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Legends

Legends. For ETD data In the spectra v = precursor ions, charge-reduced ones too; * = charge-reduced ion from a coeluting precursor ion with different, usually (2+), charge; m = neutral sugar losses In the sequences residue in bold = corresponding z . or z+1 ion detected;

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Legends

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  1. Legends For ETD data In the spectra • v = precursor ions, charge-reduced ones too; • * = charge-reduced ion from a coeluting precursor ion with different, usually (2+), charge; • m = neutral sugar losses In the sequences • residue in bold = corresponding z. or z+1 ion detected; • residue underlined = corresponding c or c-1. ion detected; For both HCD and ETD data The Table following the spectra contains all the masses used in the database search (Protein Prospector uses the 20 most abundant ions from each half of the spectra) as well as their assignments

  2. Apolipoprotein E Q03247 Thr-31 (& Thr-32) v 817.0358(3+) m DM(Oxidation)EGELGPEEPLT(HexNAc)T(HexNAc)QQPR

  3. Apolipoprotein E Q03247 Thr-307 v 541.2650(3+) v v m * LRPS(HexNAc)PTSPPSENH

  4. Insulin-like growth factor-binding protein 5 Q05717 Thr-171 v 486.9032(3+) v * m v FVGGAENT(HexNAc)AHPR

  5. Collagen alpha-1(XI) chain (Fragment) Q28083 Thr-86 v 859.8793(2+) v NYGTESYQT(HexNAc)EAPR

  6. Coagulation factor V Q28107 Ser-1151 & Thr-1154 v 759.0452(3+) v * m RS(HexNAc)PPT(HexNAc)QPSQIPNYDLR

  7. Coagulation factor V Q28107 Thr-1171 HCD 860.4367(2+) v ETD c13 z11 c9* c12 v c8* c11 b10 m c7* z9* z10 AIPT(HexNAc)DVSQIFPSLE

  8. The glycopeptide was identified from HCD data with a HexNAc neutral loss, as presented below, mass differences are in ppm. Site assignment from ETD as presented above.

  9. Complement component C7 Q29RQ1 Thr-696 HCD 428.2453(3+) EAPLTPKVPK+HexNAc

  10. The glycopeptide was identified from HCD data with a HexNAc neutral loss, as presented below, mass differences are in ppm. Single potential site.

  11. Augurin Q32KM8 Thr-47 v 943.9625(2+) v m EAPAPT(HexNAc)MTPVAVQESR

  12. Complement factor I Q32PI4 Thr-57 v 747.8566(4+) v ETEASSEVKPT(HexNAc)STQDTSQKDFVDKK

  13. Complement component C9 Q3MHN2 Thr-24 & Ser-26 v 911.7614(3+) v m * GPT(HexNAc)PS(HexNAc)YDPAERQGTPLPIDC(Carbamidomethyl)R

  14. Thrombospondin-4 Q3SWW8 Thr-270 & Ser-282 & Thr-284 v 793.1561(4+) v m m FQSPT(HexNAc)PNTLMPVVPAAS(HexNAc)PT(HexNAc)PPVRR

  15. Apolipoprotein C-IV Q3SYR5 Thr-35 1010.9789(2+) HCD v ETD y8 y13 y10 z15* z16 m y15 z8* y11 m * y14 Q(Gln->pyro-Glu)QEEPEGT(HexNAc)LSPQPAPAR

  16. The glycopeptide was identified from HCD data with a HexNAc neutral loss, as presented below, mass differences are in ppm. Site assignment from ETD as presented above.

  17. Inter-alpha-trypsin inhibitor heavy chain H4 Q3T052 Q5EA67 Ser-629 & Ser-635 v 566.2913 (4+) v v FGHS(HexNAc)VGDRTS(HexNAc)RKPGGGLK

  18. Inter-alpha-trypsin inhibitor heavy chain H4 Q3T052 Q5EA67 Ser-677 (& Ser-683; & Ser-686 or Thr-688) v v m 1078.4978(3+) LMS(HexNAc)PLAPAS(HexNAc)APS(HexNAc)PTSGPGGASHDTDFR

  19. Different colors indicate ambiguity about the site assignment: green supports Ser-686; blue indicates sugar on Thr-688.

  20. Inter-alpha-trypsin inhibitor heavy chain H4 Q3T052 Q5EA67 (Ser-683) & Ser-686 & Thr-688 & Ser-689 v v 909.7225(3+) m * AS(HexNAc)APS(HexNAc)PT(HexNAc)S(HexNAc)GPGGASHDTDFR

  21. Inter-alpha-trypsin inhibitor heavy chain H4 Q3T052 Q5EA67 (Thr-688 or Ser-689) & Ser-695 v 604.2606(3+) v m * T(HexNAc)SGPGGAS(HexNAc)HDTDFR

  22. Different colors indicate ambiguity about the site assignment: green supports Thr-688; blue indicates sugar on Ser-689.

  23. Inter-alpha-trypsin inhibitor heavy chain H4 Q3T052 Q5EA67 (Thr-688) & Thr-698 v 604.2604(3+) m v * T(HexNAc)SGPGGASHDT(HexNAc)DFR

  24. Vitronectin Q3ZBS7 Thr-63 v 570.6102(3+) * m v m AEC(Carbamidomethyl)KPQVT(HexNAc)RGDVF

  25. Both ends non-tryptic! Precursor mass error = -0.15 ppm Score = 26.3; E = 2.9e-4

  26. Vitronectin Q3ZBS7 Thr-97 & Thr-98 v 845.4210(2+) m * v QPEST(HexNAc)T(HexNAc)LAPVLQ

  27. both ends non-tryptic! Precursor mass error = -4.8 ppm Score = 28.6; E = 4.5e-4

  28. Vitronectin Q3ZBS7 Thr-107 v 680.0245(3+) m AQT(HexNAc)LETPVQAPVLNPEK

  29. Vitronectin Q3ZBS7 Thr-142 or Ser-143 v 1054.7689(3+) m v GDSEPGMGTSDLGT(HexNAc)SESPAEEETC(Carbamidomethyl)SGKPF

  30. Fragments in green indicate that the site of modification may be Thr-142.

  31. Peptidase inhibitor 16 Q58D34 Thr-408 v 925.4483(2+) v SLSNSPSASAT(HexNAc)ANAVGGR

  32. Fetuin B Q58D62 Thr-19 & Thr-20 v 914.4683(2+) v m * T(HexNAc)S(HexNAc)PPQPAARPSSLL

  33. both ends are non-tryptic Precursor mass error = -2.3 ppm Score = 22.1; E = 0.012

  34. Fetuin B Q58D62 Thr-157 v 723.9690(3+) m TC(Carbamidomethyl)PDC(Carbamidomethyl)PS(HexNAc)TSPYDLSNPR

  35. Fetuin B Q58D62 Thr-173 v 723.8355(2+) v FM(Oxidation)ETAT(HexNAc)ESLAK

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