legends for etd data in the spectra = precursor ions, charge-reduced ones too; * = charge-reduced...

LegendsFor 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

V20101018-05 #1586 RT: 16.19 AV: 1 NL: 2.43E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1640.00]

300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

542.16

812.76748.17

1625.82525.32396.36 1084.59 1229.59570.41 1357.68711.17 1609.81971.68471.36 1154.61 1496.78284.41 1313.72836.55642.65

A2I7N2

LPENVT(HexNAc)PEEQHK

541.9304 (3+)

v

*v

Thr-31

m

v

SERPINA3-6

[–] Peak Matches 284.3600 330.4020 357.3490 396.2930 412.4010 427.4260 453.3970 471.3470 525.3390 553.4990

y2(0.19)

c3(0.14) z3(0.081) y3(0.17)

c4(0.091) z4(0.085) b5(0.20)

557.0180 560.9840 570.3810 573.9700 620.8430 630.5760 639.4910 646.0260 654.3960 661.3990

c5(0.056)

z5(0.099)

700.2930 703.1810 711.2810 748.1100 768.3580 777.4350 795.3820 968.4160 971.4230 1002.5100

z+110+2(0.47)

c11

+2(0.25) c-111

+2(0.76) c7(-0.081)

1056.5410 1066.6180 1084.5460 1100.6460 1154.6090 1229.6450 1268.6100 1357.6680 1398.7360 1495.6940 z+17(0.057)

c8(0.099) z8(0.064) c9(0.055) z9(0.022) c10(0.020) z+110(0.098)


400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

630.56

946.01

871.891893.02780.82403.51 1488.79

1261.701098.69 1560.83517.42 1374.76664.47 1743.01962.74

A5PK77

Thr-387

630.6404 (3+)

SLNAT(HexNAc)SAPHAGFNRPF

v

v*

v

SERPINA11 protein

Identification from HCD, site assignment from ETD

[–] Peak Matches 370.4900 403.5120 419.4590 517.4200 530.4010 533.5150 563.5170 612.6260 622.2350 636.6290

c4(0.28) z3(0.29) z+13(-0.72)

y3(0.22) z4(0.16)

y4(0.23)

657.0390 664.4730 673.9270 676.7710 680.5880 687.9410 707.6510 721.5830 738.5840 745.5570

z5(0.14)

y5(0.24)

c12+2(0.10)

c-112+2(0.61)

c5(0.29) z6(0.23) z+16(-0.78)

z+112+2(0.20)

c13+2(0.70)

z12+2(0.70)

780.8210 794.6180 827.9700 837.8010 845.4530 871.8880 894.4780 905.3680 928.8240 1098.6890 z+113

+2(-0.055) z13

+2(0.45) c6(0.23)

z+114

+2(-0.096) z14

+2(0.41) y14

+2(0.050) c15+2(0.45)

z+115+2(0.039)

z15+2(0.54)

z8(-0.63) z+110(0.14) c-19(0.16)

1184.7670 1227.7120 1245.6950 1261.6990 1374.7580 1488.7870 1560.8350 1674.8720 1743.0070 1789.0220

z11(0.19) c11(0.12)

c12(0.093) c13(0.079) z12(0.088)

z+113(0.091) z+114(0.085)


300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

515.55

773.42

1546.84325.41 765.73 1221.711030.62846.67671.77 1529.921012.75 1406.961293.70423.45 1123.76310.45 581.44 899.88791.70

VAHAT(HexNAc)APPASLGIH

A5PKA3

Thr-89

515.6072(3+)

v

v*m

v

CCDC80 protein

[–] Peak Matches 281.5140 310.4540 325.4070 357.7820 396.4570 423.4470 498.3700 510.4810 520.8870 534.0720

z3(0.29) z+13(-0.72)

c3(0.21) y3(-0.78)

c4(0.22) z4(0.20)

z5(0.20) b9

+2(0.22)

547.1420 551.3210 557.3670 581.4440 587.4620 616.6150 632.7240 639.5400 650.6360 657.7060

z6(0.13)

b12

+2(0.71)

671.7650 679.8990 687.0280 700.5000 704.1880 715.6890 728.5750 732.8220 846.6680 965.7660

z12

+2(0.054) z+112

+2(-0.45) c5(0.14) c13

+2(0.30) z+113

+2(-0.18) z13

+2(0.33) z9(0.21) z+19(-0.80)

c8(0.26)

1012.7480 1030.6210 1036.7740 1123.7620 1221.7060 1236.7910 1293.7010 1360.7880 1406.9610 1430.8470

c9(0.23) c10(0.19) z11(0.082) c11(0.13) c12(0.021)

c13(0.20) z+113(0.12)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

779.64

1558.591149.17

1060.13

1342.60 1541.64997.41608.33326.24 521.29 1954.961239.49 1660.66986.53 1731.551428.51632.38 831.89

x5 x2

A6QLD8

Thr-605

780.0562(3+)

QYVISSPPPNLENPT(HexNAc)PEPR

v

*

m

ADAMTSL4 protein

[–] Peak Matches 309.2340 326.2390 363.1380 385.3640 408.3520 478.2770 488.2240 499.5110 521.2930 546.3090

c2(0.078)

z3(0.17) c3(0.13)

c4(-0.015)

565.3920 575.1930 592.3060 608.3330 632.3840 667.6010 682.5560 763.3840 772.3240 786.2830

c5(-0.0072)

z5(-0.092)

986.5260 997.4100 1060.1280 1068.3920 1097.6950 1100.5610 1126.4410 1134.1620 1152.6520 1213.6240 c9(-0.0046) z7(-0.061)

c10(-0.012) z8(-0.073)

c11(-0.034)

1239.4950 1342.5970 1354.6260 1428.5100 1530.3420 1541.6360 1558.5860 1660.6570 1731.5510 1954.9620 z9(-0.10) c12(-0.10) z+110(-0.023)

y13(-0.16) z14(-0.28) c16(-0.014)

mixedGPs_HCDETDTop6 #1902 RT: 15.64 AV: 1 NL: 4.48E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1685.00]

300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

556.66

835.99

569.59 1102.88777.40

1179.02741.73 1673.18590.01 1031.92486.78 1399.23344.54 960.74 1554.111263.94 1371.85

x5

E1BB91Uncharacterized protein

Thr-2929

557.3142(3+)v

v

v*

TAT(HexNAc)ARPAAAAKPAAAK

From Orbitrap Elite

Similar to Collagen alpha-3(VI) chain

[–] Peak Matches 289.6030 344.5380 378.6070 397.4650 428.5270 486.7800 493.6880 517.6820 529.7040 546.6740

y3(0.42) z4(0.33) z+14(-0.68)

z+110+2(0.77)

c-13(0.45) c3(-0.56)

565.5310 569.5900 575.1660 590.0050 593.0600 613.0260 633.5160 640.6860 718.5540 735.4870

c4(0.25) z6(0.24) z+16(-0.77)

z+113+2(0.15)

z13+2(0.66)

z7(0.30) z+17(-0.71)

c14+2(0.080)

c-114+2(0.58)

741.7340 749.1530 771.6780 777.3960 782.8810 799.5260 802.1450 818.8600 889.9520 960.7390 z+114

+2(-0.18) z14

+2(0.32) y14

+2(-0.27) c15+2(0.75)

z+115+2(-0.040)

z15+2(0.46)

z9(0.42) z+19(-0.59)

b6(0.73) c6(0.42) c7(0.48) c8(0.23)

1031.9190 1096.8910 1102.8780 1108.0090 1112.8400 1179.0230 1399.2320 1554.1110 c9(0.37)

c10(0.29) z+112(0.35)

z+113(0.32) c13(0.46) z+115(0.25)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

945.69

1396.88

1317.35

1417.86

583.33854.52

442.32

1167.56512.27 1584.86 1852.891668.711042.49 1982.96288.28 598.48 1555.67835.64427.41

x5 x2

E1BCW0Uncharacterized protein

IQPPPT(HexNAc)EALLT(HexNAc)LPGPT(HexNAc)AAGPAGR

Thr-355, Thr-360 & Thr-365

v

v

m

*

945.4916(3+)

Similar to Hepatocyte growth factor activator

[–] Peak Matches 268.0920 288.2750 398.3780 401.2940 427.4130 442.3190 456.3260 482.3120 512.2680 528.4070

z+13(0.11)

z+15(0.078)

z6(-0.0021) y6(0.12)

539.3820 550.6230 583.3330 588.3260 598.4810 670.1010 701.3890 716.3530 835.6410 854.5190

c5(0.29) z7(0.026)

c6(0.057)

983.5200 1042.4910 1054.4810 1167.5570 1251.6320 1280.6740 1297.7720 1308.8570 1317.3550 1331.3870 c7(0.016) z+110(-0.025) c8(-0.061) c9(-0.069) z12(-0.013) c10(-0.036)

1353.3820 1382.4700 1387.1730 1390.4070 1400.5050 1584.8600 1668.7150 1794.9300 1852.8940 1982.9630

c11(0.023) z14(-0.14) c13(-0.044) z16(-0.084) z+117(-0.065)


200 300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

548.51

822.011094.80

813.64

723.51 1644.10920.92 1076.83 1160.96483.71 1627.14

712.88346.57 1299.01 1371.07976.93892.79 1569.171230.03625.92371.56203.49 331.82

x5 x5

Ser-50

E1BI67Uncharacterized protein

APC(Carbamidomethyl)S(HexNAc)SRPLALPAAK

547.9600(3+)v

v

v

*

Similar to human Interleukin-18-binding protein

[–] Peak Matches 346.5720 349.2050 371.5640 373.7620 483.7060 529.6050 533.5610 544.7270 554.7180 566.2290

c3(0.42)

z5(0.40) z+15(-0.61)

c-18+2(-0.041)

c8+2(-0.54)

z6(0.38) z+16(-0.63)

574.4880 579.5070 591.0120 619.8040 625.9170 629.8160 636.6410 667.8500 673.0130 685.0040

c-19

+2(-0.78)

b4(0.56)

c4(0.38) z7(0.42) z+17(-0.58)

c-111+2(-0.35)

712.8800 720.9780 723.5140 731.7440 757.4890 777.5410 787.2890 790.4300 920.9190 976.9310

b12+2(0.016)

c-112+2(0.10)

c12+2(-0.40)

c5(0.22)

c13+2(0.59)

z9(0.34) z+19(-0.67)

c7(0.48)

1007.9200 1050.8880 1066.7260 1076.8330 1079.8130 1094.8000 1160.9580 1299.0100 1371.0700 1442.1070 z10(0.31) z+110(-0.70)

c9(0.39) z+111(0.28) c11(0.36) c12(0.36)


300 400 500 600 700 800 900 1000 1100 1200 1300 1400m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

472.51

700.58

343.33 687.69

708.72943.60586.59

1400.731074.661357.75

734.48 796.58 1172.631287.76927.57244.35 359.43 813.68499.35317.42 1101.68 1197.731021.70

x5 x2

Thr-429

E1BKQ9Uncharacterized protein

v

v

v*

472.5819(3+)

IDAT(HexNAc)LSPRDPK

Similar to human Polypeptide N-acetylgalactosaminyltransferase 5

226.3310 244.3540 317.4210 343.3280 359.4280 392.5440 441.5440 453.3450 455.4600 463.4720

y2(0.19) c-12(-0.78)

c3(0.24) z3(0.15) z+16

+2(0.64) y3(0.24)

481.5670 484.4730 495.5260 499.3510 515.4200 525.5890 530.3750 536.4710 545.5280 551.0070

z4(0.076) y4(0.13)

z8

+2(0.22) z+18

+2(-0.29)

586.5890 590.9280 599.2390 607.6860 612.4700 621.4100 644.0930 672.7220 683.4770 698.1450

b9+2(-0.20)

z+19+2(-0.22)

z9+2(0.28)

y5(0.12) c4(0.10)

z+110+2(-0.23)

c10+2(0.26)

z10+2(0.27)

c-110+2(0.76)

z6(0.12)

734.4790 743.5460 796.5810 813.6840 918.6090 927.5740 943.5960 1074.6610 1172.6280 1287.7640

c5(0.086)

z7(0.14)

c7(0.13)

c8(0.082) z+19(0.012) b9(0.049)

z+110(0.12)

F1MER7Uncharacterized protein


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

954.84

1410.91

1431.96

1366.76475.29 800.56

1468.69684.41403.30 1085.61 1779.99 1909.851239.61715.33316.24 603.30 900.57 1581.46

x5 x2

Thr-3374

954.8297(3+)

GPSGSLPAT(HexNAc)PAPAGSAPTVQVTPQLETK

v

v

*

m

Similar to human Basement membrane-specific heparan sulfate proteoglycan core protein

[–] Peak Matches 281.2450 299.2860 316.2410 363.3190 385.3650 403.2990 475.2900 481.3260 489.3030 603.2960

b4(0.15) c4(0.079)

c5(0.11) z+14(0.014)

z+15(-0.039)

613.3960 658.4400 666.3380 678.4040 684.4060 715.3330 754.3480 800.5620 816.3760 827.5850 c7(0.066)

c8(0.038) y6(-0.065)

z7(0.13) y7(-0.070)

900.5740 1085.6110 1239.6150 1275.0970 1303.4080 1317.3430 1323.4100 1330.4490 1346.7140 1354.5560

z+18(0.070) c10(0.064)

c-113(-0.26)

1357.8630 1366.7620 1381.8040 1396.7830 1404.4240 1414.9620 1468.6880 1483.7900 1779.9860 1909.8540

c14(0.11) z+113(0.015)

c15(-0.040) z+114(-0.010) z+118(0.037)

F1MMK9Uncharacterized protein

Thr-198

GEC(Carbamidomethyl)VPGEQDPVPT(HexNAc)PVSR


200 400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

676.64

969.71

985.63

874.39

1282.44746.331970.811154.51

1869.74364.26 1411.56 1735.78616.30560.35 859.52 1086.40458.37 1469.62 1584.641352.49247.30

x5 x2

v

*

cmCys!

m

676.3133(3+)

Similar to human Protein AMBP

[–] Peak Matches 247.2950 345.3720 364.2590 458.3750 527.3450 548.3030 560.3480 617.2900 658.2770 702.4270

z+12(0.15) z3(0.17) c3(0.13) y4(0.10)

c5(0.098) c6(0.019)

746.3260 783.3770 791.7440 830.3720 841.2800 852.5610 859.5250 874.3850 883.6260 887.4870

c7(0.012) z5(-0.054)

y6(0.073) c8(0.013)

904.7080 912.6890 920.7510 942.4420 956.1830 958.5860 961.1500 969.7070 977.6530 997.2010

z7(-0.060)

y7(0.066)

1086.3950 1154.5090 1170.5920 1282.4390 1411.5590 1665.7420 1735.7800 1782.8530 1869.7430 1954.8610

c10(-0.057) z9(-0.072) y9(-0.0081) c12(-0.13) z10(-0.20)

z11(-0.12) z+114(-0.091)

c15(0.032) c16(-0.11) z+116(-0.045)

mixedGPs_HCDETDTop6 #2511 RT: 19.88 AV: 1 NL: 1.28E4T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1730.00]

200 400 600 800 1000 1200 1400 1600m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

572.53

837.82 1142.79

1700.981126.74984.79 1558.95758.70358.38 1359.96 1489.01674.52 927.77443.45 552.10 1295.891180.71284.46175.39

F1N1I6Uncharacterized protein

Thr-27 & Thr-34

572.6365(3+)v

vv*

LAT(HexNAc)PARPGAT(HexNAc)QAR

Similar to human Gelsolin

[–] Peak Matches 284.4610 358.3810 443.4540 485.7790 543.6700 552.0990 581.0700 586.3360 590.0970 604.6910

z3(0.19)

b4(0.028)

609.9760 639.5240 648.4160 662.5560 668.5770 674.5180 681.7360 710.5800 726.3310 733.5640

z4(0.23) z+14(-0.77)

c5(0.15)

z5(0.20)

741.3600 750.0270 758.7050 766.5960 794.4290 823.4270 826.3600 841.8300 927.7680 984.7870

y5(0.65)

z+111+2(-0.18)

z11+2(0.33)

y11+2(0.21)

z+112+2(0.027)

z12+2(0.53)

c7(0.24) c8(0.24)

1044.7190 1055.7920 1083.8740 1100.9530 1126.7430 1142.7890 1359.9640 1489.0120 1516.8860 1558.9450 z+18(0.18) c9(0.21)

c10(0.25)

z+111(0.13) c12(0.14)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

558.35

1107.68

391.30 729.92

421.33 905.68805.70665.50 841.21 1051.02

244.20 491.951681.721610.84 1810.831212.45 1300.63 1987.951477.68378.27

x5 x2

Uncharacterized protein F1N1I6

VT(HexNAc)EARPGSMVVEHPEFLK

Thr-44

558.0357(4+)

v

v

v

Similar to human Gelsolin

[–] Peak Matches 244.2010 391.3030 421.3260 520.2360 541.1680 550.2460 575.0600 606.9190 621.2600 625.0560

z2(0.023) z3(0.056) c2(0.097) z4(-0.053) z9

+2(-0.13) z+19

+2(-0.63) c3(-0.026)

c9+2(-0.22)

c-19+2(0.28)

z10+2(0.10)

z+110+2(-

0.40) c4(-0.049)

c10+2(0.24)

c-110

+2(0.74)

650.4290 665.4950 674.5160 754.4090 805.7010 829.2500 838.1580 841.2120 849.1920 856.1870 z11

+2(0.099) z+111

+2(-0.40)

b11+2(-

0.34)

c11+2(0.17)

c-111

+2(0.67) z6(0.0082)

z+114+2(-

0.22) z14

+2(0.28)

z+115+2(-

0.23) z15

+2(0.28) y15

+2(0.25) c14

+2(0.26) c-114

+2(0.76)

905.6830 913.6700 920.7200 931.5740 973.6010 994.1150 1015.5900 1018.5810 1051.0180 1072.7480 z16

+2(0.23) z+116

+2(-0.28)

y16+2(0.20)

b7(-0.79)

c15+2(0.27)

c-115

+2(0.78) c7(0.090)

c16

+2(0.13) c-116

+2(0.64) c8(0.065) c17

+2(0.49)

1074.9640 1081.2060 1099.3910 1150.6150 1212.4530 1610.8390 1681.7160 1712.8480 1810.8300 1839.8410

z9(-0.37)

z10(-0.17) z+114(0.0031)

z+115(-0.16)

z+116(-0.086)

c15(-0.050)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

635.41

842.14

1271.82

1254.81833.22

953.17705.47 1134.77

1191.97978.75

273.26 1022.22585.35498.33 714.651341.77924.62 1848.96774.73427.41 1958.081410.71327.29 1699.95

1600.86

x5 x5

O18977Tenascin-X

Thr-3146 or Thr-3147

RVGPASTVGVTASLT(HexNAc)TERPLAPR

v635.6015(4+)

v

v

[–] Peak Matches 273.2580 327.2860 347.3850 427.4100 440.3770 498.3350 585.3550 614.5290 671.0510 694.4210

c2(0.055) z3(0.096) z6

+2(0.17) z+16

+2(-0.34)

c4(0.13) z4(0.10) c5(0.020) c6(0.0083) z9

+2(0.20) z+19

+2(-0.30)

z10+2(0.18)

z+110+2(-

0.32) z+16(-0.015)

705.4680 714.6490 722.6030 774.7280 785.5030 800.8060 823.5420 828.9990 836.3010 878.4240

z+111+2(-

0.24) z11

+2(0.26) y11

+2(0.21)

c8(0.040)

b15+2(-0.12)

z+113+2(-

0.12) z13

+2(0.38)

z+17(0.064)

z15+2(-0.048)

z+115+2(-

0.55)

924.6220 943.6800 953.1720 978.7520 1022.2220 1057.7790 1107.7440 1113.6220 1134.7650 1169.8320 z+18(0.096) b10(0.096) c17

+2(0.13) c-117

+2(0.64)

z17+2(0.22)

z+117+2(-

0.28)

z18+2(0.18)

z+118+2(-

0.33)

z19+2(0.21)

z+119+2(-

0.29)

c20+2(0.14)

c-120+2(0.64)

c12(-0.015) y20

+2(-0.48)

b21+2(0.15)

z21+2(0.16)

z+121+2(-

0.34)

1183.8270 1191.9660 1200.7310 1227.7050 1254.8100 1313.7100 1341.7650 1410.7140 1848.9640 1958.0850 b13(0.18) z22

+2(-0.31) b22

+2(0.69)

y22+2(-0.18)

c22+2(0.31)

c13(0.061) z9(0.060)

c14(-0.044) z+110(0.028)

The green assignments indicate glycosylation of Thr-1346.


400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

844.68

1238.21

1258.72

696.50

597.39 1006.281099.54 1689.06 1937.791434.48468.32 1837.741157.95369.33 1534.52978.64711.75493.26 1795.57613.44

x5 x2

P00735Prothrombin

Thr-193

844.7391(3+)

EEC(Carbamidomethyl)SVPVC(Carbamidomethyl)GQDRVT(HexNAc)VEVIPR

v

v

*

[–] Peak Matches 300.4260 313.1410 369.3340 385.3490 468.3150 484.3990 493.2580 539.2080 571.3690 597.3900

z3(0.097) y3(0.093) z4(0.0095) y4(0.075)

z5(0.042)

613.4390 696.4980 706.6830 711.7490 721.3550 725.4890 781.3950 783.6630 818.3940 828.5750

y5(0.072) z6(0.082)

y6(-0.69)

c7(0.023)

978.6360 1006.2750 1050.6420 1099.5420 1149.6460 1157.9480 1164.4590 1166.8060 1195.2070 1208.7320

c8(0.23) z16

+2(0.25) z+116

+2(-0.25) z+117

+2(0.60) z8(-0.070)

z+119+2(0.63)

1213.7460 1222.0800 1230.7330 1278.5390 1371.6790 1434.4790 1534.5250 1689.0610 1837.7420 1937.7950

c11(0.030) z+110(-0.069) c12(-0.13)

c14(-0.063)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

732.56

1076.77

989.651465.62

926.471223.56

470.25 860.501398.57 1891.861726.86

1486.61540.28306.30 1791.72407.42 711.34 1706.01

x5 x5

P00735Prothrombin

Thr-205

SGGSTT(HexNAc)SQSPLLETC(Carbamidomethyl)VPDR

v

732.3419(3+)

*

v

m

[–] Peak Matches 275.2240 306.3030 387.3070 390.2900 407.4240 470.2550 486.3990 540.2790 668.2390 706.3760

z+12(0.089) c4(0.16) y3(0.11) b5(0.13) c5(0.24) z4(0.0067) y4(0.13)

711.3400 737.9910 741.9890 747.4380 784.2340 798.4670 857.9700 860.5000 876.4300 882.3790 c6(0.024)

y6(0.093)

c7(0.12)

z7(0.13) y7(0.042)

926.4660 973.4840 989.6500 997.6310 1009.3590 1026.2210 1037.7070 1045.1190 1053.7440 1081.6550

c8(0.060) z8(0.031) y8(0.18)

1223.5590 1270.5550 1336.6800 1398.5700 1446.7340 1465.6220 1486.6090 1726.8650 1891.8560 1978.8210 c11(-0.016) z11(-0.067) c12(0.021) z12(-0.11)

c13(-0.080) z+113(-0.11) c15(0.085) z+115(-0.039) z+116(-0.11)

Fragments in blue support the site assignment


400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

803.49

1196.21

1160.27 1606.74

1052.69

373.39 684.46 1700.971002.311564.801301.64 1415.37217.12 850.42558.24 710.49 1918.801784.72465.17

x5 x2 x5

SGGSTTS(HexNAc)QSPLLETC(Carbamidomethyl)VPDRGR

803.3839(3+)

Prothrombin P00735

Thr-205 & Ser-206, mixture!

v

v*

[–] Peak Matches 217.1230 356.3830 373.3870 445.2670 465.1750 508.3900 558.2380 684.4560 710.4910 729.4950

z+12(-0.0065)

z+13(0.16)

c6(0.15)

z+16(0.077) c-16(0.18)

773.4800 779.3780 793.9260 798.3090 813.3660 820.7280 843.8290 850.4250 859.2040 879.7530

c7(-0.039)

z7(0.43) z+17(-0.58)

z+115+2(-2.4e-

4) z15

+2(0.50) y7(-0.22)

945.4600 952.1310 1002.3110 1052.6850 1071.8370 1087.6940 1096.5630 1103.3160 1115.8340 1124.8260

z+18(0.0029) z+115

+2(0.17) z15

+2(0.67)

z+116+2(-

0.18) z16

+2(0.33)

z17+2(0.18)

z+117+2(-

0.33)

z+118+2(0.034)

c-119+2(-0.45)

z18+2(0.54)

y18+2(-0.72)

z+119+2(-

0.21) z19

+2(0.29) c-120

+2(-0.70)

1132.3270 1145.1600 1152.1410 1160.2720 1187.7230 1223.5660 1588.5710 1606.7410 1700.9670 1726.6910

y19+2(-0.22)

y20

+2(-0.78) z+110(0.14) c11(-0.0090)

c15(-0.089)

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


400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

988.24

1460.34

1481.43

1379.72546.24

1331.72913.52 1898.961065.56659.41 1239.62 1611.76 1724.74821.54 1811.94744.44616.41327.36 509.34

x5 x2

P01030Complement C4

987.8339(3+)

Thr-420

DIGDKLYWGSVTTSPSNVLSPT(HexNAc)PAPR

v

v

m

[–] Peak Matches 327.3610 397.4270 432.5350 483.3340 503.3480 509.3410 525.3050 528.3500 546.2390 616.4080

z3(0.17)

z5(0.014) b9

+2(0.55) c5(-0.049)

653.5190 659.4100 693.3900 729.4270 744.4410 763.4400 778.5930 821.5380 837.4470 841.4690

c6(0.038)

z+15(0.049) y5(0.052)

c-17(0.11)

y6(0.028)

913.5200 1008.5710 1065.5550 1151.5140 1239.6220 1273.3220 1331.7210 1351.6700 1360.1270 1364.2270

z+17(0.057) c8(0.056) c9(0.019) c-110(-0.047) z+110(-0.036)

z22+2(0.17)

z+122+2(-

0.34) z+123

+2(0.55) c-112(-0.0067)

z+124+2(0.44)

1367.3550 1371.9280 1379.7210 1416.2520 1464.3850 1510.6540 1611.7600 1724.7370 1811.9380 1898.9580

y24+2(0.16)

z+125

+2(0.025) z25

+2(0.53) z+113(-0.12)

z+114(-0.062)

c16(-0.11) z+116(-5.3e-4)

z+117(-0.013)

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: y6 was detected modified.


300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

556.26

731.98459.35 574.34

833.74 1093.43416.29818.49 849.40 1208.48

372.41 947.51 1667.771463.71 1521.631352.56720.33 1190.50501.34962.62874.46662.37

P01044Kininogen-1

Thr-586

555.9546(3+)

KLISDFPET(HexNAc)TSPK

v

vv

m

m

[–] Peak Matches 315.2760 331.3120 372.3710 416.3120 432.4160 435.4050 459.4050 501.3320 517.3590 523.0200 z3(0.097) y3(0.11) c3(0.074) z4(0.085) y4(0.17)

c4(0.076)

530.3250 537.3720 546.9950 569.5480 574.3570 592.2120 601.0770 609.0700 623.3710 631.3950

c5(0.0011)

720.2600 724.1310 732.1050 768.9430 818.5180 849.4300 947.5510 962.4820 1081.8520 1093.5140

z5(-0.094)

c12+2(0.050)

c-112+2(0.55)

c7(0.041) z6(0.034) c8(0.031) y7(0.014)

z8(-0.0034)

1112.4970 1190.4480 1208.5390 1251.6280 1295.5250 1352.7360 1408.6830 1463.7520 1522.6480 1537.7170

z9(-0.0053) c9(-0.019) z10(-0.051) c10(0.042) z11(0.023)

z+112(-0.10) y12(-0.046)


300 400 500 600 700 800 900 1000 1100 1200 1300 1400m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

493.05

731.61987.44

1320.76709.78 1148.70331.43 659.64 1462.74968.33402.26 510.78 820.54 1079.37865.42 1235.51 1390.62

x2 x2

P02672Fibrinogen alpha chain

Thr-464

493.2675(3+)

VITKTVT(HexNAc)NADGR

v

*

[–] Peak Matches 331.4320 349.2760 358.7670 371.3000 374.7870 398.9260 402.2630 441.3610 459.4570 473.8750

c3(0.20) z3(0.28) z+13(-0.72)

z4(0.077)

c4(0.13) b7

+2(0.099)

504.2540 510.7830 516.2160 520.9320 530.0850 532.2030 548.4110 554.7520 560.3430 574.0050

z5(-0.013)

b8

+2(-0.71) y5(-0.044)

c5(-0.034) c-19

+2(-0.32) z9

+2(-0.78)

601.2590 604.5870 625.4220 645.4890 659.6410 682.0890 700.7050 719.7270 723.9380 738.0740

z10

+2(0.11) z+110

+2(-0.39) c6(0.20) c-111

+2(-0.71) z11

+2(0.24) z+111

+2(-0.27)

820.5390 942.3480 960.4880 963.6620 968.3270 977.8180 984.3830 987.4430 1148.7040 1320.7620

z6(0.18)

c7(0.090)

c9(0.052) z9(0.14)

c11(0.061)

P02672Fibrinogen alpha chain

SSHEFDGRT(HexNAc)GLAPEFAA

Thr-525


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

665.79

605.22 989.72926.61

1997.86852.61 1392.55589.28458.26

1219.54 1331.48777.36 1667.69 1852.85329.30 1539.71720.32534.31 1194.571079.53413.40

x5 x2

v

v

v

*m

665.6400(3+)

[–] Peak Matches 329.3050 413.3950 443.4670 458.2580 534.3110 571.2710 589.2770 605.2170 649.2400 656.4470

c3(0.15)

c4(0.059) b8

+2(-0.44) y5(0.055)

z6(0.0028)

c5(-0.051) y6(-0.076)

661.3760 677.3830 703.3860 720.3190 760.4590 777.3580 788.2380 791.3280 810.1650 831.3000

z+17(0.020) b6(0.12) c-111

+2(-0.44) c6(0.024)

z+18(0.071) b7(0.17)

c7(0.042) c13

+2(-0.14) c-113

+2(0.37)

852.6090 880.5640 889.1790 896.6910 903.1590 926.6100 933.4370 946.7180 962.2130 980.7130 c-114

+2(0.22) c14

+2(-0.29) z15

+2(0.24) z+115

+2(-0.26) c15

+2(0.18) c-115

+2(0.68) c8(0.020)

z+116+2(-0.22)

z16+2(0.29)

c16+2(0.27)

c-116+2(0.77)

1219.5430 1277.4780 1294.5320 1331.4800 1392.5480 1407.5560 1539.7150 1667.6880 1704.6710 1852.8480

z10(-0.065) b10(-0.061) z+111(-0.16)

c10(-0.034)

z+112(-0.12) c11(-0.094) y12(-0.12)

z+113(-0.018) z14(-0.079) c14(-0.11)

P06868Plasminogen


500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

884.32

1749.92

1709.92

977.70 1064.741678.021193.76

1548.981439.871326.01592.50 793.71680.62531.58 1207.541177.92893.33 1019.90

x10 x2

TIPSC(Carbamidomethyl)ESSPLST(HexNAc)ER

883.9084(2+)

Thr-366

v

v

[–] Peak Matches 497.3440 531.5790 577.6160 592.5040 793.7080 977.6950 1064.7440 1193.7620 1317.4480 1326.0060

z3(0.23) z+13(-0.77)

z+15(0.31) z+17(0.22) z+18(0.23) z+19(0.21)

1353.8710 1439.8680 1455.8910 1473.4510 1480.6480 1532.0210 1548.9790 1565.9090 1609.0150 1649.8340

z+110(0.29) z11(0.26) z+111(-0.75)

y11(0.26)

c12(-0.036)

c-113(0.30) c13(-0.71)

z13(0.089)

1660.9910 1678.0240 1692.9180 1705.8540

P06868Plasminogen


200 400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

1025.84

1538.71

1509.28

709.43 1436.36538.27903.40

410.26595.39 767.36 882.46 1266.95 1735.741066.50 1665.61917.47636.59323.32 458.37

x5 x2

1025.4580(3+)

Thr-378

MDVPVPPEQT(HexNAc)PVPQDC(Carbamidomethyl)YHGNGQSYR

v

v

m

[–] Peak Matches 262.5320 323.3210 337.9960 410.2630 453.4970 458.3660 538.2670 542.4540 552.4230 595.3850

c-12(-0.56) z+12(0.15) y2(-0.19) z+13(0.060)

z+14(0.0050) b5(0.19)

z+15(0.10)

610.3080 636.5890 709.4260 724.3640 734.3500 753.4610 767.3580 781.4940 790.5060 839.8730 y5(0.014)

z+16(0.100) y6(0.027) z12

+2(-0.44) c7(0.065)

y7(0.14)

882.4630 903.4010 1010.4770 1066.5030 1266.9520 1308.8470 1341.4790 1406.8550 1411.5730 1415.2680

c8(0.024) z+18(-0.0058) c9(-0.021) z+19(0.033) y20+2(-0.10)

z+121+2(-0.24)

z21+2(0.27)

z+111(-0.049) z23

+2(0.21) z+123

+2(-0.29) c11(-0.10) y23

+2(0.62)

1428.7410 1436.3630 1464.2570 1470.7730 1479.8150 1485.2230 1493.2760 1501.2660 1665.6110 1735.7420

z24

+2(0.10) z+124

+2(-0.40) y12(0.63) b12(-0.44)

z+114(-0.096) c14(-0.12)


300 400 500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

584.54

530.30868.67

417.30 876.731169.44647.38 1106.55847.28

1336.58 1736.90747.18 921.52 1035.59 1494.85486.35387.40 1595.751239.45 1367.65288.30

x2

P07224Vitamin K-dependent protein S

Thr-104

584.6357(3+)

TAARLST(HexNAc)NAYPDLR

v

v

[–] Peak Matches 261.2550 288.2980 373.3380 387.4040 417.3050 445.3830 486.3500 520.1010 530.3010 559.1240 c3(0.099) y2(0.095)

z3(0.19) c4(0.048)

c5(-0.040)

567.2820 575.1220 577.6410 603.1150 617.3440 635.1730 640.1370 647.3790 689.3070 709.2870

c6(-0.029)

z5(0.052)

718.4630 738.2490 747.1790 776.5010 782.5150 832.4580 840.6190 859.9900 921.5190 1035.5880

z6(0.099)

z+111+2(-0.20)

z11+2(0.30)

z12+2(0.12)

z+112+2(-0.39)

z7(0.051)

c7(0.019) c8(0.045)

1106.5470 1137.4680 1150.4870 1153.4330 1169.4390 1223.5050 1336.5820 1494.8490 1564.8820 1595.7490 c9(-0.033) z+18(-0.074)

z9(-0.061) z10(-0.069)

z+112(0.085)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

814.78

1200.71

1119.78

618.36

547.27

477.27 1824.681306.53 1895.75882.45 981.50 1461.61400.35 1560.64922.50703.48 1782.78

x5 x2

P07456

Thr-99 (& Thr-106)

814.3936(3+)

DVSASTT(HexNAc)VLPDDVT(HexNAc)AYPVGK

m

v

Insulin-like growth factor 2

[–] Peak Matches 319.2800 355.3170 373.3010 390.3600 400.3450 416.3090 428.3350 434.3740 458.2550 462.3680 c3(0.12)

b4(0.13) c4(0.16) y4(0.090)

477.2690 547.2740 559.3580 563.2930 578.3180 618.3650 634.3590 703.4830 839.4120 863.4790 c5(0.039) z5(-0.026)

y5(-0.026) c6(0.040) z6(0.028) y6(0.0031)

882.4520 981.4970 1021.5520 1070.2610 1097.6740 1106.2380 1111.8250 1119.7830 1136.5100 1156.6660 c7(0.047) c8(0.024) z8(0.019)

z9(-0.050)

1185.3420 1203.7450 1251.4540 1306.5290 1421.4900 1461.6050 1560.6410 1824.6790 1895.7540 1966.8380

z10(-0.13) c11(-0.11) c12(-0.17) z12(-0.12) z13(-0.15) c14(-0.18) c15(-0.14) z+115(-0.14)


300 400 500 600 700 800 900 1000 1100 1200 1300 1400m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

571.14

1427.30

884.31 946.04

1204.67703.41445.22 803.42 1325.081103.82662.85

506.38 1011.69755.66 1239.75314.36218.15 376.32

P07456

(Ser-154, Thr-163 &) Thr-168

S(HexNAc)HRPLIALPT(HexNAc)QDPAT(HexNAc)HGGASSK

Insulin-like growth factor 2

v570.8846(5+)

vv

vm

[–] Peak Matches 218.1490 305.2950 314.3590 445.2240 490.2240 506.3770 607.8860 648.2030 662.8460 672.1860

z2(0.023) z3(0.14) z7

+2(0.21) z+17

+2(-0.30) c2(0.020)

z6(-0.014) b7

+2(0.45) y6(0.12)

z11+2(0.11)

z+111+2(-0.39)

z+112+2(-0.12)

z12+2(0.38)

735.7880 755.6580 803.4160 819.5990 826.4350 850.1350 857.0080 879.4520 884.3100 908.1520

c10

+2(0.24) c-110

+2(0.74) z+120

+3(0.0010) z20

+3(0.34) c11

+2(0.15) c-111

+2(0.66) c18

+3(0.35) c-118

+3(0.69) c19

+3(0.37) c-119

+3(0.71) c20

+3(0.68)

c21+3(0.37)

b6(0.65) c-121

+3(0.71)

921.1750 940.6040 965.1290 976.2010 995.5390 1011.6940 1021.1670 1027.5530 1103.8200 1113.1720

z+116

+2(0.17) z16

+2(0.68) c7(-0.024)

z17

+2(0.17) z+117

+2(-0.33) b15

+2(-0.74) c15

+2(0.10) c-115

+2(0.61)

1140.4170 1172.6680 1181.8820 1204.6670 1215.4230 1239.7480 1274.6640 1318.3170 1325.0760 1361.7770

b16

+2(-0.42) c16

+2(0.28) c-116

+2(0.79)

c-19(-0.025) z+120

+2(0.048) z20

+2(0.55) z+111(-0.13)

c19

+2(0.53) c20+2(0.66)

c21

+2(0.61)

P07456Insulin-like growth factor 2


400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

649.24

973.70

951.74

1298.56579.38 908.21 1928.96

863.13 1115.571366.651252.60731.44509.30 1437.68 1903.03421.42 1215.641002.57

1727.94314.58 1647.69

x5 x2

(Thr-163) & Ser-174

ALPT(HexNAc)QDPATHGGASS(HexNAc)K

648.6398(3+)v

v

v

*m

[–] Peak Matches 314.5760 326.4690 376.7650 421.4170 509.3020 579.3840 589.3720 603.4760 627.4030 636.2700

z2(0.21) z+12(-0.80)

z+13(0.057) y9

+2(-0.44) z4(0.11)

c4(0.14) c10

+2(0.59) z5(-0.026)

638.3900 666.9310 673.0160 682.5290 688.6000 694.3780 709.5280 714.4110 731.4420 742.2720

z+112

+2(0.71)

z+16(0.053) y6(0.19) b5(0.044) c5(0.049)

831.4170 863.1280 871.1920 882.0120 908.2110 936.7750 955.6820 1002.5720 1115.5730 1215.6430 z+17(0.033) y13

+2(-0.46) c15

+2(0.29) c-115

+2(0.79) y15

+2(-0.17)

z9(0.11) c9(0.015) y10(0.040)

z+111(0.094)

1252.6010 1282.7190 1298.5550 1309.5950 1343.6520 1366.6530 1437.6840 1524.7440 1814.7310 1858.7920 c10(-0.016)

c11(-0.043) z+112(0.045) c12(-0.0067) c13(-0.013) c14(0.015) c15(-0.11)


400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

607.37

881.74

845.39910.32

1803.93557.41 959.64741.55 1263.61444.41 1489.74671.52 1376.691149.59 1690.82331.38 1560.78808.611015.73460.47 1332.71261.39 363.39

P12763Alpha-2-HS-glycoprotein

Thr-217

606.9723(3+)

v

vm

EVVDPT(HexNAc)KC(Carbamidomethyl)NLLAEK

[–] Peak Matches 261.3860 276.4110 331.3780 345.5090 363.3900 444.4070 460.4650 557.4100 573.4910 588.2240

z+12(0.24) y2(0.26) z3(0.20) c3(0.30)

z4(0.15) y4(0.19) z5(0.068) c5(0.12)

y5(0.13)

597.6410 601.0880 671.5160 687.5990 716.5680 729.8530 738.7000 741.5480 747.0720 751.3010

z6(0.13)

y6(0.20) c-110

+2(-0.74) z+111

+2(-0.17) z11

+2(0.34) y11

+2(0.70)

788.0910 800.7540 808.6110 837.7990 845.3920 861.5260 865.8120 873.1930 893.1910 959.6360

z12+2(0.19)

z+112+2(-0.31)

z+113+2(-0.14)

z13+2(0.37)

c13+2(-0.030)

y13+2(-0.048)

c-113+2(0.47)

c6(0.11)

z8(0.13)

989.5880 1149.5930 1212.5950 1263.6130 1376.6940 1476.7070 1489.7430 1560.7770 1674.8580 1690.8210

c7(0.073) c8(0.047)

c9(0.024) z9(-0.025)

y10(-0.015) c10(0.021)

z+111(-0.018) c11(-0.014) c12(-0.017) z+113(-0.0039)


300 400 500 600 700 800 900 1000 1100 1200m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

618.81

1220.77

1106.86920.73849.77 1209.51

1007.73606.67 692.68 750.69238.56 504.57 1155.87449.73306.59 408.17 827.69 1078.63876.79

x5


Thr-314

618.7888(2+)

HT(HexNAc)FSGVASVE

v

v

[–] Peak Matches 238.5590 255.6200 306.5860 322.5120 325.6550 408.1670 441.5670 449.7300 454.6120 459.6040

b2(-0.63)

c2(0.38)

600.6570 606.6660 692.6780 716.7450 750.6860 827.6940 849.7740 876.7880 901.6850 920.7280

c3(0.38)

c-14(0.37) c4(-0.64)

c5(0.34)

c6(0.36)

c7(0.28)

928.7290 963.6940 1007.7270 1017.7660 1030.6250 1033.8050 1035.9160 1078.6340 1106.8620 1155.8680

c8(0.25)

c9(0.31)


300 400 500 600 700 800 900 1000 1100 1200m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

618.82

1220.70

1106.69

1209.58

1033.68717.64490.50 547.51 928.94645.55 1155.55

836.47402.45 561.70 1063.71358.64 458.57 749.82692.55304.55256.58

x5 x2


v

v

Ser-320

618.7886(2+)

HTFSGVAS(HexNAc)VE

m

[–] Peak Matches 256.5810 304.5480 307.4870 319.5540 358.6350 376.5590 402.4530 433.6820 458.5700 490.4960

c2(0.44)

c-13(0.25) c3(-0.76)

c4(0.26)

547.5150 600.6530 645.5470 717.6390 836.4740 920.0310 928.9350 965.7280 983.8270 1001.7950

c5(0.25)

c-16(0.22) c6(-0.78)

c7(0.27) z+17(0.086)

z+18(0.37)

1007.6210 1018.7130 1033.6820 1063.7100 1106.6850 1119.7410 1133.8030 1155.5550 1165.7820 c8(0.14)

c9(0.14)

Alpha-2-HS-glycoprotein P12763


200 400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

646.58

969.98

1292.71

905.43868.44332.61 1168.75 1608.99 1809.11419.48 734.64571.67 1904.121024.60 1522.011422.94288.58

x5 x2

v

v

646.6395(3+)

Ser-324

SGVASVESS(HexNAc)SGEAFHVGK

[–] Peak Matches 332.6090 419.4830 425.5110 453.5620 518.5580 571.6720 627.6390 638.3240 642.6690 665.3300

c4(0.42) c5(0.26) z+14(0.26)

c6(0.26) z5(0.36) z+15(-0.65)

z6(0.32) z+16(-0.69)

710.6720 734.6360 771.7270 786.2960 791.3450 795.6700 804.8970 808.3980 828.5840 833.4470

z12+2(-0.65) c8(0.27)

z7(0.34) z+17(-0.67)

z+114+2(0.024)

z14+2(0.53)

z8(0.17)

840.3680 863.0960 868.4410 889.7810 905.4280 914.9450 918.0550 952.8350 1024.6010 1168.7520 z+115

+2(-0.024) z15

+2(0.48) b16

+2(0.55) z+116

+2(-0.14) z16

+2(0.36) c17

+2(0.51) z9(-0.50) z17

+2(0.12) z+117

+2(-0.38) c9(0.12) c11(0.22)

1205.8310 1276.7150 1292.7070 1297.8490 1522.0090 1608.9890 1653.0050 1780.0460 1809.1100 1837.1060 z10(0.28) z+110(-0.73)

z11(0.12) c12(0.27) z+113(0.30) z+114(0.25) c15(0.27)

c17(0.28)


200 400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

646.62

969.79

518.26840.13

771.40 1297.49 1922.851422.521168.53 1679.65419.30 571.32 734.41 1836.761521.591368.541118.43189.19 287.36

x2

Alpha-2-HS-glycoprotein P12763

Ser-325

SGVASVESSS(HexNAc)GEAFHVGK

646.6392(3+)

v

v

[–] Peak Matches 189.1920 287.3600 332.3940 419.2950 425.3450 440.3870 475.3360 518.2630 571.3240 603.3210

z+12(0.069) z3(0.18) z+15

+2(0.70) c4(0.20) c5(0.070) z+14(0.094) y4(0.13)

c6(-0.030) z5(0.013)

z10+2(0.039)

z+110+2(-

0.46)

628.3770 642.3800 658.4430 734.4060 771.3990 777.2340 804.9210 821.4920 829.4670 840.1350

z6(0.032) y6(0.076) c8(0.038) z7(0.0080)

z+114+2(0.048)

b9(0.55) z14

+2(0.55) c9(0.092) z+18(0.047)

z15+2(0.25)

z+115+2(-

0.26)

868.2050 889.6980 904.7520 918.1930 1111.4540 1118.4290 1168.5350 1205.4790 1292.5010 1297.4890

b16+2(0.31)

z+116+2(-

0.23) z16

+2(0.28)

c17+2(-0.17)

c-117

+2(0.34)

z+117+2(-

0.24) z17

+2(0.26) c10(-0.057) z9(-0.095) c11(0.0022) z10(-0.077) z11(-0.087) c12(-0.086)

1368.5450 1422.5190 1515.5730 1521.5880 1608.6510 1652.6340 1679.6510 1778.8110 1809.7040 1836.7560

c13(-0.068) z+112(-0.12) c14(-0.11) z+113(-0.12) z+114(-0.088)

c15(-0.11) z+115(-0.12) z+116(-0.033)


200 400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

623.46

1217.74888.72

948.65817.00716.35 1058.78

596.421145.26

376.281647.84287.29

1776.86400.36 1896.771290.66 1437.71500.501550.80 1688.81 1997.81

P17690Beta-2-glycoprotein 1

Ser-32 (& Thr-33)

TC(Carbamidomethyl)PKPDELPFS(HexNAc)T(HexNAc)VVPLKR

v

vv

623.3235(4+)

m

m

[–] Peak Matches 287.2900 376.2830 400.3630 500.5000 596.4220 601.3450 605.3750 645.5150 653.6290 695.4960

z2(0.095) c3(0.12) z3(0.084) z7

+2(0.20) z+17

+2(-0.31)

z5(0.022)

c5(0.032) c-110

+2(0.052) c10

+2(-0.45)

z8+2(0.16)

z+18+2(-

0.35) y8

+2(0.26) z6(0.027)

716.3470 737.2560 752.5040 758.0580 764.0570 795.9330 802.6930 806.9660 845.4270 888.7150

c6(0.0074)

c7(0.045) z12

+2(0.23) z+112

+2(-0.27)

899.1690 946.1640 948.6460 1046.7750 1055.4510 1058.7850 1103.2880 1136.2610 1145.2550 1167.2990 c12

+2(0.25) c-112

+2(0.76)

z13+2(0.17)

z+113+2(-

0.33)

c13+2(0.20)

c-113

+2(0.70)

c15+2(0.26)

c-115+2(0.77)

c9(-0.068) z15

+2(0.22) z+115

+2(-0.29)

c16+2(0.23)

c-116

+2(0.74)

c17+2(0.20)

c-117+2(0.70)

1196.3130 1202.4950 1209.2130 1229.7070 1290.6600 1647.8380 1776.8590 1796.7070 1891.9250 1896.7680

c10(-0.092)

z+18(-0.055)

z+111(-0.082) z+112(-0.10) c12(-0.12) z+113(-0.065)


200 400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

729.75

1072.29

952.31566.30

992.26451.341775.77

1115.51 1287.59899.56 1903.861458.69 1622.63523.30213.19 829.52669.44350.39

x5 x2

GKFTDFWESATSPT(HexNAc)QSPP

(Ser-90 or) Thr-92

P19035Apolipoprotein C-III

729.3362(3+)

v

m

*

[–] Peak Matches 204.3160 213.1860 350.3880 413.2920 451.3380 523.2990 566.3040 669.4440 680.3730 698.4230

y2(0.063) c3(0.17) z+14(0.089) c4(0.072)

c5(0.011)

713.4350 717.4100 799.4540 829.5210 838.5090 855.5260 870.6170 883.5360 887.6370 899.5590

c6(0.073) z+15(0.080)

b13+2(0.15)

y6(0.13) c13

+2(0.62)

c-114+2(-0.27)

c14+2(-0.77)

c7(0.12)

944.8020 952.3120 984.3380 992.2590 1002.5210 1023.1350 1028.5570 1057.1330 1076.7590 1115.5080

c15

+2(-0.13) c-115

+2(0.38) z+18(0.058)

c8(0.073)

c9(-0.0076)

1142.5310 1160.4700 1186.5000 1287.5890 1458.6900 1472.6330 1622.6300 1737.6950 1775.7740 1903.8620

z+110(-0.062) c10(-0.053) c11(-0.011)

z+113(-0.092) z+114(-0.054) c14(-0.038) c15(-0.0088)

The green assignment indicates modification on Ser-90 (though the presence of b13 is very unlikely), while the blue assignment identifies Thr-92 as the glycosylation site.


400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

900.32

1328.20

1285.641800.82

586.30458.32 759.47

986.49 1440.63644.44387.34 1681.75 1941.781553.681166.80839.57529.23261.15 689.59

x5 x2

FSPVST(HexNAc)M(Oxidation)EPLDLQLM(Oxidation)DGQAQQK

Ser-24 or Ser-27 or Thr-28

P28800Alpha-2-antiplasmin

900.0894(3+)

v

v

*

m

[–] Peak Matches 261.1510 275.1160 329.4120 350.2580 387.3380 400.3130 432.7110 449.2380 458.3170 529.2270

y2(-0.055)

z3(0.13)

z4(0.069)

534.9430 566.3460 586.2970 630.3420 644.4390 659.1850 689.5920 759.4740 773.3090 839.5670

b3(-0.30) c5(-0.34) c-15(0.66)

z5(-0.0099)

z+16(0.10) y6(-0.16)

z+17(0.11)

c6(0.15)

906.4170 986.4900 1018.4810 1146.4410 1166.7980 1241.1550 1249.1690 1259.4550 1268.3180 1285.6390 z+18(0.018) c7(0.040) z9(0.0062) z10(-0.092)

z11(-0.16)

1304.4020 1314.7150 1332.6590 1440.6250 1553.6790 1681.7460 1714.7120 1795.5990 1800.8160 1941.7840

c11(-0.031) c12(-0.061) c13(-0.053) z+115(-0.12) c14(0.72)

c15(-0.13)

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.


500 600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

963.26

1926.07

1012.621909.95

1353.57550.28 1579.86

1451.461225.72 1709.90636.40 1881.001207.80 1509.60 1596.94861.44 1083.51464.35

x5 x2


LSEAGVQAAAAT(HexNAc)STAMSR

Thr-398

v

v

m

m

962.9673(2+)

[–] Peak Matches 464.3540 550.2810 636.3980 1012.6180 1083.5070 1155.5940 1207.8040 1225.7170 1353.5730 1417.9250

y4(0.13) z+15(0.016) z6(0.11) z+18(0.16) z+19(0.0083)

z+111(0.14) z+112(-0.058)

1445.4160 1451.4560 1509.6050 1536.6980 1579.8620 1596.9420 1709.9010 1724.0200 1766.6590 1777.8380

z13(-0.24) z+114(-0.12)

z15(0.11)

z+116(0.100) y16(-0.79) c-117(-0.18)

1795.9290 1798.4940 1851.9690 z17(0.10)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

776.26

1061.80

1142.25

1315.671011.48818.50 1909.881386.70 1595.82418.32 1173.58703.43 1467.71531.33 832.55 1708.89 1795.77401.32 1950.15


Thr-400

SALELSEAGVQAAAATST(HexNAc)AMSR

775.7141(3+)

v

m

[–] Peak Matches 247.2330 272.2850 289.3050 375.2540 378.3600 401.3210 418.3230 448.3640 514.3870 531.3330

z+12(0.093) b3(0.12) c3(0.12)

z+13(0.18) b4(0.12) c4(0.093) z4(0.15) b5(0.100) c5(0.019)

618.3270 690.5240 703.4320 747.4160 752.3320 780.9510 818.5040 832.5530 839.5050 875.6030 c6(-0.019)

c7(0.028) z5(-0.0049)

c8(0.079)

z6(0.14) c9(0.16)

940.4430 1011.4820 1019.7950 1027.2860 1053.8050 1061.7970 1076.2610 1082.5050 1127.2870 1146.1830 z7(0.026) z8(0.028)

y8(-0.19)

z9(0.014)

1173.5780 1244.7020 1315.6670 1386.6990 1467.7080 1508.6780 1574.8340 1580.8530 1595.8230 1909.8840

c12(-0.033) c13(0.054) c14(-0.018) c15(-0.023) y13(-0.0028) z14(-0.036) c17(0.032) z+115(0.095) y15(0.054) z+118(-0.033)


600 700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

953.31

1905.94

1309.62 1861.951180.601065.61831.58 1703.82

1438.65 1775.751525.68 1590.74902.651162.59 1657.79606.57 772.78700.48 1047.69 1394.211285.70

x5 x2


Ser-489

LGPPSEEDYAQPS(HexNAc)SPK

952.9440(2+)

v

v

m

[–] Peak Matches 584.4830 606.5670 612.7920 831.5770 902.6530 1065.6080 1162.5940 1168.4570 1180.5970 1300.6580

z+14(0.27)

z+16(0.17) z+17(0.21) z+18(0.098)

z+19(0.060) c-112(0.065)

1309.6210 1429.6100 1438.6460 1525.6790 1590.7350 1686.8810 1703.8200 1731.8810 1734.8610 1757.7840

z+110(0.042)

z+111(0.024) z+112(0.025) c-113(0.031)

y14(0.091)

1775.7460 1830.9670 1834.9500 z15(-0.027) c15(-0.051)

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

V20101018-11 #2935 RT: 25.56 AV: 1 NL: 3.30E3T: FTMS + c NSI d Full ms2 [email protected] [100.00-1375.00]

100 200 300 400 500 600 700 800 900 1000 1100 1200 1300m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

860.48

201.12

680.51

186.07

598.35

173.131159.66

300.19 1063.55430.74 959.54532.28

470.26662.50369.21 897.53263.14 697.42

581.81

1180.19 1349.55837.38

309.02

210.30

P50448Factor XIIa inhibitor

681.8776(2+)

TVVPATVTKPF+HexNAc

y8G(2+)

y8G

[–] Peak Matches 126.0540 138.0540 144.0640 168.0640 173.1270 186.0721 201.1220 204.0850 255.1680 263.1360

P(-7.6)

VT-28(-8.4) TV-28(-8.4) a2(-8.4)

TV(-6.8) VT(-6.8) b2(-6.8)

y2(-11)

300.1890 351.2000 369.2100 391.2310 430.7430 452.2450 470.2580 492.2780 532.2820 598.3500

b3(-9.3)

PATV-H2O(-7.6) VPAT-H2O(-7.6)

PATV(-8.8) VPAT(-8.8)

y3(-7.6) y8+2(-10)

PATVT-H2O(-12)

PATVT(-6.2)

y4(-7.4)

PATVTK(-9.8) ATVTKP(-9.8)

616.3410 662.4960 680.5090 697.4180 763.4280 766.2310 775.9680 837.3830 855.2230 860.4790

VPATVTK(-9.0)

y7(-9.0)

y8(-10)

895.4710 897.5320 931.6850 959.5440 1063.5550 1159.6610 1180.1870 1233.0100 1319.8740

b9(-9.4)

y9(-13)

MH(-9.6)

This HCD spectrum identified this NON-tryptic glycopeptide


650 700 750 800 850 900 950 1000 1050 1100 1150 1200 1250 1300 1350m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

681.84

1346.791214.86989.78 1320.84

779.691144.851023.34

950.87 1292.92879.82 1063.83 1118.04 1169.30851.74 1260.63806.67745.58701.85

x2

Factor XIIa inhibitor P50448

TVVPATVT(HexNAc)KPF

The following ETD spectrum was good enough for site assignment.

Thr-74

z5*z6 z7 v

v

c8

c10

*

681.8776(2+)


400 600 800 1000 1200 1400 1600 1800 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

939.76

1408.94

1380.38

1878.991200.31

1291.35

1111.53758.43394.31 508.25 1841.821707.84635.43 829.58 1034.55 1989.951455.68 1542.73307.35586.39

x5 x5

P81187Complement factor B

T(HexNAc)PLPEAGPQSPC(Carbamidomethyl)SLEGVEIKGGSFR

Thr-26

939.4554(3+)

v

v

*m

[–] Peak Matches 307.3460 322.3480 394.3050 409.3760 426.7860 451.3810 466.3570 478.4820 508.2540 523.3570

z+12(0.17) y2(0.16) z+13(0.097) y3(0.16)

z+14(0.15) y4(0.12)

z+15(0.0026) y5(0.095)

624.3470 629.3760 635.4280 715.5740 749.4670 758.4330 764.4400 786.5380 829.5800 843.4810

c4(0.026) z6(0.089)

z+17(0.037) c5(0.040) y7(-0.0013)

c6(0.15)

878.5570 977.5780 1034.5470 1111.5260 1200.3060 1208.3570 1275.6630 1291.3530 1299.0360 1308.2900

z+18(0.084) z+19(0.037) z+110(-0.016) c9(-0.037) z23

+2(0.21) z+123

+2(-0.29) y23

+2(0.25) z12(-0.019) y12(-0.35)

1355.9260 1364.8680 1373.8410 1455.6780 1707.8420 1784.8130 1841.8200 1878.9850 1941.9360 1989.9480

c12(-4.2e-4) z+116(0.0050) c15(-0.024) c16(-0.039)

z+119(-0.022)

P81644Apolipoprotein A-II


200 400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Re

lativ

e A

bu

nd

an

ce

606.37

887.68

844.19 908.75587.36

1230.611800.881051.60

799.71

1686.84472.35 936.60766.49 1345.62 1557.781458.661102.57359.36

696.41488.49 951.58261.25 1301.58 1441.71

FQT(HexNAc)VADYGKDLVEK

Thr-40

605.9726(3+)v

v

*

[–] Peak Matches 201.3020 261.2470 276.3630 359.3600 472.3480 488.4880 543.4580 554.3790 587.3550 597.2510

z+12(0.10)

y2(0.21) b2(0.23)

z3(0.15) z+16

+2(0.65) z4(0.059) y4(0.18)

z5(0.039) c3(-0.037)

619.4810 653.5730 696.4120 715.5120 731.8210 748.5140 763.1780 766.4890 773.6170 785.1410

y11+2(0.65)

c4(0.056) z6(0.10) y6(0.39)

z+112

+2(-0.21) z12

+2(0.30) c-15(0.10) z+17(0.18)

791.1310 799.7080 808.2500 813.7620 827.2650 844.1860 882.5140 891.7440 936.5970 1051.5980

z+113

+2(-0.15) z13

+2(0.35) c13

+2(0.27) c-113

+2(0.78) c6(0.094)

z+18(0.093) z+19(0.067)

1102.5700 1122.5670 1211.6670 1221.6380 1230.6140 1345.6240 1458.6600 1557.7790 1653.8870 1686.8420 c8(0.065) z+110(-7.3e-4)

z+111(0.0019) c9(0.014) c10(-0.0030) c11(-0.051) c12(-5.1e-4) z+113(0.065) c13(0.020)

legends for etd data in the spectra = precursor ions, charge-reduced ones too; * = charge-reduced...

Documents

etd slide

chain slide

klisdfpethexnactspk

ccdc80 protein slide

adamtsl4 protein slide

binding protein slide

human gelsolin slide

site assignment slide