxypeptidase N subunit 2 P22792 Details Alpha-mannosidase 2 Q16706 Details Prolyl endopeptidase FAP Q12884 Details Cholesteryl ester transfer protein P11597 Details Monocyte differentiation antigen CD14 P08571 Details Serum paraoxonase/lactonase 3 Q15166 Details Receptor-type tyrosine-protein phosphatase S Q13332 Details Integrin beta-1 P05556 Details BDNF/NT-3 growth factors receptor Q16620 Details Carbonic anhydrase-related protein 11 O75493 Details Alpha-1-acid glycoprotein 2 P19652 Details Aggrecan core protein P16112 Details Apolipoprotein M O95445 Details Poliovirus receptor P15151 Details Tyrosine-protein kinase Mer Q12866 Details N-acetylmuramoyl-L-alanine amidase Q96PD5 Details Carboxypeptidase Q Q9Y646 Details Coagulation factor XII P00748 Details Complement C4-A P0C0L4 Details Interleukin-1 receptor antagonist protein P18510 Details Transferrin receptor protein 1 P02786 Details Apolipoprotein D P05090 Details Selenoprotein P P49908 Details Afamin P43652 Details Neural cell adhesion molecule L1 P32004 Details Macrophage receptor MARCO Q9UEW3 Details Alpha-1B-glycoprotein P04217 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 Leucine-rich alpha-2-glycoprotein P02750 Details Lumican P51884 Details Kallistatin P29622 Details Pigment epithelium-derived factor P36955 Details Apolipoprotein L1 O14791 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 H3 Q06033 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 A disintegrin and metalloproteinase with thrombospondin motifs 13 Q76LX8 Details UDP-glucuronosyltransferase 2B10 P36537 Details Phospholipid transfer protein P55058 Details Lysophosphatidic acid receptor 4 Q99677 Details Nucleoside diphosphate phosphatase ENTPD5 O75356 Details Prostaglandin-H2 D-isomerase P41222 Details Apolipoprotein B-100 P04114 Details Hemopexin P02790 Details Histidine-rich glycoprotein P04196 Details Haptoglobin P00738 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