Table II. N-Linked sialoglycopeptide changes in human breast cancer tissues were compared with noncancerous tissues using spectral counting.
The altered sialoglycopeptides were compared with total N-linked glycopeptides isolated from the same tissues.
| IPI | Protein name | Peptide sequencee | Pa | SGb |
TGb |
CA/NCd |
|||
|---|---|---|---|---|---|---|---|---|---|
| CAc | NCc | CAc | NCc | SG | TG | ||||
| Consistent changes in SG and TG | |||||||||
| IPI00000877 | 150-kDa oxygen-regulated protein | R.VFGSQN↓LTTVK.L | 1.00 | 6 | 1 | 10 | 1 | 6.0 | 10.0 |
| IPI00005707 | Urokinase receptor-associated protein UPARAP | R.VTPACN↓TSLPAQR.W | 1.00 | 4 | 2 | 4 | 1 | 2.0 | 4.0 |
| IPI00009030 | Lysosome-associated membrane glycoprotein 2 | M.GLQLN↓ITQDK.V | 1.00 | 2 | 0 | 4 | 0 | 100.0 | 100.0 |
| IPI00009135 | Lymphatic endothelium-specific hyaluronan receptor LYVE-1 | K.ANQQLN↓FTEAK.E | 1.00 | 0 | 4 | 0 | 2 | 0.0 | 0.0 |
| IPI00009802 | Versican core protein | R.FEN↓QTGFPPPDSR.F | 1.00 | 29 | 3 | 28 | 1 | 9.7 | 28.0 |
| IPI00010351 | Macrophage scavenger receptor types I and II | K.VLNN↓ITNDLR.L | 1.00 | 3 | 0 | 4 | 0 | 100.0 | 100.0 |
| IPI00011229 | Cathepsin D | K.GSLSYLN↓VTR.K | 1.00 | 5 | 0 | 9 | 4 | 100.0 | 2.3 |
| IPI00022418 | Fibronectin | R.DQCIVDDITYNVN↓DTFHK.R | 1.00 | 6 | 0 | 7 | 0 | 100.0 | 100.0 |
| IPI00022418 | Fibronectin | Y.NNHN↓YTDCTSEGR.R | 1.00 | 6 | 0 | 6 | 0 | 100.0 | 100.0 |
| IPI00022418 | Fibronectin | R.HEEGHMLN↓CTCFGQGR.G | 1.00 | 20 | 8 | 11 | 7 | 2.5 | 1.6 |
| IPI00022418 | Fibronectin | K.LDAPTNLQFVN↓ETDSTVLVR.W | 1.00 | 14 | 6 | 15 | 7 | 2.3 | 2.1 |
| IPI00023673 | MAC-2-binding protein | K.GLN↓LTEDTYKPR.I | 1.00 | 16 | 6 | 6 | 0 | 2.7 | 100.0 |
| IPI00023673 | MAC-2-binding protein | R.ALGFEN↓ATQALGR.A | 1.00 | 4 | 2 | 7 | 3 | 2.0 | 2.3 |
| IPI00027412 | Carcinoembryonic antigen-related cell adhesion molecule 6 | K.ANYRPGENLN↓LSCH.A | 1.00 | 3 | 0 | 2 | 0 | 100.0 | 100.0 |
| IPI00027827 | Extracellular superoxide dismutase [Cu-Zn] | L.EGFPTEPN↓SSSR.A | 1.00 | 5 | 12 | 0 | 3 | 0.4 | 0.0 |
| IPI00028908 | Nidogen-2 | Y.TQGQQIGYLPLN↓GTR.L | 1.00 | 1 | 3 | 0 | 2 | 0.3 | 0.0 |
| IPI00031008 | Tenascin | K.VEAAQN↓LTLPGSLR.A | 1.00 | 2 | 0 | 4 | 0 | 100.0 | 100.0 |
| IPI00103356 | Integrin-like protein | K.LTN↓NSNQFQTEVGK.Q | 1.00 | 9 | 0 | 5 | 0 | 100.0 | 100.0 |
| IPI00153057 | Asporin | K.ITDIEN↓GSLANIPR.V | 1.00 | 5 | 2 | 7 | 3 | 2.5 | 2.3 |
| IPI00166729 | α-2-Glycoprotein 1, zinc | R.GDVLHNGN↓GTYQ.S | 1.00 | 10 | 5 | 4 | 2 | 2.0 | 2.0 |
| IPI00180844 | CD36 antigen (collagen type I receptor, thrombospondin receptor) | K.EN↓VTQDAEDNTV.S | 1.00 | 14 | 28 | 4 | 7 | 0.5 | 0.6 |
| IPI00180844 | CD36 antigen (collagen type I receptor, thrombospondin receptor) | V.MMN↓SSNIQVK.Q | 1.00 | 3 | 11 | 6 | 15 | 0.3 | 0.4 |
| IPI00180844 | CD36 antigen (collagen type I receptor, thrombospondin receptor) | L.FYPYN↓NTADGVYK.V | 1.00 | 1 | 7 | 5 | 12 | 0.1 | 0.4 |
| IPI00217766 | Scavenger receptor class B, member 2 | V.MYLN↓ESVHIDK.E | 0.96 | 3 | 0 | 4 | 0 | 100.0 | 100.0 |
| IPI00291262 | Clusterin | K.EDALN↓ETR.E | 1.00 | 8 | 3 | 4 | 0 | 2.7 | 100.0 |
| IPI00291262 | Clusterin | K.ELPGVCN↓ETMM.A | 1.00 | 33 | 17 | 16 | 4 | 1.9 | 4.0 |
| IPI00298237 | Tripeptidyl-peptidase I | K.FLSSSPHLPPSSYFN↓ASGR.A | 1.00 | 2 | 1 | 10 | 2 | 2.0 | 5.0 |
| SG changed but TG did not change | |||||||||
| IPI00010274 | α-Tryptase | E.LEEPVN↓ISSR.V | 0.94 | 6 | 11 | 7 | 6 | 0.5 | 1.2 |
| IPI00019399 | Serum amyloid A-4 protein | Y.LFGN↓SSTVLEDSK.S | 1.00 | 5 | 0 | 4 | 3 | 100.0 | 1.3 |
| IPI00020987 | Prolargin | V.ESFQN↓ATGLR.W | 1.00 | 1 | 3 | 6 | 6 | 0.3 | 1.0 |
| IPI00022200 | Collagen α3(VI) chain | R.GPPGVN↓GTQGFQGCPGQR.G | 1.00 | 2 | 6 | 9 | 7 | 0.3 | 1.3 |
| IPI00023824 | Fibulin-2 | K.DVDECALGTHN↓CSEAETCH.N | 1.00 | 2 | 1 | 2 | 2 | 2.0 | 1.0 |
| IPI00024284 | Basement membrane-specific heparan sulfate proteoglycan core protein | R.ALVN↓FTR.S | 1.00 | 8 | 2 | 4 | 4 | 4.0 | 1.0 |
| IPI00101462 | Hypothetical protein | K.YKN↓NSDISSTR.G | 1.00 | 1 | 4 | 3 | 2 | 0.3 | 1.5 |
| IPI00101462 | Hypothetical protein | R.GLTFQQN↓ASSMCVPDQDTAIR.V | 1.00 | 0 | 7 | 2 | 2 | 0.0 | 1.0 |
| IPI00032328 | Kininogen (α-2-thiol proteinase inhibitor) (contains bradykinin) | R.HGIQYFNN↓NTQH.S | 1.00 | 43 | 15 | 14 | 11 | 2.9 | 1.3 |
| IPI00328113 | Fibrillin 1 | R.VLPVN↓VTDYCQLVR.Y | 1.00 | 2 | 4 | 9 | 5 | 0.5 | 1.8 |
| IPI00328113 | Fibrillin 1 | L.DSEERN↓CTDIDECR.I | 1.00 | 3 | 7 | 11 | 8 | 0.4 | 1.4 |
| IPI00328113 | Fibrillin 1 | K.AWGTPCEMCPAVN↓TSEYK.I | 1.00 | 1 | 3 | 2 | 2 | 0.3 | 1.0 |
| IPI00382606 | Factor VII active site mutant immunoconjugate | R.EEQYN↓STYR.V | 1.00 | 5 | 10 | 13 | 16 | 0.5 | 0.8 |
| SG changed but TG showed opposite changes | |||||||||
| IPI00004617 | Ig γ-3 chain C region | R.EQQFN↓STFR.V | 1.00 | 5 | 1 | 1 | 5 | 5.0 | 0.2 |
| IPI00019906 | Basigin | K.ALMN↓GSESR.F | 1.00 | 4 | 2 | 1 | 2 | 2.0 | 0.5 |
| IPI00032258 | Complement C4 (contains C4a anaphylatoxin) | R.GLN↓VTLSSTGR.N | 1.00 | 10 | 3 | 1 | 3 | 3.3 | 0.3 |
a Probability score of peptide.
b SG represents sialoglycopeptides, whereas TG represents total glycopeptides.
c CA stands for cancer, and NC stands for noncancer.
d CA/NC is the ratio of peptide spectral counts from breast cancer versus from noncancer. If the peptides were only detected in breast cancer but not in noncancer, the ratio was assigned to be 100.
e ↓represents identified glycosylation sites.