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. A2I7N2 LPENVT(HexNAc)PEEQHK 541.9304 (3+)  *  Thr-31   SERPINA3-6

4. A5PK77 Thr-387 630.6404 (3+) SLNAT(HexNAc)SAPHAGFNRPF   *  SERPINA11 protein Identification from HCD, site assignment from ETD

6. VAHAT(HexNAc)APPASLGIH A5PKA3 Thr-89 515.6072(3+)   *   CCDC80 protein

8. A6QLD8 Thr-605 780.0562(3+) QYVISSPPPNLENPT(HexNAc)PEPR  *  ADAMTSL4 protein

10. E1BB91Uncharacterized protein Thr-2929 557.3142(3+)    * TAT(HexNAc)ARPAAAAKPAAAK From Orbitrap Elite Similar to Collagen alpha-3(VI) chain

12. E1BCW0Uncharacterized protein IQPPPT(HexNAc)EALLT(HexNAc)LPGPT(HexNAc)AAGPAGR Thr-355, Thr-360 & Thr-365    * 945.4916(3+) Similar to Hepatocyte growth factor activator

14. Ser-50 E1BI67Uncharacterized protein APC(Carbamidomethyl)S(HexNAc)SRPLALPAAK 547.9600(3+)    * Similar to human Interleukin-18-binding protein

16. Thr-429 E1BKQ9Uncharacterized protein    * 472.5819(3+) IDAT(HexNAc)LSPRDPK Similar to human Polypeptide N- acetylgalactosaminyltransferase 5

18. F1MER7Uncharacterized protein Thr-3374 954.8297(3+) GPSGSLPAT(HexNAc)PAPAGSAPTVQVTPQLETK   *  Similar to human Basement membrane-specific heparan sulfate proteoglycan core protein

20. F1MMK9Uncharacterized protein Thr-198 GEC(Carbamidomethyl)VPGEQDPVPT(HexNAc)PVSR  * cmCys!  676.3133(3+) Similar to human Protein AMBP

22. F1N1I6Uncharacterized protein Thr-27 & Thr-34 572.6365(3+)    * LAT(HexNAc)PARPGAT(HexNAc)QAR Similar to human Gelsolin

24. Uncharacterized proteinF1N1I6 VT(HexNAc)EARPGSMVVEHPEFLK Thr-44 558.0357(4+)    Similar to human Gelsolin

26. O18977Tenascin-X Thr-3146 or Thr-3147 RVGPASTVGVTASLT(HexNAc)TERPLAPR  635.6015(4+)  

27. The green assignments indicate glycosylation of Thr-1346.

28. P00735Prothrombin Thr-193 844.7391(3+) EEC(Carbamidomethyl)SVPVC(Carbamidomethyl)GQDRVT(HexNAc)VEVIPR   *

30. P00735Prothrombin Thr-205 SGGSTT(HexNAc)SQSPLLETC(Carbamidomethyl)VPDR  732.3419(3+) *  

31. Fragments in blue support the site assignment

32. SGGSTTS(HexNAc)QSPLLETC(Carbamidomethyl)VPDRGR 803.3839(3+) ProthrombinP00735 Thr-205 & Ser-206, mixture!   *

33. The blue assignments indicate Thr-205 as the modification site, the green fragments identify Ser-206 glycosylated.

34. P01030Complement C4 987.8339(3+) Thr-420 DIGDKLYWGSVTTSPSNVLSPT(HexNAc)PAPR   

35. Fragments in green identify Ser-418 as the modification site, fragments in blue place the carbohydrate on Thr-420. HCD data also confirm the site as Thr-420: y 6 was detected modified.

36. P01044Kininogen-1 Thr-586 555.9546(3+) KLISDFPET(HexNAc)TSPK     

38. P02672Fibrinogen alpha chain Thr-464 493.2675(3+) VITKTVT(HexNAc)NADGR  *

40. P02672Fibrinogen alpha chain SSHEFDGRT(HexNAc)GLAPEFAA Thr-525    *  665.6400(3+)

42. P06868Plasminogen TIPSC(Carbamidomethyl)ESSPLST(HexNAc)ER 883.9084(2+) Thr-366  

44. P06868Plasminogen 1025.4580(3+) Thr-378 MDVPVPPEQT(HexNAc)PVPQDC(Carbamidomethyl)YHGNGQSYR   

46. P07224Vitamin K-dependent protein S Thr-104 584.6357(3+) TAARLST(HexNAc)NAYPDLR  

48. P07456 Thr-99 (& Thr-106) 814.3936(3+) DVSASTT(HexNAc)VLPDDVT(HexNAc)AYPVGK   Insulin-like growth factor 2

50. P07456 (Ser-154, Thr-163 &) Thr-168 S(HexNAc)HRPLIALPT(HexNAc)QDPAT(HexNAc)HGGASSK Insulin-like growth factor 2  570.8846(5+)    

52. P07456Insulin-like growth factor 2 (Thr-163) & Ser-174 ALPT(HexNAc)QDPATHGGASS(HexNAc)K 648.6398(3+)    * 

54. P12763Alpha-2-HS-glycoprotein Thr-217 606.9723(3+)    EVVDPT(HexNAc)KC(Carbamidomethyl)NLLAEK

56. P12763Alpha-2-HS-glycoprotein Thr-314 618.7888(2+) HT(HexNAc)FSGVASVE  

58. P12763Alpha-2-HS-glycoprotein   Ser-320 618.7886(2+) HTFSGVAS(HexNAc)VE 

60. Alpha-2-HS-glycoproteinP12763   646.6395(3+) Ser-324 SGVASVESS(HexNAc)SGEAFHVGK

62. Alpha-2-HS-glycoproteinP12763 Ser-325 SGVASVESSS(HexNAc)GEAFHVGK 646.6392(3+)  

64. P17690Beta-2-glycoprotein 1 Ser-32 (& Thr-33) TC(Carbamidomethyl)PKPDELPFS(HexNAc)T(HexNAc)VVPLKR   623.3235(4+)  

66. GKFTDFWESATSPT(HexNAc)QSPP (Ser-90 or) Thr-92 P19035Apolipoprotein C-III 729.3362(3+)   *

67. The green assignment indicates modification on Ser-90 (though the presence of b 13 is very unlikely), while the blue assignment identifies Thr-92 as the glycosylation site.

68. FSPVST(HexNAc)M(Oxidation)EPLDLQLM(Oxidation)DGQAQQK Ser-24 or Ser-27 or Thr-28 P28800Alpha-2-antiplasmin 900.0894(3+)   * 

69. The green assignment indicates modification on Ser-24, the pink assignment puts the modification to Thr-28. The ion is very weak, thus, the site assignment is ambiguous.

70. P28800Alpha-2-antiplasmin LSEAGVQAAAAT(HexNAc)STAMSR Thr-398     962.9673(2+)

72. P28800Alpha-2-antiplasmin Thr-400 SALELSEAGVQAAAATST(HexNAc)AMSR 775.7141(3+)  

74. P28800Alpha-2-antiplasmin Ser-489 LGPPSEEDYAQPS(HexNAc)SPK 952.9440(2+)   

75. The fragment in green identifies Ser-489 as the modification site.

76. P50448Factor XIIa inhibitor 681.8776(2+) TVVPATVTKPF+HexNAc y 8G (2+) y 8G

77. This HCD spectrum identified this NON-tryptic glycopeptide

78. Factor XIIa inhibitorP50448 TVVPATVT(HexNAc)KPF The following ETD spectrum was good enough for site assignment. Thr-74 z5*z5* z6z6 z7z7   c8c8 c 10 * 681.8776(2+)

79. P81187Complement factor B T(HexNAc)PLPEAGPQSPC(Carbamidomethyl)SLEGVEIKGGSFR Thr-26 939.4554(3+)   * 

81. P81644Apolipoprotein A-II FQT(HexNAc)VADYGKDLVEK Thr-40 605.9726(3+)   *