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

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

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

VAHAT(HexNAc)APPASLGIH A5PKA3 Thr (3+)   *   CCDC80 protein

A6QLD8 Thr (3+) QYVISSPPPNLENPT(HexNAc)PEPR  *  ADAMTSL4 protein

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

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

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

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

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

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

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

Uncharacterized proteinF1N1I6 VT(HexNAc)EARPGSMVVEHPEFLK Thr (4+)    Similar to human Gelsolin

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

The green assignments indicate glycosylation of Thr-1346.

P00735Prothrombin Thr (3+) EEC(Carbamidomethyl)SVPVC(Carbamidomethyl)GQDRVT(HexNAc)VEVIPR   *

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

Fragments in blue support the site assignment

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

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

P01030Complement C (3+) Thr-420 DIGDKLYWGSVTTSPSNVLSPT(HexNAc)PAPR   

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.

P01044Kininogen-1 Thr (3+) KLISDFPET(HexNAc)TSPK     

P02672Fibrinogen alpha chain Thr (3+) VITKTVT(HexNAc)NADGR  *

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

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

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

P07224Vitamin K-dependent protein S Thr (3+) TAARLST(HexNAc)NAYPDLR  

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

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

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

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

P12763Alpha-2-HS-glycoprotein Thr (2+) HT(HexNAc)FSGVASVE  

P12763Alpha-2-HS-glycoprotein   Ser (2+) HTFSGVAS(HexNAc)VE 

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

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

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

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

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.

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

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.

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

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

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

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

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

This HCD spectrum identified this NON-tryptic glycopeptide

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 * (2+)

P81187Complement factor B T(HexNAc)PLPEAGPQSPC(Carbamidomethyl)SLEGVEIKGGSFR Thr (3+)   * 

P81644Apolipoprotein A-II FQT(HexNAc)VADYGKDLVEK Thr (3+)   *