Table I.
N-Linked glycosite information for each protein identified via the CSC technology
The table lists the protein number (corresponds to supplemental Table S1), the protein name, the number of N-linked glycosylation sites confirmed in the current study, the number of potential N-linked glycosylation sites annotated in Swiss-Prot, whether these N-linked sites listed in Swiss-Prot are potential (i.e. the protein contains the NX(S/T) motif but no experimental evidence is available) or whether there is experimental (exp) evidence, and whether the glycopeptides identified in the current study are consistent with the extracellular domain (i.e. orientation) annotated in Swiss-Prot. Proteins are sorted by the number of potential N-linked glycosylation sites in increasing order. Y, observed glycopeptides map to predicted extracellular domain; N, observed glycopeptides map to predicted intracellular domain; NA, not applicable due to GPI or ECM; Amb, annotation regarding orientation is ambiguous. MHC, major histocompatibility complex.
| Protein number | Protein name | No. identified sites | No. potential sitesa | No. sites with exp evidence | Orientation consistent? | Protein number | Protein name | No. identified sites | No. potential sitesa | No. sites with exp evidence | Orientation consistent? |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 45 | Solute carrier family 2, facilitated glucose transporter member 1 | 1 | 1 | 0 | Y | 9 | CD80 antigen | 5 | 6 | 0 | Y |
| 63 | Sphingosine 1-phosphate receptor 2 (Edg-5) | 1 | 1 | 0 | Y | 15 | Ectonucleotide pyrophosphatase/phosphodiesterase family member 1 | 3 | 6 | 0 | Y |
| 70 | Ephrin-A5 | 1 | 1 | 1 | NA | 35 | Neural cell adhesion molecule 1 | 1 | 6 | 1 | Y |
| 87 | Lipid phosphate phosphohydrolase 2 | 1 | 1 | 0 | Amb | 37 | Neuroplastin | 3 | 6 | 1 | Y |
| 95 | Solute carrier family 2, facilitated glucose transporter member 3 | 1 | 1 | 0 | Y | 48 | Transmembrane protein 16F | 3 | 6 | 0 | Y |
| 99 | Mast cell antigen 32 | 1 | 1 | 0 | Y | 96 | Tyrosine-protein kinase receptor UFO | 1 | 6 | 0 | Y |
| 113 | Sphingosine 1-phosphate receptor 5 or 8 | 1 | 1 | 0 | Y | 102 | Cleft lip and palate transmembrane protein 1 homolog | 1 | 6 | 0 | Y |
| 117 | Ephrin-B1 | 1 | 1 | 0 | Y | 114 | OX-2 membrane glycoprotein | 1 | 6 | 0 | Y |
| 123 | Aquaporin-1 | 1 | 1 | 0 | Y | 128 | Calcitonin gene-related peptide type 1 | 1 | 6 | 0 | Y |
| 125 | Myelin protein zero-like protein 1 | 1 | 1 | 0 | Y | 10 | CD97 antigen | 3 | 7 | 0 | Y |
| 3 | Adipocyte adhesion molecule | 1 | 2 | 0 | Y | 25 | Hematopoietic progenitor cell antigen CD34 | 1 | 7 | 0 | Y |
| 18 | Ephrin type-A receptor 2 | 2 | 2 | 0 | Y | 33 | N-Acetylated α-linked acidic peptidase 2 | 3 | 7 | 0 | Y |
| 20 | Excitatory amino acid transporter 1 | 2 | 2 | 0 | Y | 56 | Poliovirus receptor-related protein 1 | 2 | 7 | 0 | Y |
| 21 | Junctional adhesion molecule A | 1 | 2 | 0 | Y | 73 | Latrophilin 2 | 1 | 7 | 0 | Y |
| 44 | Sodium/potassium-transporting ATPase subunit β-3 | 1 | 2 | 0 | Y | 86 | VPS10 domain-containing receptor SorCS2 | 1 | 7 | 0 | Y |
| 46 | Translocon-associated protein α | 1 | 2 | 0 | Y | 103 | Cadherin-2 | 1 | 7 | 0 | Y |
| 47 | Transmembrane 4 L6 family member 1 | 1 | 2 | 0 | Y | 112 | Plexin A1 | 1 | 7 | 0 | Y |
| 52 | Zinc transporter ZIP10 | 2 | 2 | 0 | Y | 119 | Emilin-1 | 2 | 7 | 0 | NA |
| 59 | Junctional adhesion molecule C | 1 | 2 | 0 | Y | 1 | 4F2 cell surface antigen heavy chain | 4 | 8 | 0 | Y |
| 62 | Solute carrier family 12 member 2 | 1 | 2 | 0 | Y | 7 | CD166 antigen | 4 | 8 | 0 | Y |
| 67 | Neutral amino acid transporter A | 2 | 2 | 0 | Y | 23 | Fibronectin | 4 | 8 | 0 | NA |
| 79 | Transmembrane 9 superfamily member 3 | 1 | 2 | 0 | Y | 34 | Neogenin | 2 | 8 | 0 | Y |
| 91 | Glypican-1 | 2 | 2 | 0 | NA | 42 | Prostaglandin F2 receptor negative regulator | 2 | 8 | 0 | Y |
| 104 | Trophoblast glycoprotein | 1 | 2 | 0 | Y | 16 | Embigin | 8 | 9 | 0 | Y |
| 107 | Major prion protein | 1 | 2 | 0 | NA | 17 | Endothelin-converting enzyme 1 | 3 | 10 | 0 | Y |
| 109 | Tetraspanin-4 | 1 | 2 | 0 | Y | 60 | Tyrosine-protein kinase-like 7 | 2 | 10 | 0 | Y |
| 120 | Transmembrane protein 87A | 2 | 2 | 0 | Y | 122 | Epidermal growth factor receptor | 1 | 10 | 3 | Y |
| 6 | Basigin | 2 | 3 | 0 | Y | 30 | Integrin αV | 4 | 11 | 0 | Y |
| 12 | Choline transporter-like protein 2 | 2 | 3 | 0 | Y | 39 | β-type platelet-derived growth factor receptor | 3 | 11 | 0 | Y |
| 19 | Ephrin type-B receptor 4 | 1 | 3 | 0 | Y | 97 | Lysosome membrane protein 2 | 1 | 11 | 0 | Y |
| 24 | H-1 class I histocompatability antigen, D-K α chain | 2 | 3 | 0 | Y | 5 | Basement membrane-specific heparan sulfate proteoglycan core protein | 4 | 12 | 0 | NA |
| 32 | Macrophage mannose receptor 2 | 2 | 3 | 0 | Y | 31 | Integrin β1 | 2 | 12 | 0 | Y |
| 57 | Protein ITFG3 | 3 | 3 | 0 | Y | 38 | Oncostatin M-specific receptor subunit β | 3 | 12 | 0 | Y |
| 80 | Epithelial membrane protein 1 | 1 | 3 | 0 | Amb | 94 | Receptor-type tyrosine-protein phosphatase μ | 1 | 12 | 0 | Y |
| 81 | Synaptophysin-like protein 1 | 1 | 3 | 0 | Y | 4 | Aminopeptidase N | 5 | 13 | 0 | Y |
| 105 | β-Sarcoglycan | 1 | 3 | 0 | Y | 27 | Integrin α3 | 6 | 13 | 0 | Y |
| 106 | LMBR1 domain-containing 1 | 1 | 3 | 0 | Y | 74 | Lymphocyte antigen 75 | 1 | 13 | 0 | Y |
| 108 | CMP-N-acetylneuraminate-β-galactosamide-α-2,3-sialyltransferase | 1 | 3 | 0 | Y | 28 | Integrin α5 | 5 | 14 | 0 | Y |
| 110 | Immunoglobulin superfamily member 3 | 1 | 3 | 0 | Y | 13 | Chondroitin sulfate proteoglycan 4 | 5 | 15 | 0 | Y |
| 115 | Anthrax toxin receptor 1 | 1 | 3 | 0 | Y | 65 | Integrin α11 | 1 | 16 | 0 | Y |
| 127 | Cadherin-10 | 1 | 3 | 0 | Y | 88 | Insulin-like growth factor 1 receptor | 2 | 16 | 0 | Y |
| 11 | Cell adhesion molecule 1 | 2 | 4 | 0 | Y | 69 | Teneurin-3 | 2 | 17 | 0 | Y |
| 61 | CD82 antigen | 2 | 4 | 0 | Y | 98 | Leucyl-cystinyl aminopeptidase | 1 | 17 | 0 | Y |
| 64 | Tissue factor | 2 | 4 | 0 | Y | 68 | Lysosomal membrane glycoprotein 1 | 1 | 18 | 2 | Y |
| 77 | Solute carrier family 12 member 7 | 1 | 4 | 0 | Y | 72 | Insulin receptor | 1 | 18 | 0 | Y |
| 78 | Solute carrier family 12, member 4 | 1 | 4 | 0 | Y | 92 | Cation-independent mannose 6-phosphate receptor | 1 | 20 | 0 | Y |
| 83 | Ephrin type-B receptor 2 | 1 | 4 | 0 | Y | 126 | Tenascin | 1 | 20 | 1 | NA |
| 84 | Thrombomodulin | 1 | 4 | 0 | Y | 82 | Probable G-protein-coupled receptor 126 | 1 | 23 | 0 | Y |
| 85 | Thrombospondin-1 | 1 | 4 | 0 | NA | 41 | Prolow density lipoprotein receptor-related protein 1 | 3 | 51 | 0 | Y |
| 100 | Kin of IRRE-like protein 1 | 1 | 4 | 0 | Y | 22 | Fat 1 cadherin | 3 | 0 (30)a | 0 | Amb |
| 101 | Tetraspanin-3 | 1 | 4 | 0 | Y | 76 | Protein unc-84 homolog B | 1 | 0 (1)a | 0 | Amb |
| 118 | Transmembrane protein 87B | 1 | 4 | 0 | Y | 14 | Collectin-12 | 4 | 0 (12)a | 0 | Y |
| 2 | Acid sphingomyelinase-like phosphodiesterase 3b | 2 | 5 | 0 | NA | 40 | Plexin B2 | 6 | 0 (15)a | 0 | Amb |
| 29 | Integrin α7 | 1 | 5 | 0 | Y | 49 | Transmembrane protein 2 | 2 | 0 (15)a | 0 | Amb |
| 36 | Neuropilin-1 | 2 | 5 | 0 | Y | 116 | Claudin domain-containing protein 1 | 1 | 0 (2)a | 0 | Amb |
| 50 | Vascular cell adhesion protein 1 (isoform 1) | 2 | 5 | 0 | Y | 66 | MHC H-2K-k protein | 1 | 0 (3)a | 0 | Amb |
| 51 | Voltage-dependent calcium channel subunit α-2/δ-1 | 3 | 5 | 0 | Y | 90 | Neurotrophin receptor-associated death domain | 1 | 0 (3)a | 0 | Amb |
| 54 | Cadherin-15 | 2 | 5 | 0 | Y | 93 | Protocadherin 7 | 1 | 0 (3)a | 0 | Amb |
| 55 | Cation-dependent mannose 6-phosphate receptor | 1 | 5 | 0 | Y | 26 | Immunoglobulin superfamily containing leucine-rich repeat region | 2 | 0 (4)a | 0 | Amb |
| 58 | Golgi apparatus protein 1 | 2 | 5 | 0 | Y | 53 | Zinc transporter ZIP14 | 2 | 0 (5)a | 0 | N |
| 71 | Fibroblast growth factor receptor 4 | 1 | 5 | 0 | Y | 89 | cDNA sequence BC051070 | 1 | 0 (5)a | 0 | Amb |
| 75 | P2X purinoceptor 7 | 1 | 5 | 0 | Y | 43 | Protocadherin γ C3 | 1 | 0 (8)a | 0 | Amb |
| 111 | Zinc transporter ZIP6 | 1 | 5 | 0 | Y | 121 | Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit STT3B | 3 | 0 (8)a | 0 | Amb |
| 124 | Semaphorin-7A | 1 | 5 | 0 | NA | 8 | CD276 antigen | 2 | 1 (4)a | 0 | Y |
a If no N-linked glycosylation sites are predicted in Swiss-Prot or if fewer are predicted than were observed, then the number of predicted N-linked glycosylation sites from EnsembleGly is provided. The first number is from Swiss-Prot; the number in parentheses is from EnsembleGly.