63
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

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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; - PowerPoint PPT Presentation

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Page 1: Legends

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

Page 2: Legends

V20101001-14 #2633 RT: 23.14 AV: 1 NL: 1.70E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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817.35

1204.22

1123.74

1633.75991.46

392.27 512.28 594.09 708.24 1759.921460.60280.22 1014.58 1591.53 1858.051286.41832.51

x5 x2

Q03247Apolipoprotein E

DM(Oxidation)EGELGPEEPLT(HexNAc)T(HexNAc)QQPR

Thr-31 (& Thr-32)

817.0358(3+)v

m

Page 3: Legends

[–] Peak Matches 280.2230 349.2920 385.3910 392.2700 408.4650 466.1540 503.5190 512.2790 545.4120 583.3410

c2(0.13) z+13(0.17) b3(0.16) c-13(0.33) c3(-0.67) c4(-0.0062) z4(0.0089)

594.0890 596.4030 665.3270 708.2360 714.3560 800.5430 821.4550 832.5100 848.1960 862.5220 c-15(-0.11) c6(-0.051) y5(0.094) c8(0.16) 991.4580 1014.5820 1093.9840 1115.6000 1121.4820 1123.7450 1159.7920 1175.6110 1189.8570 1197.7480

c9(0.054) z+16(-0.050) 1208.3120 1441.7920 1453.6640 1460.5990 1591.5260 1617.6340 1633.7500 1744.7880 1759.9150 1858.0500

z+19(-0.11) b13(-0.050) c-113(0.048)

Page 4: Legends

V20101005-05 #1364 RT: 14.66 AV: 1 NL: 1.73E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1635.00]

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

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541.51

803.55

812.031624.04

790.991607.05711.02 1082.86

872.81 1494.03384.691370.09

470.58 1241.03 1565.031153.96703.05 1354.881421.12959.74340.76 669.65269.57 1275.13576.73450.54

x5 x5

Apolipoprotein E Q03247

Thr-307

v

m

v v

*

541.2650(3+)

LRPS(HexNAc)PTSPPSENH

Page 5: Legends

[–] Peak Matches 204.4970 226.6110 254.4800 269.5660 340.7620 345.6870 370.1700 384.6910 450.5410 470.5850

z2(0.38) z+12(-0.63)

y2(-0.55) b2(-0.63)

c3(0.42) z+13(0.54)

z4(0.41) z+14(-0.60)

485.7180 516.6750 522.0380 558.2680 561.1410 576.7350 596.6370 601.1690 641.9840 669.6480

y4(-0.48) c-19

+2(-0.075) c9

+2(-0.58) 703.0470 711.0200 721.2380 742.8430 747.4030 751.6660 771.1630 776.8040 794.9750 872.8100

c12+2(0.47) z+112

+2(0.056) z12

+2(0.56) z7(0.35) z+17(-0.65)

c5(-0.27) c-15(0.73) c6(0.33)

1063.7380 1066.8180 1080.7500 1082.8630 1153.9600 1221.7650 1241.0330 1370.0940 1486.0430 1494.0330

c9(0.34) c10(0.38) z+110(0.50) c11(0.40) z+112(0.35)

Page 6: Legends

V20101001-12 #1335 RT: 14.25 AV: 1 NL: 2.36E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1475.00]

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

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487.13

722.16

730.18689.66

378.36973.72578.37

882.47393.42 628.77 1460.751011.70300.47 1082.72955.711301.71769.56415.60 1377.801197.59936.69272.46 842.56570.73

x5 x2

Q05717Insulin-like growth factor-binding protein 5

Thr-171

486.9032(3+)

v

v

vm *

FVGGAENT(HexNAc)AHPR

Page 7: Legends

[–] Peak Matches 272.4550 300.4710 320.4260 378.3640 393.4170 415.6040 449.3960 464.4120 482.5890 505.2700

y2(0.28) c-13(0.24) c3(-0.77) c4(0.15) z3(0.21)

y5+2(0.72)

c5(0.15) y6

+2(-0.33) z4(0.16) 512.9600 526.4350 534.3210 541.5360 549.4620 570.7340 578.3700 582.7860 599.1660 602.0100

z8

+2(-0.22) z+18

+2(-0.72) y8+2(-0.30) z+19

+2(-0.034) z9

+2(0.47) c6(0.077) y9

+2(0.097) z+110

+2(-0.11) z10

+2(0.39) 612.6040 620.6620 628.7690 648.5900 666.2480 689.6650 702.3890 769.5630 882.4740 936.6930

z+111

+2(-0.22) z11

+2(0.28) z+15(0.18) z6(0.055) 955.7070 973.7230 996.5590 1011.6980 1067.6120 1082.7170 1140.6500 1197.5950 1301.7070 1377.8040

c8(0.096) z7(0.24) z+17(-0.77) c9(0.11) z8(0.22)

z+18(-0.79) z+19(0.12) z+110(0.046) c11(0.095)

Page 8: Legends

V20101001-08 #1770 RT: 17.14 AV: 1 NL: 3.24E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1730.00]

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860.20

1719.79

1139.67

1674.69457.53 1268.63761.601369.741052.64 1560.761426.76889.60 1249.82328.47 787.63665.31

x5 x2

Q28083Collagen alpha-1(XI) chain (Fragment)

Thr-86

NYGTESYQT(HexNAc)EAPR

v

v

859.8793(2+)

Page 9: Legends

[–] Peak Matches 328.4750 457.5310 633.4180 761.6040 889.5970 1052.6350 1121.6720 1139.6670 1249.8240 1268.6280

z+13(0.28) z+14(0.29) z+15(0.24) z+16(0.17) z+17(0.15) z+18(0.15) z+19(0.064) 1285.6800 1290.8950 1369.7370 1426.7630 1441.7790 1499.7990 1517.7850 1560.7560 1588.8450 1613.9060

z+110(0.13) z+111(0.13) y11(0.13) c-112(0.099) z12(0.16) 1622.9650 1630.8200 1647.8520

Page 10: Legends

V20101006-04 #2507 RT: 22.62 AV: 1 NL: 3.72E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

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759.33

1117.251138.22

388.311518.73962.52

1889.951314.59550.25 1727.791274.591402.70874.47 1187.67 1620.33273.27 658.36 1870.90 1983.96404.45

x5 x5

Q28107Coagulation factor V

Ser-1151 & Thr-1154

759.0452(3+)v

v

m *

RS(HexNAc)PPT(HexNAc)QPSQIPNYDLR

Page 11: Legends

[–] Peak Matches 229.3540 273.2690 288.4280 388.3130 404.4470 507.4480 550.2460 601.6560 658.3570 665.5050

z+12(0.077) b3

+2(0.63) y2(0.22) z+13(0.094) z4(-0.029) c4(0.0051) z+15(0.18)

675.7450 694.3120 737.5980 751.4250 768.2820 776.8620 821.8680 839.5970 860.3210 874.4720

y6(-0.53) z7(0.018) 962.5160 1002.6700 1012.7920 1020.1330 1029.7000 1037.6580 1085.0230 1089.5040 1094.9630 1102.8170

c5(0.037) z8(0.16) c-114

+2(0.19) c14

+2(-0.31) z9(-0.041)

1121.2950 1187.6700 1274.5880 1314.5900 1400.3550 1402.7010 1500.7420 1518.7290 1727.7910 1889.9480

c7(0.080) c8(-0.034) z11(-0.066) c9(0.020) c13(0.024)

Page 12: Legends

V20101018-11 #4705 RT: 37.46 AV: 1 NL: 6.99E3T: FTMS + c NSI d Full ms2 [email protected] [100.00-1735.00]

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204.08445.22

186.07

925.49592.29

1072.56741.37

888.44812.41261.14

959.47413.20 628.29280.16

314.13 660.36 1054.55500.23 1672.03547.28

1332.651256.64 1444.711143.35

V20101018-11 #4706 RT: 37.46 AV: 1 NL: 5.04E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1735.00]

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860.77

1677.94

1589.91

1702.85

1144.691476.81

1031.641501.88

1389.82 1517.971422.781276.741118.74772.68 903.72614.69 1371.801004.78 1248.43430.45 683.73534.38

x10 x5

HCD

ETD

860.4367(2+)

v

vm

AIPT(HexNAc)DVSQIFPSLE

c7* z9*

z11c9*c8*b10

c11

c12

c13

z10

Q28107Coagulation factor V

Thr-1171

Page 13: Legends

[–] Peak Matches 126.0540 138.0540 144.0640 148.0590 167.0800 185.0910 186.0740 204.0850 261.1420 280.1630

P(-7.6) y1(-9.7) PS-H2O(-9.0) PS(-5.8) y2(-9.6) PSL-H2O(-9.2)

298.1730 314.1320 413.1990 445.2250 500.2300 592.2920 597.3180 628.2870 660.3650 741.3710

PSL(-11) PTD(-8.5) PTDV(-9.9) y4(-9.6) PTDVS(-10) y5(-9.6) b6(-10) PTDVSQ(-11)

IPTDVSQ(-9.1) PTDVSQI(-9.1)

794.3970 812.4070 860.4510 870.4270 888.4380 907.4830 925.4910 941.4660 959.4740 1044.5630

b8-H2O(-9.2) b8(-9.7)

PTDVSQIF-28(-0.28) TDVSQIFP-28(-0.28)

PTDVSQIF-H2O(-9.9) TDVSQIFP-H2O(-9.9)

TDVSQIFP(-9.2) PTDVSQIF(-9.2)

b9-H2O(-5.9) b9(-8.6) a10(-9.0)

1054.5510 1072.5570 1238.6330 1256.6390 1332.6530 1396.8860 1444.7090 1659.7890 1662.8540 1672.0290 b10-H2O(-5.5) b10(-9.6) b12-H2O(-6.9) b12(-10) y12(-11)

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.

Page 14: Legends

V20101018-06 #1962 RT: 18.22 AV: 1 NL: 1.38E4T: FTMS + c NSI d Full ms2 [email protected] [100.00-1295.00]

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

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531.32

208.95

440.28

429.08359.03

126.05186.07

144.06 568.38

244.16 879.56395.26669.42 818.47312.19 522.31 782.51590.31 836.47 1140.57969.27 1030.27

HCD

428.2453(3+)

EAPLTPKVPK+HexNAc

Thr-696

Q29RQ1Complement component C7

Page 15: Legends

[–] Peak Matches 126.0540 138.0540 144.0640 155.0800 168.0640 173.0910 183.0750 186.0740 201.0850 204.0850 P(-7.6) a2-H2O(-9.7) a2(-6.2) b2-H2O(-7.7) b2(-9.9) 226.1530 244.1630 280.1270 312.1890 395.2610 410.2670 427.7420 429.0850 431.2770 440.2830

PK(-8.9) y2(-11) b3-H2O(-7.8) PLT(-8.9) LTP(-8.9) y8-H2O+2(-10) y8

+2(-8.5) LTPK(-8.5)

522.3110 526.3130 531.3160 540.3220 550.3670 568.3760 577.7570 589.3090 590.3110 636.3990

MH-H2O+2(-10) MH+2(-8.5) y5(-10) PLTPKV(-14) LTPKVP(-14)

641.3670 669.4230 754.3820 782.5080 818.4700 836.4740 879.5580 969.2660 1030.2720 1140.5700

y6(-9.5) y7(-7.0) b8-H2O(-8.6) y8(-9.3)

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

Single potential site.

Page 16: Legends

V20101001-07 #2662 RT: 23.27 AV: 1 NL: 8.00E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1900.00]

400 600 800 1000 1200 1400 1600 1800m/z

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944.39

1888.10

1871.01

1829.01

1102.71 1742.03674.65

1669.05971.72603.48 1573.921415.87 1530.92773.67504.54 1283.791057.49 1164.33376.54 857.91

x5 x5

Q32KM8Augurin

943.9625(2+)

Thr-47

EAPAPT(HexNAc)MTPVAVQESR

v

v

m

Page 17: Legends

[–] Peak Matches 376.5370 504.5440 543.3260 603.4770 615.5500 642.5400 658.4740 674.6480 697.5350 773.6700

z+13(0.35) z+14(0.30) z+15(0.17) z+16(0.30) z+17(0.25) 971.7180 1102.7100 1390.8100 1406.9310 1415.8710 1530.9190 1573.9230 1639.8470 1642.8730 1669.0450

z+19(0.20) z+110(0.15) z+111(0.25) z13(0.16) c14(0.074) 1681.9660 1685.9190 1714.9120 1717.0940 1728.9420 1742.0270 1797.0120 1814.0050 1817.0370 c-115(0.12) z15(0.17)

Page 18: Legends

V20101018-12 #1539 RT: 15.88 AV: 1 NL: 1.59E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

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748.16

1185.23

622.331473.861372.271120.72806.58 997.19

1309.05948.891695.72649.19375.27 1611.73259.27 1079.61864.44590.90473.37 1871.661717.66

x5 x2

Q32PI4Complement factor I

747.8566(4+)

Thr-57

ETEASSEVKPT(HexNAc)STQDTSQKDFVDKK

v

v

Page 19: Legends

[–] Peak Matches 259.2700 275.3350 375.2750 448.3490 473.3670 490.7310 590.9040 598.3890 622.3310 636.4140

z2(0.081) y2(0.13) z+13(0.051) c4(0.15) z4(0.083) z+110

+2(0.090) z10

+2(0.59) y10+2(0.069) c6(0.063) y5(0.042)

649.1910 655.5180 668.9600 712.2840 729.2800 735.4830 751.3030 762.7590 806.5770 814.1510

y11+2(-0.31)

z+112+2(-

0.073) z12

+2(0.43) z6(0.10) c7(-0.0075) y6(-0.095) c-119

+3(-0.72)

z+113+2(-

0.12) z13

+2(0.38)

z+114+2(0.18)

z14+2(0.68) y14

+2(0.25)

915.0260 948.8870 954.1010 973.6690 985.6660 1120.7240 1128.7830 1185.2310 1229.5740 1295.4750

z+123+3(-

0.084) z23

+3(0.25)

z+124+3(0.094)

z24+3(0.43)

b24+3(0.78)

y24+3(0.30)

c24+3(0.32)

c-124+3(0.65)

z+118+2(0.16)

z18+2(0.66)

y18+2(0.71)

c19+2(0.75)

z+119+2(0.14)

c-120+2(0.19)

c20+2(-0.31)

z19+2(0.65)

z+111(-0.17)

1309.0490 1367.6360 1372.2710 1379.6170 1408.9640 1423.6690 1430.4020 1478.3710 1611.7340 1695.7190

c22+2(0.44)

z+123+2(0.11)

z23+2(0.61)

c11(-0.037) y23

+2(-0.050)

z+112(-0.037)

y24+2(0.21)

c24+2(0.23)

c-124+2(0.73)

z+114(-0.052) c14(-0.073)

Page 20: Legends

V20101006-04 #2744 RT: 24.23 AV: 1 NL: 3.75E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

400 600 800 1000 1200 1400 1600 1800m/z

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10

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100

Rel

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911.80

1338.34

1367.35

1266.761779.73757.41 956.49 1026.57435.35 1709.82548.24 863.49 1823.76335.25 1426.581141.63 1594.69659.45 1978.08

x5 x2

Q3MHN2Complement component C9

Thr-24 & Ser-26

GPT(HexNAc)PS(HexNAc)YDPAERQGTPLPIDC(Carbamidomethyl)R

911.7614(3+)

v

v

*

m

Page 21: Legends

[–] Peak Matches 335.2500 413.3010 435.3470 450.2150 548.2430 563.2600 573.3780 659.4490 663.3130 674.3020

y2(0.10) z+13(0.18) y3(0.038) z+14(-0.0067) y4(-6.1e-4) c4(0.090) 688.2600 690.4840 757.4120 773.5890 806.4840 819.6180 956.4870 1026.5720 1141.6270 1249.9070

z6(0.033) y13

+2(0.53) y6(0.19) z+18(2.2e-5) c6(0.11) z+110(0.060) 1258.2040 1266.7560 1282.1200 1296.6530 1308.6940 1314.6330 1322.7760 1331.6760 1350.6800 1426.5820

z19

+2(0.029) z+119

+2(-0.47) z11(-0.0073) c-19(0.12) z+112(-0.13)

1438.5650 1594.6900 1709.8180 1779.7290 1821.3820 1823.7630 c10(-0.057) c11(-0.033) z+115(-0.0095) c13(-0.074)

Page 22: Legends

V20101006-04 #3471 RT: 29.05 AV: 1 NL: 2.97E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

0

10

20

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100

Rel

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793.56

1577.90477.24

1043.33

1347.87293.25 1506.891206.55686.51

1966.08925.80 1439.91457.34 1872.971638.87586.46204.18

x5

FQSPT(HexNAc)PNTLMPVVPAAS(HexNAc)PT(HexNAc)PPVRR

Thr-270 & Ser-282 & Thr-284

Q3SWW8Thrombospondin-4

793.1561(4+)

v

v

m

m

Page 23: Legends

[–] Peak Matches 293.2530 457.3410 477.2410 586.4570 641.5370 650.3220 658.5220 686.5080 694.6500 721.7380

c2(0.092) z+16+2(0.082)

z6+2(0.59) c4(-0.0046)

z8+2(-0.015)

z+18+2(-

0.52) y8

+2(0.18) z+19+2(0.15)

z9+2(0.65) y9

+2(0.79) z+110

+2(-0.14) z10

+2(0.36) 768.0190 778.0760 819.7890 824.2250 827.5090 865.7330 869.0870 878.4780 882.5700 898.8450

y11+2(0.17)

z+112+2(-

0.15) z12

+2(0.35) y12+2(0.065)

z13+2(0.12)

z+113+2(-

0.39) c6(0.053)

925.7980 984.4930 990.0540 992.3210 1027.5490 1033.6610 1046.1570 1090.3240 1147.3250 1206.5480

y14+2(0.29) c7(-0.15)

z17+2(0.24)

z+117+2(-

0.26)

z18+2(0.22)

z+118+2(-

0.28) c9(-0.052)

1322.5130 1347.8680 1439.9060 1476.3870 1484.3530 1506.8890 1549.4720 1569.4860 1966.0760 1983.6320

z20+2(0.18)

z+120+2(-

0.33)

z22+2(0.17)

z+122+2(-

0.33) c23

+2(0.12) c-123

+2(0.63) z+115(0.045)

Page 24: Legends

V20101001-11 #2277 RT: 21.19 AV: 1 NL: 3.96E3T: FTMS + c NSI d Full ms2 [email protected] [100.00-2000.00]

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

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10

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30

40

50

60

70

80

90

100

Rel

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204.09

186.08

660.85

736.40823.44 1663.41343.21 511.30

1817.851597.291330.95936.52498.18 1446.40 1963.96227.10 999.82 1279.53637.24

V20101001-11 #2278 RT: 21.19 AV: 1 NL: 2.16E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

700 800 900 1000 1100 1200 1300 1400 1500 1600 1700 1800 1900 2000m/z

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

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bund

ance

1010.79

1893.79

909.63 1781.911978.93

1766.831516.631298.56808.531652.751227.93 1495.141108.67 1405.98935.53 1563.69

x10 x5

HCD

ETD

1010.9789(2+)

Q3SYR5Apolipoprotein C-IV

Thr-35

Q(Gln->pyro-Glu)QEEPEGT(HexNAc)LSPQPAPAR

v

mmy11

y15

z16

y14

y13

*

z15*

z8*

y8 y10

Page 25: Legends

[–] Peak Matches 126.0540 138.0540 144.0650 168.0650 175.1180 186.0750 204.0850 227.1010 240.0950 343.2070

P(-7.6) y1(-5.4) PE(-7.2) EP(-7.2)

b2(-12) QE-H2O(-12) y3(-5.3)

367.1590 369.1400 385.1710 498.1800 511.2960 660.8460 673.6800 736.4050 772.5460 823.4400

PEGT-H2O(-6.0) b3(-1.3) QEE-H2O(-1.3)

EPEG-28(-2.0) PEGT(-2.0) b4(-6.2) y5(-5.3) y13

+2(-4.5) y7(-6.9) y8(-2.5)

936.5180 960.7190 977.4170 999.8160 1320.6850 1328.7810 1330.9540 1446.3990 1459.7060 1558.6950 y9(-8.7) b9-H2O(-4.2) y13(-4.3)

1595.8220 1597.0380 1597.2900 1658.8700 1661.8940 1663.4090 1667.9560 1817.8480 1963.9630 1977.5890

MH(-10)

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.

Page 26: Legends

V20101018-03 #1105 RT: 12.47 AV: 1 NL: 9.53E2T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

0

10

20

30

40

50

60

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90

100

Rel

ativ

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566.42

1010.58

1125.08740.67359.20

808.15 953.35849.53244.26 729.89398.93 920.43 1177.64649.36

1459.72415.311905.491678.721351.43

1582.61 1791.64259.18 431.20 1264.44

x5 x5

FGHS(HexNAc)VGDRTS(HexNAc)RKPGGGLK

Q3T052Q5EA67

Ser-629 & Ser-635

566.2913 (4+)

Inter-alpha-trypsin inhibitor heavy chain H4

v

v v

Page 27: Legends

[–] Peak Matches 244.2610 359.1960 398.9300 415.3070 543.9110 552.0130 594.3540 649.3630 671.8720 677.0230

z2(0.083)

c3(0.013) c-18

+3(0.023) z+14(-0.033) c8

+3(-0.31)

z8+2(0.18)

z+18+2(-0.32) z5(0.064)

z9+2(0.11)

y14+3(-0.39)

z+19+2(-0.40)

y9+2(0.20) z10

+2(0.025) z+110

+2(-0.48) b15

+3(0.046) c4(0.069) z11

+2(-0.51)

681.9560 687.6360 726.3230 729.8880 797.6190 805.3620 808.1550 812.3870 841.9640 849.5330

z+116+3(0.27)

z16+3(0.60) b10

+2(0.50) z12+2(-0.0049)

z+112+2(-0.51) z+18(0.12) c6(-0.022) z14

+2(0.22) z+114

+2(-0.29)

c11+2(-0.0027)

y8(-0.12) c-111

+2(0.50)

903.0620 920.4310 926.2190 932.1040 944.2520 953.3490 961.8800 983.0500 989.2040 1010.5840

b7(-0.32) c7(0.020) b14+2(-0.71)

c14+2(-0.13)

z+115+2(-0.15)

z15+2(0.36)

c-114+2(0.38)

c16

+2(0.088) c-116

+2(0.59)

1022.2950 1073.3110 1076.6330 1087.6970 1177.6410 1351.4340 1459.7250 1467.5910 1678.7250 1905.4920

z+116+2(0.27)

z16+2(0.77) c8(0.12) z+19(0.086) c9(0.081) z+112(-0.061) c10(-0.080)

c14(-0.45) z+115(-0.50) z15(0.51) c-114(0.56)

Page 28: Legends

V20101005-03 #2920 RT: 25.43 AV: 1 NL: 1.40E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

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60

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80

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100

Rel

ativ

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1618.271079.39

1517.28

990.461293.58

1201.54 1459.49 1947.76523.21 933.44638.34 1776.77775.35306.29 422.21 540.36 1351.06789.35649.59 1634.28 1832.251159.60

x5 x5

1078.4978(3+)

Ser-677 (& Ser-683; & Ser-686 or Thr-688)

LMS(HexNAc)PLAPAS(HexNAc)APS(HexNAc)PTSGPGGASHDTDFR

vv

m

Q3T052Q5EA67

Inter-alpha-trypsin inhibitor heavy chain H4

Page 29: Legends

[–] Peak Matches 296.3890 306.2930 322.3210 350.3870 422.2140 429.2820 448.5400 523.2070 540.3590 595.3210

z2(0.12) y2(0.13) z+13(0.011) z+14(-0.044) z10

+2(-0.52) 613.4390 638.3440 649.5890 654.2700 753.3980 762.4210 775.3490 789.3540 797.4130 832.4970

z+15(0.066) c4(0.27) c5(0.014) z+16(0.012) z+114+2(0.57)

933.4450 990.4610 1047.7910 1201.5390 1210.2400 1287.5380 1291.3510 1293.5800 1459.4940 1487.9530

z+18(0.039) z+19(0.033) z+110(0.34) z+112(0.016) y21+2(0.70) z13(-0.0094)

b22+2(0.25)

c9(-0.29) c-19(0.71)

z23+2(-0.0094)

z+123+2(-0.51)

c11(-0.24) c-111(0.77)

z+125+2(0.28)

z25+2(0.78)

1496.2550 1499.9340 1502.4410 1508.8190 1517.2760 1553.7610 1572.4900 1581.3670 1776.7660 1947.7650

y15(0.77) z+126+2(0.57) z+116(-0.0011) c14(-0.18)

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

Page 30: Legends

V20101018-15 #1719 RT: 16.24 AV: 1 NL: 1.88E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

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bund

ance

1364.31909.81

1263.70

1176.27

1818.65638.36

990.51775.391739.591035.40523.21 1528.59 1954.74422.31 1693.61307.36 1491.42673.77 862.47484.68 579.25

x5 x5

AS(HexNAc)APS(HexNAc)PT(HexNAc)S(HexNAc)GPGGASHDTDFR

909.7225(3+)

(Ser-683) & Ser-686 & Thr-688 & Ser-689v

v

*

m

Q3T052Q5EA67

Inter-alpha-trypsin inhibitor heavy chain H4

Page 31: Legends

[–] Peak Matches 281.3030 307.3620 322.3060 411.0640 422.3100 484.6800 507.6650 523.2110 531.4880 539.2760

z+12(0.19) y2(0.12) z+13(0.11) z+14(-0.040) z10

+2(-0.51) y10+2(-0.25)

560.4370 579.2510 638.3630 653.3480 673.7670 731.5140 768.5040 775.3900 780.4070 789.4070

z+15(0.085) y5(0.059) z+16(0.053) 862.4680 933.4870 990.5100 1035.3980 1092.5840 1176.2670 1200.4830 1218.8840 1246.3200 1255.1290

z+17(0.099) c-16(0.058) z+18(0.081) z+19(0.082) z+116

+2(0.62) z+118+2(0.26)

z18+2(0.76) z12(-0.032)

1263.6980 1275.2930 1313.7240 1319.8100 1325.6530 1328.7550 1347.4190 1528.5910 1739.5920 1818.6490

z19+2(-0.75) y19

+2(0.18) c8(-0.084) c11(-0.18)

Page 32: Legends

V20101018-07 #1249 RT: 13.41 AV: 1 NL: 1.41E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1825.00]

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

Rel

ativ

e A

bund

ance

604.63

906.54

885.36

1206.65789.31 1653.92

1176.67522.48421.53 1391.86

1290.75

774.66 1507.901038.641576.83637.49 1077.99932.74322.62 538.57 1721.211338.35

x5 x5

T(HexNAc)SGPGGAS(HexNAc)HDTDFR

(Thr-688 or Ser-689) & Ser-695

v

v

*

m

604.2606(3+)

Q3T052Q5EA67

Inter-alpha-trypsin inhibitor heavy chain H4

Page 33: Legends

[–] Peak Matches 306.6080 322.6210 386.5330 409.5610 421.5280 522.4810 538.5730 563.4540 569.6120 572.8290

z2(0.44) z+12(-0.57) y2(0.43) c2(0.37) z3(0.33)

z+13(-0.68) z4(0.24) z+14(-0.77) y4(0.31) c4(0.19)

585.6280 594.5860 612.6070 615.1090 620.6080 637.4860 677.5800 681.3230 702.6240 707.9620

c5(0.32) z5(0.22) b10

+2(0.22) z+15(-0.79)

c6(0.27) y11+2(-0.48) z+112

+2(-0.18) z12

+2(0.32)

746.2480 748.6720 774.6580 789.3090 804.9240 823.6710 847.0290 865.8760 1038.6440 1064.6990 z+113

+2(-0.073) z13

+2(0.43) c7(0.32) z6(0.33) z+16(-0.68) z13

+2(-0.33) c8(0.19) z7(0.26) z+17(-0.75)

1176.6740 1191.6960 1201.8000 1206.6520 1290.7510 1391.8620 1403.8950 1491.9370 1507.8960 1653.9180

c10(0.21) c11(0.27) z12(0.30) z+112(-0.71) z+113(0.30) c13(0.23)

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

Page 34: Legends

V20101018-07 #1310 RT: 13.87 AV: 1 NL: 1.30E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1825.00]

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

Rel

ativ

e A

bund

ance

604.51

885.38

906.52

1208.68

876.87 972.79840.62

1653.851135.81677.62 1391.82796.85421.611087.68 1508.04 1611.05306.57 1066.53 1345.981226.02506.57

x5 x5

604.2604(3+)

(Thr-688) & Thr-698

T(HexNAc)SGPGGASHDT(HexNAc)DFR

v

v*

m

Q3T052Q5EA67

Inter-alpha-trypsin inhibitor heavy chain H4

Page 35: Legends

[–] Peak Matches 306.5700 322.5880 377.5660 409.5320 421.6100 437.4990 468.5700 506.5680 559.6470 562.6040

z2(0.40) z+12(-0.61) y2(0.40) c2(0.34) z3(0.41)

z+13(-0.59) y3(0.28) c-14(0.34) c4(-0.66)

585.3230 593.9450 596.4530 599.4200 620.5030 633.5620 677.6180 698.6760 702.9690 711.6570

z9+2(-0.30) c5(0.21) y10

+2(0.29) c6(0.31) z+112

+2(0.16) z12

+2(0.67) 746.4660 748.5740 796.8460 805.3340 835.6990 840.6230 860.8450 889.2290 972.7860 977.6940

z+113+2(0.15)

z13+2(0.65) c7(0.23) c8(0.32) z5(0.27)

z+15(-0.73) c9(0.35) z6(0.29) z+16(-0.72)

1087.6790 1135.8110 1192.7200 1208.6820 1391.8200 1405.8650 1491.8420 1508.0420 1611.0500 1653.8460

c10(0.21) z8(0.33) z+18(-0.67)

z9(0.22) z+19(-0.79) y9(0.16) c11(0.23) z+113(0.21) c13(0.16)

Page 36: Legends

Vitronectin Q3ZBS7

Thr-63V20101005-05 #2223 RT: 20.87 AV: 1 NL: 2.59E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1725.00]

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

Rel

ativ

e A

bund

ance

571.07

1141.55

826.72674.48 1334.73731.55

378.22 856.19 980.54754.49 1124.57

1653.63881.61645.39 1097.68 1316.74 1694.931403.85 1508.76 1608.91940.66 1039.71 1290.74360.34 389.53 553.29

x5 x5

570.6102(3+)

AEC(Carbamidomethyl)KPQVT(HexNAc)RGDVF

v

v

*

m

m

Page 37: Legends

[–] Peak Matches 360.3390 364.3620 378.2220 389.5310 405.3440 453.1080 489.0670 494.3400 505.4940 524.3560

b3(-0.78) z3(0.20) c3(0.078) b4(-0.15) 553.2940 556.3280 562.3980 577.3130 587.8350 593.3780 596.4050 603.4070 606.1960 630.3880

z5(0.028) y5(0.074) c5(0.12) 645.3910 674.4780 731.5540 754.4930 759.8290 781.6380 811.0230 830.5180 881.6090 980.5430

c-19+2(0.068)

c9+2(-0.44)

c10+2(0.14)

c-110+2(0.64)

c6(0.20) c-111

+2(0.21) c11

+2(-0.30) c12

+2(0.25) c-112

+2(0.76) c7(0.099) z6(0.20) z7(0.062)

1097.6830 1111.1270 1124.5670 1134.6840 1141.5520 1316.7380 1334.7350 1347.6610 1403.8480 1508.7600

y8(0.0088) c8(0.14) z+110(0.040) c10(-0.0075)

Both ends non-tryptic!

Precursor mass error = -0.15 ppmScore = 26.3; E = 2.9e-4

Page 38: Legends

V20101018-04 #2689 RT: 24.01 AV: 1 NL: 2.99E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1705.00]

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

Rel

ativ

e A

bund

ance

845.53

1647.831266.32

1560.731447.73

1180.63763.52 1066.61459.67 1348.74372.50 543.05 710.67 826.61 1161.731048.57857.28

x10 x2

Q3ZBS7Vitronectin

Thr-97 & Thr-98

QPEST(HexNAc)T(HexNAc)LAPVLQ

v

v

* m

845.4210(2+)

Page 39: Legends

[–] Peak Matches 372.5000 459.6710 543.0510 570.0150 575.5240 763.5180 826.6070 1066.6070 1180.6270 1200.9800 c3(0.31) c4(0.45) c5(0.17) c-16(0.14) c7(0.069) 1221.9020 1236.9320 1245.2090 1249.2190 1257.8490 1266.3170 1348.7400 1431.7650 1447.7330 1471.7810

y8(0.56) c9(0.092) c10(0.017) 1487.7600 1516.8070 1560.7340 1618.7160 1628.0120

c11(-0.066)

both ends non-tryptic!

Precursor mass error = -4.8 ppmScore = 28.6; E = 4.5e-4

Page 40: Legends

V20101018-16 #3211 RT: 26.86 AV: 1 NL: 1.09E4T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

679.71

998.37

918.31

471.26 1188.53 1519.72851.53763.401568.68 1996.02

1276.62 1909.90584.32 1060.47 1356.66 1779.871078.67261.29 1604.85401.36

x5 x5

AQT(HexNAc)LETPVQAPVLNPEK

Thr-107

Q3ZBS7Vitronectin

680.0245(3+)

v

m

Page 41: Legends

[–] Peak Matches 261.2880 373.4120 401.3570 471.2630 521.2340 584.3170 600.4200 628.4150 634.4710 663.5030

z+12(0.14) y3(0.20) z4(0.031) c3(-0.023) z5(5.7e-4) y5(0.085) c4(0.13) 699.4740 719.4880 746.4490 748.5870 763.4040 797.5950 847.4890 851.5280 867.5630 874.9640

y6(0.070) b5(0.092) c5(0.021) b6(0.085) z8(0.053) y8(0.070) 910.7040 918.3110 954.7080 961.4950 976.1430 984.3220 1002.7350 1060.4700 1078.6720 1188.5330

c7(0.011) c8(-0.082) z10(0.070) c9(-0.078) 1276.6160 1356.6630 1359.5360 1405.6180 1455.6600 1519.7210 1568.6820 1779.8720 1909.8980 1951.8500 z12(-0.086) c11(-0.038) z13(-0.13) c12(-0.11) z+114(-0.12) c13(-0.17) c15(-0.077) z+116(-0.17)

Page 42: Legends

V20101001-09 #3021 RT: 26.19 AV: 1 NL: 2.23E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

400 600 800 1000 1200 1400 1600 1800m/z

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

1055.22

1553.79

1537.731581.891481.30

1444.34910.61520.30376.33 1612.03691.26 849.46 1220.81 1743.57 1944.981300.16391.45 1124.09535.20

x5 x5

Q3ZBS7Vitronectin

GDSEPGMGTSDLGT(HexNAc)SESPAEEETC(Carbamidomethyl)SGKPF

Thr-142 or Ser-143

v

1054.7689(3+)

vm

Page 43: Legends

[–] Peak Matches 376.3340 389.1640 391.4520 433.4510 503.2590 520.2970 535.2020 560.1740 629.2810 648.4120

z+13(0.11) b4(0.034) y3(0.22) z+14(0.21) c5(0.049) z+15(0.020) y5(-0.085) c6(-0.057) 672.4130 676.4180 691.2640 726.5990 729.8290 748.4700 781.4280 797.3430 849.4610 910.6050

c7(-0.0076) c8(0.18) z+17(0.073) c9(0.12) z+18(0.21) 936.3670 1039.5370 1220.8060 1388.1250 1423.6240 1444.3420 1451.1830 1472.4040 1481.2980 1487.4590

c10(-0.0057) z+19(0.097) c-113(0.31) c13(-0.70) z+113(0.019) b27

+2(0.60) 1495.9080 1507.9320 1523.7320 1529.4040 1537.7330 1546.4740 1612.0330 1639.7030

c28

+2(0.31) b14(-0.67)

c-115(0.38) c15(-0.63) z+115(0.024)

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

Page 44: Legends

V20101001-09 #1756 RT: 17.45 AV: 1 NL: 1.37E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1865.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

925.84

1834.10

1546.931806.081004.87 1162.87 1692.021434.03629.63 1634.031249.04558.67 1091.81 1488.921338.07933.79906.62

x10 x5

v

v

925.4483(2+)

Thr-408

Q58D34Peptidase inhibitor 16

SLSNSPSASAT(HexNAc)ANAVGGR

Page 45: Legends

[–] Peak Matches 558.6660 610.6020 629.6300 906.6170 933.7860 1004.8730 1091.8080 1162.8670 1249.0350 1389.9010

z+16(0.37) z+17(0.29) z+18(0.32) z+19(0.37) z+110(0.28) z+111(0.30) z12(0.44) z+112(-0.57)

1434.0350 1488.9180 1546.9250 1615.0470 1630.1750 1634.0270 1650.2060 1674.9980 1692.0180 1747.1810

z+114(0.35) z15(0.20)

z16(0.27) z+116(-0.73) c-116(-0.75)

y16(0.43) b17(-0.78) c-117(0.22) c17(-0.79)

z17(0.34) z+117(-0.66)

1779.1150 1788.3590

Page 46: Legends

V20101018-09 #2691 RT: 23.68 AV: 1 NL: 4.02E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1840.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

914.79

1608.90

657.641023.70 1513.77 1829.011625.95

1426.841786.031372.00

613.55 1286.87728.66 1210.021130.44798.82421.43 1007.58

x10 x5

T(HexNAc)S(HexNAc)PPQPAARPSSLL

914.4683(2+)

Q58D62Fetuin B

Thr-19 & Thr-20

v

vm*

Page 47: Legends

[–] Peak Matches 421.4340 613.5460 638.6850 657.6420 728.6580 1023.6970 1286.8710 1343.1220 1372.0000 1407.8140

z+16(0.25) z+17(0.23) z10(0.13) 1426.8420 1495.8470 1508.8450 1513.7740 1592.8330 1600.9050 1608.9020 1625.9530 1655.9640 1714.0500 c10(0.12) z+113(0.050) c11(0.025) c12(0.12) c13(0.18) 1730.0330 1741.9780 1754.0270 1757.9960

Precursor mass error = -2.3 ppmScore = 22.1; E = 0.012

both ends are non-tryptic

Page 48: Legends

Q58D62Fetuin B

Thr-157V20101018-14 #2427 RT: 21.42 AV: 1 NL: 1.10E4T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

724.29

1056.71

570.27370.28

1601.49 1801.60685.30 1486.44984.16 1139.35457.18 1963.70586.42 1448.50848.43 1714.611323.43272.29

x2

723.9690(3+)v

m

TC(Carbamidomethyl)PDC(Carbamidomethyl)PS(HexNAc)TSPYDLSNPR

Page 49: Legends

[–] Peak Matches 204.0930 272.2870 370.2760 376.3330 386.3760 457.1780 473.2690 491.1830 570.2740 586.4180

y2(0.12) z3(0.080) c3(0.17) y3(0.16) z4(-0.050) y4(0.022) c4(-0.0089) z5(-0.038) y5(0.087) 641.4020 685.3000 701.4350 706.2960 727.3000 729.4120 748.2550 774.2280 776.3700 848.4270

z6(-0.039) y6(0.077) c6(-0.020) z7(0.025) 955.1950 976.5870 984.1620 994.1750 1027.2130 1032.4550 1038.3600 1041.0920 1049.0890 1068.5820

z9(-0.032) c7(-0.027) y9(0.58) 1133.4940 1139.3470 1149.4730 1423.4990 1448.4990 1486.4360 1601.4870 1714.6090 1801.5980 1963.7010 z10(-0.041) c8(-0.087) y10(-0.080) z11(-0.15) c11(-0.15) c12(-0.12) c13(-0.084) c14(-0.13)

Page 50: Legends

V20101018-06 #1910 RT: 17.86 AV: 1 NL: 2.18E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1460.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

723.90

1430.79

532.49907.69

1283.72 1405.761136.631045.59

1008.72 1228.701358.80403.62 990.70836.65

1085.07788.72433.61247.47 899.55573.35 706.39289.74

x2 x2

Q58D62Fetuin B

Thr-173

FM(Oxidation)ETAT(HexNAc)ESLAK

723.8355(2+)

v

v

Page 51: Legends

[–] Peak Matches 247.4670 289.7440 403.6170 417.5290 433.6120 532.4860 836.6450 907.6920 916.6700 965.9610

z+14(0.36) y4(-0.74) z+15(0.19) z+16(0.22) z+17(0.23) c-16(0.29) c6(-0.72)

990.7010 1008.7180 1023.8400 1045.5890 1085.0670 1132.5020 1136.6300 1152.6770 1211.7390 1228.6990

z+18(0.21) y8(0.32) c-17(0.16) c-18(0.043) z9(0.086) y9(0.11) 1245.6770 1283.7190 1317.7290 1358.7960 1375.7830 1385.8070 c-19(0.13) z10(0.14) c10(0.14)

Page 52: Legends

V20101018-06 #2518 RT: 21.98 AV: 1 NL: 9.06E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1470.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

728.08

526.28654.41

1204.461058.53944.51 1438.61

1351.52

1253.581073.51

358.33 1132.68995.67482.40 881.48272.35 768.29635.26 711.36

x5 x5

Fetuin B Q58D62

Ser-262

SFFNS(HexNAc)QAPTPR

727.8453(2+)

v

v

Page 53: Legends

[–] Peak Matches 272.3510 312.2790 334.3140 358.3270 448.4310 475.3950 482.3960 498.3590 526.2850 654.4120

y2(0.18) z+13(0.12) z+15(-0.013) z+16(0.055) 944.5080 1058.5270 1073.5140 1092.7030 1186.5970 1204.4640 1214.6100 1220.5830 1236.5330 1253.5770

z+17(0.040) z+18(0.016) y8(-0.0082) z9(-0.11) y9(-0.0076) 1282.7120 1286.5640 1296.5660 1334.5540 1351.5200 1367.7220 1380.8150 1383.8130 1393.5520

c-110(-0.032) z10(-0.12) y10(0.063)

Page 54: Legends

V20101018-15 #1196 RT: 12.54 AV: 1 NL: 1.30E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1800.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

596.28

864.81735.91

429.48 793.29893.95

1788.011192.61 1358.85 1585.081095.80996.71 1470.91500.54 1656.93692.67219.38 1569.93906.80403.76 1400.861287.86

x5 x2

Fetuin B Q58D62

Thr-273

GENAT(HexNAc)VNQRPANPSK

v

v

v

595.9606(3+)

Page 55: Legends

[–] Peak Matches 219.3770 358.5370 385.6990 403.7630 429.4840 500.5430 502.7170 534.4180 555.5650 586.8840

z+12(0.24) y7+2(0.48)

z4(0.26) z+14(-0.75)

z5(0.28) z+15(-0.72) y10

+2(-0.24) b9+2(-0.39)

615.1730 633.3810 648.5010 667.5730 671.7720 692.6710 701.3520 704.7360 735.9110 748.5280

b11+2(0.45) c-15(0.37)

c5(-0.63) z+112

+2(0.030) z12

+2(0.53) 754.6980 785.1210 793.2870 807.4250 828.8830 858.4080 876.8490 882.6470 906.8050 996.7150

z+17(0.28) c-113+2(0.24)

c13+2(-0.26) z+113

+2(0.38) c14

+2(-0.017) c-114

+2(0.49) z+18(0.17) c7(0.39) z+19(0.19)

1034.7680 1095.8020 1173.6780 1192.6110 1358.8520 1470.9130 1569.9260 1585.0760 1656.9290 1715.0980 c8(0.29) z+110(0.21) b9(0.13) c11(0.19) z+112(0.16) c13(0.16) z+113(0.28) c14(0.14)

Page 56: Legends

V20101018-14 #1356 RT: 14.05 AV: 1 NL: 1.02E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

777.28

1165.18

1144.20

1101.19527.24 730.47 1036.68

398.28 1553.51629.38 1316.52972.841201.59 1805.641535.72386.34 1702.70 1932.87241.09 585.19415.51 639.57 899.46 1382.39

x5 x2

Q58D62Fetuin B

(Thr-295) & Thr-299

777.0660(3+)

LQQQNTAPT(HexNAc)NSPT(HexNAc)KAVPK

v

v

m

*

Page 57: Legends

[–] Peak Matches 241.0920 258.4030 328.3430 386.3400 398.2850 415.5080 473.3090 514.1950 527.2390 551.0340

c-12(0.23) c2(-0.77) z+13(0.12) c-13(0.11) z4(0.033) z6

+2(-0.23) z+16

+2(-0.74) c-14(-0.091) z+15(-0.12) 585.1910 629.3820 730.4710 742.6020 759.4740 769.2630 795.8690 812.7160 830.5440 833.5140

c5(0.045) c6(0.087) z6(0.070) 972.8430 997.5410 1015.5550 1036.6810 1047.9140 1056.1840 1063.8270 1078.7150 1101.1890 1121.7170

z+115+2(-0.15)

z15+2(0.36) z+18(-0.012) z16

+2(0.16) z+116

+2(-0.34)

z+117+2(0.14)

c17+2(0.63)

z17+2(0.64)

1130.4630 1149.0730 1201.5890 1316.5240 1535.7170 1553.5100 1702.6990 1805.6370 1816.9610 1932.8720

c-19(-0.0043) c10(-0.12) z+113(-0.18) c13(0.78) z+114(0.044) c14(-0.079)

Page 58: Legends

V20101018-05 #3703 RT: 30.28 AV: 1 NL: 8.09E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-2000.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

804.73

1185.65673.37

1104.83637.28

1291.47425.29 1041.66544.33346.33 1740.69895.42 1517.64 1608.661307.59 1868.76766.39 991.23501.31 1474.65

x5 x2

AGSLTPEST(HexNAc)GAPVEEEDPFFK

Thr-34

Q95121Pigment epithelium-derived factor

v804.3722(3+)

v

m

Page 59: Legends

[–] Peak Matches 279.3280 294.3320 314.3010 329.2450 331.3850 346.3270 425.2920 538.3310 544.3290 566.3140

z+12(0.16) y2(0.15) b4(0.063) c4(0.12) z3(0.061) y4(0.029) c6(0.020) 593.3770 629.3690 637.2760 673.3670 716.4590 760.3950 766.3860 787.3220 799.4290 808.7340

z5(-0.035) c7(0.015) c8(0.011) z6(0.033) 895.4190 1024.3140 1041.6650 1090.6260 1097.2340 1104.8330 1121.5000 1134.2870 1141.2330 1162.6490

z7(0.023) z8(-0.12) b10(0.33) c10(-0.032) 1170.7330 1291.4700 1307.5930 1364.5760 1388.6360 1517.6360 1608.6610 1646.7060 1740.6940 1775.7300

z11(-0.13) y11(-0.022) y12(-0.061) c13(-0.054) c14(-0.097) c15(-0.070) z+114(-0.091) c16(-0.088)

Page 60: Legends

V20101001-09 #1864 RT: 18.20 AV: 1 NL: 1.96E3T: ITMS + c NSI d sa Full ms2 [email protected] [50.00-1420.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

702.81

1316.83

1405.941015.82 1362.83

1158.761102.88 1287.79610.67 913.80 982.79

1203.90797.55 860.81605.14511.55 641.50 759.47

x10 x5

TEGSTT(HexNAc)VSVPHS

z6*z5* c6

z7 c8*z8*

z9*

c11

z11z10

-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

*

v

v

Page 61: Legends
Page 62: Legends

V20101001-09 #1863 RT: 18.20 AV: 1 NL: 1.49E3T: FTMS + c NSI d Full ms2 [email protected] [100.00-1420.00]

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

0

10

20

30

40

50

60

70

80

90

100

Rel

ativ

e A

bund

ance

204.09

186.08

1201.56

126.05340.16

144.06

971.48231.10 526.26826.39

439.23243.11 703.82 1159.95945.49771.56290.76

1018.31616.31

TEGSTTVSVPHS + HexNAc

HexNAc

y3

y4y5

y2

b2

y10

b9-2xH2O

702.8290(2+)

F1MNV4This 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+

Page 63: Legends