1. Legends For ETD data In the spectra  = precursor ions, charge-reduced ones too; * = charge-reduced ion from a coeluting precursor ion with different, usually (2+), charge;  = 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. Q03247Apolipoprotein E DM(Oxidation)EGELGPEEPLT(HexNAc)T(HexNAc)QQPR Thr-31 (& Thr-32) 817.0358(3+)  

4. Apolipoprotein EQ03247 Thr-307     * 541.2650(3+) LRPS(HexNAc)PTSPPSENH

6. Q05717Insulin-like growth factor-binding protein 5 Thr-171 486.9032(3+)    * FVGGAENT(HexNAc)AHPR

8. Q28083Collagen alpha-1(XI) chain (Fragment) Thr-86 NYGTESYQT(HexNAc)EAPR   859.8793(2+)

10. Q28107Coagulation factor V Ser-1151 & Thr-1154 759.0452(3+)    * RS(HexNAc)PPT(HexNAc)QPSQIPNYDLR

12. HCD ETD 860.4367(2+)    AIPT(HexNAc)DVSQIFPSLE c7*c7*z9*z9* z 11 c9*c9* c8*c8* b 10 c 11 c 12 c 13 z 10 Q28107Coagulation factor V Thr-1171

13. 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.

14. HCD 428.2453(3+) EAPLTPKVPK+HexNAc Thr-696 Q29RQ1Complement component C7

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

16. Q32KM8Augurin 943.9625(2+) Thr-47 EAPAPT(HexNAc)MTPVAVQESR   

18. Q32PI4Complement factor I 747.8566(4+) Thr-57 ETEASSEVKPT(HexNAc)STQDTSQKDFVDKK  

20. Q3MHN2Complement component C9 Thr-24 & Ser-26 GPT(HexNAc)PS(HexNAc)YDPAERQGTPLPIDC(Carbamidomethyl)R 911.7614(3+)   * 

22. FQSPT(HexNAc)PNTLMPVVPAAS(HexNAc)PT(HexNAc)PPVRR Thr-270 & Ser-282 & Thr-284 Q3SWW8Thrombospondin-4 793.1561(4+)    

24. HCD ETD 1010.9789(2+) Q3SYR5Apolipoprotein C-IV Thr-35 Q(Gln->pyro-Glu)QEEPEGT(HexNAc)LSPQPAPAR    y 11 y 15 z 16 y 14 y 13 * z 15 * z8*z8* y8y8 y 10

25. 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.

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

28. 1078.4978(3+) Ser-677 (& Ser-683; & Ser-686 or Thr-688) LMS(HexNAc)PLAPAS(HexNAc)APS(HexNAc)PTSGPGGASHDTDFR    Q3T052 Q5EA67 Inter-alpha-trypsin inhibitor heavy chain H4

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

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

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

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

34. 604.2604(3+) (Thr-688) & Thr-698 T(HexNAc)SGPGGASHDT(HexNAc)DFR   *  Q3T052 Q5EA67 Inter-alpha-trypsin inhibitor heavy chain H4

36. VitronectinQ3ZBS7 Thr-63 570.6102(3+) AEC(Carbamidomethyl)KPQVT(HexNAc)RGDVF   *  

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

38. Q3ZBS7Vitronectin Thr-97 & Thr-98 QPEST(HexNAc)T(HexNAc)LAPVLQ   *  845.4210(2+)

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

40. AQT(HexNAc)LETPVQAPVLNPEK Thr-107 Q3ZBS7Vitronectin 680.0245(3+)  

42. Q3ZBS7Vitronectin GDSEPGMGTSDLGT(HexNAc)SESPAEEETC(Carbamidomethyl)SGKPF Thr-142 or Ser-143  1054.7689(3+) 

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

44.   925.4483(2+) Thr-408 Q58D34Peptidase inhibitor 16 SLSNSPSASAT(HexNAc)ANAVGGR

46. T(HexNAc)S(HexNAc)PPQPAARPSSLL 914.4683(2+) Q58D62Fetuin B Thr-19 & Thr-20    *

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

48. Q58D62Fetuin B Thr-157 723.9690(3+)   TC(Carbamidomethyl)PDC(Carbamidomethyl)PS(HexNAc)TSPYDLSNPR

50. Q58D62Fetuin B Thr-173 FM(Oxidation)ETAT(HexNAc)ESLAK 723.8355(2+)  

52. Fetuin BQ58D62 Ser-262 SFFNS(HexNAc)QAPTPR 727.8453(2+)  

54. Fetuin BQ58D62 Thr-273 GENAT(HexNAc)VNQRPANPSK    595.9606(3+)

56. Q58D62Fetuin B (Thr-295) & Thr-299 777.0660(3+) LQQQNTAPT(HexNAc)NSPT(HexNAc)KAVPK    *

58. AGSLTPEST(HexNAc)GAPVEEEDPFFK Thr-34 Q95121Pigment epithelium-derived factor  804.3722(3+)  

60. TEGSTT(HexNAc)VSVPHS z6* z5* c6 z7 c8* z8* z9* c11 z11 z10 -HexNAc 702.8290(2+) F1MNV4This UniProt entry (recently deleted) indicated a Leu -> Val substitution at position-403 of kininogen-1, here we show ETD data confirming the mutation *  

62. TEGSTTVSVPHS + HexNAc HexNAc y3 y4 y5 y2 b2 y10 b9-2xH 2 O 702.8290(2+) F1MNV4 This UniProt entry (recently deleted) indicated a Leu -> Val substitution at position-403 of kininogen-1, here we show HCD data confirming the mutation All fragments are within 10 ppm MH +