GlyGly Site Id 0 - Caltech Authors

Scan number

8487

Raw file

nak_WTonetooneSAX5_4feb11_05

Method

ITMS; CID

Pepti...

139.86

y₁₂²⁺

GlyGly Site Id 0

y₁₀

-H₂O y₉

y₈

-H₂O

A

E

K

y₇

y₅

-NH₃ y₃

y₂

D

E

gl

_

M

V

A

b₃

E

b₅

b₆ -H₂O

F

b₇ -H₂O

b₈

K

E

E

b₁₁ -NH₃

-NH₃

b₁₂ -H₂O

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800

1600

1800

120

400

y₈

100

100

1166.57

b₁₂

1521.69

y₉

b₈

1020.48

b₆

631.28

b₇

y₉-NH₃ 1278.58

873.41

40

y₅

649.27

b₇-H₂O 855.4

y₇

40

b₆-H₂O 613.27

b₁₁-NH₃ 1389.64

924.43

y₉-H₂O 1277.6

y₃

391.18

y₆-H₂O 759.35

b₅

y₂

y₁₀

1366.65

b₁₁

b₉-NH₃ 1131.55

b₁₁²⁺ 703.83

276.16

b₁₂-NH₃ 1504.66 1406.66

b₃

20

20

502.23

y₃-NH₃ 374.16

b₁₂-H₂O 1503.68

0

302.15

0

400

600

800

1000

m/z (zoom)

1200

1400

Intensity

60

1295.61

60

Relative Abundance

80

80

y₁₂²⁺ 783.87

Scan number

8211

Raw file

nak_cdc48UbconjugatesSAX5_14may10_09

Method

ITMS; CID

Pepti...

114.72

GlyGly Site Id 1

-H₂O y₁₃

y₁₂

y₁₁²⁺

y₁₀²⁺

-H₂O

y₉²⁺

y₆

y₂

gl

_

M

V b₂

A b₃

E b₄

A b₅

E

K

F

K b₉²⁺

E

E

D b₁₂²⁺

E b₁₃

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

120

200

3000

100

y₁₂²⁺ 783.87

40

1500 1000

20

y₂

y₁₃

500

b₂

y₁₃²⁺ 833.4

1665.8

y₂-H₂O 258.14 a₂

b₁₂²⁺ 761.35 y₁₁²⁺ 748.35

b₄

b₃

431.2

b₉²⁺ 574.79

y₉²⁺ 648.31

b₅

502.23

y₆

y₈-H₂O 1148.56

891.41

y₁₂

1566.73

b₁₃

1650.73

0

203.12 231.12 276.16 302.15

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

1800

Intensity

60

2000

Relative Abundance

80

2500

y₁₀²⁺ 683.83

Scan number

2577

Raw file


Method

ITMS; CID

Pepti...

123.28

-NH₃ y₉

-NH₃

D

T

GlyGly Site Id 2

-NH₃ y₇

-H₂O y₆

y₅

E

N

-H₂O y₂

y₃

gl

_

K

A

V

b₂

M

b₃

b₅

N b₇²⁺

b₆ -H₂O

b₈ -NH₃

E

b₉

E b₁₁²⁺

E b₁₂²⁺ -NH₃

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

120

200

1000

y₅

100

656.3

800 600

60

Intensity

b₇²⁺ 441.72 b₆

400

768.38

40

y₄-H₂O 524.24

y₆

785.34

b₃

421.26

b₁₁²⁺ 692.3

y₇²⁺ 450.2 b₆²⁺ 384.69 20

y₃

413.21

b₅

667.33

b₂

322.2

b₈

y₇-NH₃ 882.36

y₂-H₂O 266.16

b₉

1011.47

b₆-H₂O 750.37

y₈-NH₃ 983.4

y₇

899.38

1125.51

200

y₂

284.17

b₁₂²⁺ 756.82

y₉-NH₃ 1098.43

b₈-NH₃ 994.44

y₉

b₁₂-NH₃ 1495.61

1115.46

0

Relative Abundance

80

b₈²⁺ 506.24

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

Scan number

17971

Raw file

nak_UBX2HSAX5_8feb11_09

Method

ITMS; CID

Pepti...

95.98

y₁₃

y₁₂²⁺

y₁₁²⁺

y₁₀²⁺

GlyGly Site Id 3

y₉²⁺

y₇

y₆

y₅

y₄

y₃

y₂

y₁

A b₈

Q

S

E

Y

W

R

gl

_

A

T

Q b₃

I b₄

E

K b₆

-H₂O

E b₇

-H₂O

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

120

200

1200

y₁₁²⁺ 783.89 y₅

100

746.36

800

60

y₁₀²⁺ 727.35 y₃

530.28

40

y₉²⁺ 662.83 400

y₆

874.41

y₄

659.32

b₆

793.43

y₂

367.22

b₄

414.23

y₇²⁺ 473.23

b₈

993.51

b₇

b₃-H₂O 283.14

922.47

200

20

b₃

301.15

y₇

y₁₃

945.45

1795.88

y₁

b₁₂-H₂O 1482.7

0

181.14

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

1800

Intensity

y₁₂²⁺ 847.92

600

Relative Abundance

80

1000

b₆-H₂O 775.42

Scan number

8734

Raw file

nak_UBX6SAX3H_14jan11_13

Method

ITMS; CID

Pepti...

141.2

GlyGly Site Id 4

-H₂O y₆

y₅

-NH₃ y₄

L

L

K

-H₂O y₃

-H₂O y₂

E

D

gl

_

D

A

a₂ -H₂O

b₃

b₄

b₅

-H₂O

A

b₇ -H₂O

_

m/z (full) 200

300

400

500

600

700

800

900

1000

120

100

100

1000

60 40

400

y₄

576.26

y₃-H₂O 316.11 y₂-H₂O 187.07 b₃

b₄

413.24

y₆-H₂O 784.42

b₅

b₇

899.45

655.38

y₃

y₂

334.12

205.08

y₆²⁺ 401.72

b₇²⁺ 450.23

200

20

300.16

b₂-H₂O 169.06 y₄-NH₃ 559.24

y₆

802.43

b₆-H₂O 766.41

a₂

b₇-H₂O 881.44

0

159.08

0

100

200

300

400

500

600

m/z (zoom)

700

800

900

1000

Intensity

600

Relative Abundance

80

800

y₅

689.35

Scan number

16277

Raw file

nak_UBX3HSAX5_28jan11_31

Method

ITMS; CID

Pepti...

173.06

-H₂O y₁₂²⁺

y₁₁

-NH₃ y₁₀

T

F

K

GlyGly Site Id 5

-H₂O y₉

y₈

D

A

y₆

y₅

y₄

y₃

D

N

E

V

-NH₃ y₂

gl

_

Y

a₂ -H₂O

-H₂O

b₄ -H₂O

b₅

E

b₈

b₁₀ -H₂O

-H₂O

I b₁₂ -H₂O

b₁₁ -H₂O

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

120

200

500

y₉

100

1032.48

300

60

Intensity

y₈

917.46

b₁₀-H₂O 1309.53

769.35

40

y₁₀

1274.62

y₂-NH₃ 243.17 a₂

y₂

260.2

b₃-H₂O 394.18 y₃

b₄

654.32

y₁₂²⁺ 761.87

y₉-H₂O 1014.47

488.31

b₁₁-NH₃ 1409.59

b₈

b₁₂-NH₃ 1522.67 b₁₂-H₂O 1521.69

1084.46

y₁₀-NH₃ 1257.6

b₇-H₂O 951.42

y₄

359.27

237.12

y₁₁

1421.69

b₅

602.35

100

20

b₁₁

1426.61

y₉-NH₃ 1015.46

y₅

b₂-H₂O 247.11

200

y₁₁²⁺ 711.35 b₄-H₂O 636.31

b₁₀

1327.54

b₁₁-H₂O 1408.6

b₁₂

1539.7

y₁₂-H₂O 1504.73

0

Relative Abundance

80

400

y₆

717.38

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

Scan number

18419

Raw file

nak_UBX2LSAX6_8feb11_06

Method

ITMS; CID

Pepti...

100.77

-H₂O y₁₇²⁺

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

N

Q

D

M

GlyGly Site Id 6

-NH₃ y₁₂

y₁₁

y₁₀²⁺

D

V

E

y₉²⁺

y₈

y₇

y₆

G

G

D

y₅

gl

_

D

M

b₂

D b₇²⁺

b₈

b₉

-NH₃

K b₁₁²⁺

-H₂O

b₁₃

T b₁₅²⁺

A

Y b₁₇²⁺

D b₁₈²⁺

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

3000

100

y₁₇²⁺ 1007.92

2000

60

y₁₄²⁺ 829.35

40

b₁₁²⁺ 718.28

y₇

769.34

20

y₁₆²⁺ 950.9

y₆

712.31

b₁₇²⁺ 1000.39 b₁₂-H₂O 1474.56

b₁₅²⁺ 883.34

y₅

597.29

b₉

1064.37

a₂

b₂

247.07

y₁₁

1296.61

y₁₂

1411.63

y₁₇-H₂O 1996.82

b₁₃

1549.59

0

219.08

b₁₀-H₂O 1175.4

b₇²⁺ 425.64

500

y₂-NH₃ 245.11

b₈

965.3

y₁₂²⁺ 706.32 y₁₁²⁺ 648.81

b₄-NH₃ 472.15

1000

y₉²⁺ 534.75

y₁₀²⁺ 599.27

b₁₈²⁺ 1057.9

y₈

826.36

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

1500

Relative Abundance

80

2500

y₁₅²⁺ 886.87

Scan number

27658

Raw file


Method

ITMS; CID

Pepti...

152.07

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

F

N

T

y₁₂²⁺

GlyGly Site Id 7

y₁₁

y₁₀

y₉

y₈

y₇

y₆

S

W

S

P

V

G

y₄

y₃

E

D b₁₅²⁺

-NH₃ y₂

gl

_

L

b₂

b₄ -H₂O

E

K

b₅

-H₂O

b₈ -H₂O

-H₂O

b₉ -H₂O

L

A b₁₆²⁺

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1600

1800

2000

120

200

y₈

60

828.45

b₄-NH₃ 459.22 40

b₄-H₂O 458.24

b₇-H₂O 916.45 b₅

y₁₄²⁺ 830.91

605.29

b₉-H₂O 1189.56

y₉

915.48

y₆

632.32

b₄

a₂

b₆-H₂O 829.42

20

y₁₁²⁺ 594.8

b₉

1207.57

b₁₆²⁺ 944.96 y₁₂²⁺ 715.87

b₈-H₂O 1102.53

b₁₅²⁺ 909.44

b₂

218.15 261.16

b₉-NH₃ 1190.55

b₁₂-NH₃ 1443.69

y₁₆²⁺ 961.47 y₃

y₄

y₁₀

462.22

1101.56

333.18

y₁₁

1188.59

b₁₂-H₂O 1442.71

0

y₂-NH₃ 201.12

b₈

1120.54

476.25

233.16

y₂

y₇

731.39

1000

b₉²⁺ 604.29

y₈²⁺ 414.73

0

200

400

600

800

1000

1200

m/z (zoom)

1400

Intensity

2000

Relative Abundance

80

3000

100

y₁₅²⁺ 887.93

Scan number

27738

Raw file

nak_ubx4LightSAX5_11nov05

Method

ITMS; CID

Pepti...

87.33

y₂₀²⁺ ac

y₁₈²⁺

GlyGly Site Id 8

y₁₆

y₁₅²⁺

-NH₃ y₁₄

y₁₃

-NH₃

A

E

S

H

-H₂O y₁₁

-NH₃ y₉²⁺

y₇²⁺

y₄

y₂

gl

_

M

D

b₂

T

D

K

L

I

S

E

b₉

b₁₀

b₁₁

F

S

Q

G

N

H

A

E

A

V

A

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1800

2000

y₁₀-H₂O 1006.51 1500

y₁₈²⁺ 949.94 60

Intensity 1000

40

b₆-NH₃ 843.36 b₆-H₂O 842.37 b₁₀

1260.58

y₁₁²⁺ 556.28

20

y₁₄²⁺ 741.86

y₂₀²⁺ 1063.02

500

y₄

388.26

y₁₅²⁺ 806.38

y₃-NH₃ 300.19

y₁₂-NH₃ 1241.59

y₇²⁺ 363.2

y₁₃

1395.68

y₁₄

1482.71

y₁₁

1111.55

y₂

218.15

b₂

b₉

y₉²⁺ 448.73

289.09

1189.54

b₁₁

1389.62

y₁₄-NH₃ 1465.68

y₁₆

1682.79

0

Relative Abundance

80

2000

100

120

200

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

Scan number

10356

Raw file


Method

ITMS; CID

Pepti...

107.35

y₁₃²⁺

GlyGly Site Id 9

y₁₂²⁺

y₉

y₈

y₇

y₆

V

D

P

N

y₃

-NH₃ y₂

Y

A

gl

_

D

G

b₂

K

M

b₃ -NH₃

G

b₄

E

b₅

b₆

b₇

b₈ -H₂O

A

D

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1200

1400

1600

120

200

600

100

y₇²⁺ 393.7

500

y₇

300

b₃

40

423.21

b₈

b₇²⁺ 420.19

b₄

554.25

y₂

20

226.16

b₈²⁺ 477.71

b₆

740.31

y₈

y₁₃²⁺ 784.37

901.41

100

y₂-NH₃ 209.14

b₃-NH₃ 406.18

b₈-H₂O 936.4

y₁₂²⁺ 659.3

y₈²⁺ 451.21

200

954.41

b₇

y₃

839.38

389.23

b₅

611.27

y₆

689.33

y₉

1000.48

b₂

0

173.06

0

200

400

600

800

1000

m/z (zoom)

Intensity

60

400

Relative Abundance

80

786.39

Scan number

31000

Raw file

nak_ubx4HeavySAX6_11nov11

Method

ITMS; CID

Pepti...

88.43

y₁₆

-H₂O y₁₅²⁺

y₁₄²⁺

y₁₃²⁺

y₁₂

V

N

L

I

G

GlyGly Site Id 10

y₉

y₈

y₇

-NH₃ y₆

y₅

y₄

y₃

D

E

D

F

V

D

L

gl

_

N

L

b₂ -NH₃

b₃

b₅ -NH₃

b₆

S

K

b₁₄²⁺

M

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

100

1400

60 40

600

y₆-NH₃ 763.38

y₇

895.43

y₁₅²⁺ 933.46 b₁₄²⁺ 829.92

400

b₅-NH₃ 537.3

20

y₁₄²⁺ 876.44 y₄

534.27

b₃

y₅

633.34

327.2

b₆

667.41

y₃

419.24

y₆

780.41

b₅

200

b₂

228.13

y₈

1024.48

554.33

y₉

y₁₂

1139.5

y₁₅-H₂O 1847.9

1525.7

y₁₆

1964.97

0

b₂-NH₃ 211.11

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

800

Relative Abundance

1000

80

1200

y₁₆²⁺ 982.99 y₁₃²⁺ 819.89

Scan number

44118

Raw file


Method

ITMS; CID

Pepti...

131.4

y₁₇²⁺

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

-H₂O y₁₃

y₁₂²⁺

y₁₁

A

P

T

V

V

F

L

GlyGly Site Id 11

y₁₀

y₉

D b₁₀²⁺

E

y₇

y₆²⁺

y₄

y₃

-NH₃ y₂

gl

_

A

A

b₃

b₆

L

D

S b₁₄

I

A b₁₆

K b₁₇ -NH₃

A

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

100

2500

y₁₆²⁺ 944.51

60 40

1000

y₁₃²⁺ 795.93 y₄

y₂-NH₃ 229.13

y₃

488.29

b₃

214.12

y₂

y₆²⁺ 380.23

y₁₀²⁺ 616.32

y₁₅²⁺ 895.99

y₁₂²⁺ 746.39

y₁₄²⁺ 845.46

b₁₄²⁺ 715.36

b₁₀²⁺ 493.27

b₁₇

y₁₃

1855.98

1590.85

y₇

y₉

874.47

1116.6

y₁₀

1231.63

y₁₁

1344.71

b₁₄

1429.72

y₁₃-H₂O 1572.84

b₁₆

1613.84

b₁₇-NH₃ 1838.95

0

246.16

y₇²⁺ 437.74

b₆

511.29

500

20

559.33

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

1500

Relative Abundance

80

2000

y₁₇²⁺ 980.03

Scan number

12756

Raw file


Method

ITMS; CID

Pepti...

81.35

y₁₇²⁺

y₁₄²⁺

GlyGly Site Id 12

y₁₃²⁺

y₁₂²⁺

D b₈²⁺

A b₉²⁺

-H₂O y₁₀

-H₂O

T

E

y₈

y₇

y₆

A

E

E

-NH₃ y₂

gl

_

V

V

R

b₂

b₃

P

K

S

L

b₇

E

-NH₃

D

H b₁₇²⁺

M

L

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1400

1600

1800

2000

y₆

40

772.37

400

y₁₃²⁺ 759.32 y₉-H₂O 1083.48

20

y₂-NH₃ 243.17

y₁₂²⁺ 701.81 b₃

355.25

a₂

b₂

199.14

b₇²⁺ 447.78

y₂

260.2

y₈²⁺ 486.73

b₉²⁺ 540.81

y₇

901.41

b₇

b₁₀-NH₃ 1192.63 y₈

972.45

y₁₇²⁺ 1028.98 y₁₀-H₂O 1184.53

894.55

b₁₁-H₂O 1292.7

0

171.15

y₁₄²⁺ 815.87

y₁₀

1202.54

b₁₇²⁺ 1010.98

200

b₈²⁺ 505.29

0

200

400

600

800

1000

1200

m/z (zoom)

Intensity

600

60

800

Relative Abundance

80

1000

100

1200

120

200

Scan number

11399

Raw file


Method

ITMS; CID

Pepti...

162.93

-NH₃ y₁₄²⁺

-NH₃ y₁₃²⁺

-NH₃ y₁₂²⁺

y₁₁

E

E

D

N

GlyGly Site Id 13

y₉

-H₂O y₈

-NH₃ y₇

y₆²⁺

L

E

D

G

y₃ gl

_

L

b₂ -H₂O

b₃

b₄

D

b₆

b₈ -H₂O

b₉

T

K

S

M

b₁₃

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

120

200

60

y₇

40

880.42

1000

y₇-NH₃ 863.39 20

y₆²⁺ 383.2 b₂-H₂O 225.12

b₆

b₃

372.18

a₂

b₂

215.14 243.13

y₇²⁺ 440.71

y₃

365.19

y₈-H₂O 991.45

b₁₃²⁺ 780.84

716.27

y₉²⁺ 561.78

y₁₁²⁺ 676.31

b₄

y₁₂²⁺ 733.83

y₁₄²⁺ 862.87

b₈

y₁₃-NH₃ 1578.66

958.4

y₈

1009.46

b₈-H₂O 940.39

b₉

y₉

y₁₁

1073.43 1122.55

1351.62

y₁₂-NH₃ 1449.62

b₁₃

1560.67

y₁₄-NH₃ 1707.7

0

487.2

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

1800

Intensity

2000

Relative Abundance

80

3000

100

y₁₃²⁺ 798.35

Scan number

28532

Raw file

nak_cdc48UbconjugatescontrolSAX6_14may10_17

Method

ITMS; CID

Pepti...

106.69

y₂₄²⁺

y₂₃²⁺

y₂₂²⁺

A

D

V

y₂₀²⁺

y₁₈²⁺

y₁₆²⁺

GlyGly Site Id 14

y₁₄²⁺

y₁₃

A

S

-H₂O y₆

y₁₁ gl

_

D

K

b₄

b₅ -H₂O

D

G

b₆

F

b₈ -NH₃

L

V b₁₀ -H₂O

G

G b₁₂

L b₁₅ -H₂O

K

P

E

F

V

D

I

I

N

S

R

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

1800

2000

120

400

100

2500

60

y₁₆²⁺ 908.98 40

y₂₂²⁺ 1224.15

b₁₀

1060.53

y₂₄²⁺ 1317.18

y₁₄²⁺ 851.96

1000

y₁₁²⁺ 716.38

y₁₁

1431.76

20

y₆

b₅

b₈-NH₃ 831.35

b₁₂

1174.57

717.39

529.26

b₆

b₁₀-H₂O 1042.52

b₄

b₁₅

1445.73

b₁₅-H₂O 1427.72

b₅-H₂O 511.25

y₁₃

1631.88

0

430.19

b₁₅-NH₃ 1428.7

y₁₈²⁺ 1015.06

644.29

y₆²⁺ 359.2

y₂₃²⁺ 1281.66

500

y₆-H₂O 699.38

b₈

848.38

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

Intensity

1500

Relative Abundance

80

2000

y₂₀²⁺ 1117.1

Scan number

2348

Raw file


Method

ITMS; CID

Pepti...

186.76

-H₂O y₁₀

-H₂O y₉

y₈

V

T

K

GlyGly Site Id 15

y₇

y₆

y₅

-H₂O y₄

y₃

Y

S

S

S

T

-NH₃ y₂

gl

_

A

b₃

b₄ -H₂O

b₅ -H₂O

b₆ -H₂O

b₇ -H₂O

b₈

Q b₁₀²⁺ -NH₃

b₉ -H₂O

A

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

1200

120

200

100

2 1.5

80

b₁₀²⁺ 588.29

b₇

b₅

b₆

772.41

y₇

b₄

743.32

522.31

40

y₉²⁺ 547.76

y₆

580.26

b₉

y₄

y₉

1094.52

y₁₀-H₂O 1175.58

406.19

y₂

218.11

y₅

y₃

493.23

319.16

y₄-H₂O 388.18

b₃

272.16

b₅-H₂O 667.37

b₆-H₂O 754.4

y₈

b₉-H₂O 1029.51

y₉-NH₃ 1077.49

y₁₀

1193.59

993.47

b₇-H₂O 841.43

y₉-H₂O 1076.51

b₁₀-NH₃ 1158.55

0

y₂-NH₃ 201.09

b₄-H₂O 504.3

0.5

20

1047.52

b₈

946.47

0

200

300

400

500

600

700

m/z (zoom)

800

900

1000

1100

1200

Intensity [10e4]

60

685.38

1

Relative Abundance

859.44

GlyGly Site Id 16

Scan number

1548

Raw file


Method

ITMS; CID

Pepti...

241.84

y₁₂²⁺

-H₂O y₁₁

-H₂O y₁₀

y₉

-H₂O y₈

-H₂O y₇

-H₂O y₆

y₅

H

P

T

A

K

E

E

K

y₄

y₃

y₂

E

Q

L

gl

_

N

b₂ -NH₃

b₃

-H₂O

b₅ -H₂O

b₈ -NH₃

b₉

b₁₀ -NH₃

b₁₂ -NH₃

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

120

200

6000 4000

y₁₁

1442.76

60

Intensity

y₁₀

40

1345.71

y₆

916.48

20

b₄-H₂O 432.2

b₂

y₉²⁺ 622.83

b₂-NH₃ 235.08

y₂ b₃

y₃

416.26

288.2 349.16

y₆-H₂O 898.47 y₇-H₂O 1027.52

y₈²⁺ 587.31

b₈-NH₃ 890.4

b₈

907.43

b₁₂

y₁₀-H₂O 1327.7

y₉

1244.66

y₄

y₁₁-H₂O 1424.75 1519.75

y₈-H₂O 1155.61

545.3

b₅-H₂O 503.24

b₁₀-NH₃ 1261.58

y₇-NH₃ 1028.5

787.44

252.11

y₈

1173.62

y₆-NH₃ 899.46

y₅

b₅

521.25

2000

y₁₂²⁺ 790.41

b₁₂-NH₃ 1502.72

y₁₀-NH₃ 1328.68

y₇

1045.53

y₁₁-NH₃ 1425.73 b₁₀

1278.61

b₉

1149.56

0

Relative Abundance

80

100

y₁₁²⁺ 721.88

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

Scan number

25163

Raw file


Method

ITMS; CID

Pepti...

84.84

y₁₈²⁺

y₁₇²⁺

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

GlyGly Site Id 17

y₁₃²⁺

y₁₁²⁺

y₁₀

y₉

y₇²⁺

y₄

y₂

gl

_

S

T

A b₃

I b₄

-H₂O

S

L

Y

S

E

M

-H₂O

S

D

E

D

V

K

E

I

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1400

1600

1800

2000

120

200

100

y₁₅²⁺ 951.95 4000 3000

60

Intensity

y₁₃²⁺ 851.89

2000

y₁₀²⁺ 662.33

b₃

260.12

b₃-H₂O 242.11

y₇²⁺ 495.78 y₂

b₄

268.21 373.21

y₉²⁺ 596.8

y₁₄²⁺ 908.44

1000

20

40

y₁₆²⁺ 1008.49

b₁₀-H₂O 1065.49

y₁₁²⁺ 726.85

y₉

1192.6

y₄

y₁₈²⁺ 1094.54

647.41

y₁₀

b₅-H₂O 442.23

1323.64

0

Relative Abundance

80

y₁₇²⁺ 1044.01

0

200

400

600

800

1000

1200

m/z (zoom)

Scan number

22173

Raw file

nak_UBX6SAX6L_14jan11_16

Method

ITMS; CID

Pepti...

167.69

y₁₅²⁺

y₁₄

y₁₃

y₁₂

H

E

L

K

GlyGly Site Id 18

y₁₀

y₉

E

P

-NH₃ y₇

y₆

Q

E

y₄

gl

_

V

b₃ -H₂O

b₄

Y

b₅

b₆

T

b₈

b₉ -H₂O

-H₂O

b₁₀ -NH₃

b₁₁

I

b₁₂ -H₂O

I b₁₃ -H₂O

E b₁₄²⁺

D b₁₅²⁺

I

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000 800

120

400

100

b₁₅²⁺ 973.98

y₇-NH₃ 842.41 b₁₂

40

1589.8

b₁₂²⁺ 795.41

b₁₃

1702.89

y₄

20

489.26

b₉-H₂O 1201.61

b₅

729.41

b₆

892.48

b₃

366.18

y₇

b₄

y₉

y₁₀

1186.58

b₈

1118.57

y₁₂

1599.8

b₉

731.38

1219.62

b₁₀-NH₃ 1330.65

b₁₂-H₂O 1571.79

y₁₃

1712.88

y₁₄

1841.93

0

b₃-H₂O 348.17

b₁₁

1476.72

1057.54

y₁₅²⁺ 990

y₆

b₁₃-H₂O 1684.88

1347.68

b₇-H₂O 1003.51

859.44 479.26

b₁₀

200

b₁₁²⁺ 738.86

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

60

b₁₃²⁺ 851.95 400

Relative Abundance

80

600

b₁₄²⁺ 916.47

Scan number

19550

Raw file


Method

ITMS; CID

Pepti...

165.45

-NH₃

-H₂O y₁₄²⁺

y₁₃

G

S

GlyGly Site Id 19

-H₂O y₁₁

-NH₃ y₁₀

y₉

y₈

y₇

y₆

E

P

E

N

E

V

-NH₃ y₄

y₅

y₃

-H₂O y₂

gl

_

E

K

Q

b₃ -H₂O

I

I

b₇

b₈ -H₂O

-H₂O

-NH₃

E b₁₄²⁺

Y b₁₅²⁺

F b₁₆²⁺

E b₁₇²⁺

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

1200

100

y₁₀²⁺ 642.29

600

40

y₁₂-NH₃ 1508.68

y₁₀

1283.58

b₄-H₂O 595.32 20

y₂

y₃

423.22

b₃-H₂O 482.24

y₁₁²⁺ 706.81

b₇

b₈-H₂O 981.5

y₁₀-NH₃ 1266.55

870.47

y₁₁

b₁₂-H₂O 1450.68

1412.62

y₁₃

200

y₄

586.29

y₁₁-NH₃ 1395.6

715.33

y₁₄²⁺ 835.38

b₃

500.25

276.16

y₈

1057.48

y₅

400

b₁₄²⁺ 848.9

1612.74

y₆

b₁₅²⁺ 930.44

814.4

y₄-NH₃ 569.26

b₁₆²⁺ 1003.97

b₁₇²⁺ 1068.49

y₇

y₉

943.44

1186.53

b₁₁-NH₃ 1322.62

y₁₁-H₂O 1394.61

y₁₂-H₂O 1507.7

y₁₅-NH₃ 1765.82

0

y₂-H₂O 258.14

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

60

800

Relative Abundance

80

1000

b₈

999.51

Scan number

19544

Raw file


Method

ITMS; CID

Pepti...

159.18

GlyGly Site Id 20

y₁₅²⁺

y₁₄²⁺

y₁₃

y₁₂²⁺

y₁₁²⁺

-H₂O y₁₀

y₉

y₈

y₇

y₆

-NH₃

L

D

D

V

S

H

Y

E

M

K

y₅

y₄

E

I

y₂

gl

_

N

D

b₂ -H₂O

b₃ -H₂O

b₄

-NH₃

b₇²⁺

b₁₀

-NH₃

b₁₁ -NH₃

b₁₃²⁺

b₁₄²⁺

Q

b₁₅²⁺

P

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1800

2000

120

200

y₁₄²⁺ 924.94 1000

60

Intensity

b₁₄²⁺ 906.4 y₁₃²⁺ 867.43 y₁₁²⁺ 760.38

40

y₇²⁺ 502.28 y₆²⁺ 436.76

y₂

20

252.18

b₂

230.08

b₅-NH₃ 556.19

b₇²⁺ 380.16 b₃

y₆

b₁₁

872.52

1319.52

b₁₁-NH₃ 1302.49

y₁₂²⁺ 809.92

622.37

493.32

343.16

y₉

b₃-H₂O 325.15

y₇

1003.56

b₄

y₁₀

1432.72

1295.66

b₁₅²⁺ 970.43 y₃-NH₃ 363.21

b₂-H₂O 212.07

y₅

y₄

b₁₃²⁺ 849.86

b₆-NH₃ 655.26

500

b₃-NH₃ 326.13

458.19

y₈

1132.6

b₁₀

1188.48

y₁₃

1733.85

y₁₀-H₂O 1414.71

0

Relative Abundance

80

100

1500

y₁₅²⁺ 981.48

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

Scan number

25322

Raw file


Method

ITMS; CID

Pepti...

114.96

GlyGly Site Id 21

y₁₇²⁺

y₁₆²⁺

-H₂O y₁₅²⁺

-H₂O y₁₄²⁺

y₁₃²⁺

-H₂O y₁₂²⁺

y₁₁

y₁₀²⁺

y₉²⁺

T

I

E

N

M

E

Y

E

G

y₇²⁺

y₆

-H₂O y₅

y₄

y₃

H

H

A

S

Y

gl

_

T

V

b₂

E

K

b₃

b₇

b₉

b₁₀ -H₂O

E

L

R

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

100

120

200

60 40

y₁₁²⁺ 681.32

20

y₉²⁺ 535.26 b₂

y₁₂²⁺ 745.84

y₁₄²⁺ 868.38

b₁₀

y₁₃²⁺ 811.36

b₁₄-H₂O 1749.76

1289.6

b₇

915.48

y₇²⁺ 442.23

b₃

y₁₆²⁺ 989.44

y₁₇²⁺ 1039.97 b₉

1160.56

b₁₀-H₂O 1271.59

y₁₁

1361.62

y₁₂-H₂O 1472.66

y₁₅-H₂O 1846.78

y₁₄-H₂O 1717.74

0

330.17

y₁₅²⁺ 932.9

y₅-H₂O 591.32

y₃

451.27

201.12

0.5

y₁₀²⁺ 599.78 y₄

538.3

y₆

746.39

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity [10e4]

1

Relative Abundance

80

1.5

y₅

609.34

Scan number

34374

Raw file

nak_UBX6SAX1L_14Jan11_11

Method

ITMS; CID

Pepti...

153.94

y₁₆²⁺

GlyGly Site Id 22

y₁₄²⁺

y₁₀

-NH₃ y₉

y₈

y₇

y₆

y₅

V

L

V

G

N

L

y₃

ox

_

S

gl

M

b₂

G

b₃ -H₂O

A

b₄ -H₂O

P

I

G

S

b₈ -H₂O

b₉

b₁₀

b₁₁

b₁₃

K

b₁₅

F b₁₆

V

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1800

2000

120

200

2500

100

y₁₄²⁺ 800.99 y₁₆²⁺ 865.02

60 40

1000

y₃

401.26

b₃

292.1

b₄

1034.63

y₆

363.13

878.54

20

b₁₀²⁺ 465.24 b₄-H₂O 345.12

y₉²⁺ 574.36 b₈-H₂O 699.31

b₉²⁺ 408.7

b₂

b₁₅²⁺ 781.93 y₅

764.5

b₁₄-H₂O 1294.68

500

b₈

717.32

b₃-H₂O 274.09

y₈

b₉

816.39

b₁₁²⁺ 514.78

y₉

b₁₀

1147.72

929.48

b₁₁

1028.54

b₁₃

1199.61

y₉-NH₃ 1130.69

y₁₀

b₁₅

1246.79

b₁₆

1709.91

1562.85

0

235.07

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

Intensity

1500

Relative Abundance

80

2000

y₇

935.56

Scan number

37749

Raw file

nak_UBX6SAX1H_14Jan11_11

Method

ITMS; CID

Pepti...

126.48

y₁₆²⁺

y₁₅²⁺

-H₂O y₁₄²⁺

G

A

P

GlyGly Site Id 23

-NH₃ y₁₂

y₁₀

-NH₃ y₉

y₈

y₇

V

L

V

G

y₃

-NH₃ y₂

F

V

gl

_

S

M

b₂ -H₂O

b₃ -H₂O

b₄ -H₂O

I

G

S

b₇

b₁₁

N

L

K

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

120

200

100

1

y₁₆²⁺ 857.01

60 40

0.4

b₃-H₂O 258.09 y₂-NH₃ 229.15 b₂

b₃

276.1

b₄

b₂-H₂O 201.07

y₁₀²⁺ 615.88

y₃

347.14 393.25

y₂

a₂

1131.69

y₁₅²⁺ 828.5 b₄-H₂O 329.13

y₈²⁺ 509.81

b₇

614.3

y₁₂²⁺ 687.91

b₁₁

y₉-NH₃ 1114.66

y₁₄-NH₃ 1567.92

y₉

y₁₂

1374.81

y₇

919.54 1012.55

y₁₀

1230.76

y₁₂-NH₃ 1357.78

y₁₄-H₂O 1566.94

b₁₇-H₂O 1766.96

0

191.08

y₈

1018.6

246.18

0.2

20

219.08

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

1800

Intensity [10e4]

0.6

Relative Abundance

80

0.8

y₁₄²⁺ 792.98

Scan number

7604

Raw file


Method

ITMS; CID

Pepti...

136.93

y₁₁²⁺

y₁₀

y₉

N

S

K

ac

GlyGly Site Id 24

-H₂O y₈

y₇

y₆

y₅

y₄

-H₂O y₃

-H₂O y₂

A

D

I

E

E

gl

_

T

E

D b₆²⁺

-H₂O

b₉ -H₂O

b₁₀ -NH₃

K

b₁₁ -H₂O

_

m/z (full) 400

600

800

1000

1200

1400

120

200

100

1000

60 40

400

948.42

y₁₀²⁺ 639.3

20

y₅

633.31

y₃

405.2

y₂

b₁₀

y₁₁²⁺ 696.32 y₈-H₂O 930.41

y₄

518.28

b₉-H₂O 1112.49

1259.54

b₁₁-NH₃ 1371.55

b₁₀-NH₃ 1242.51

b₁₁-H₂O 1370.57

y₉

1190.55

0

276.16

b₉ 1130.5

200

b₂-NH₃ 241.08 b₂-H₂O 240.1

b₁₁

1388.58

y₇

819.37

y₃-NH₃ 388.17 y₃-H₂O 387.19

y₁₀

1277.59

y₆ 704.35

0

200

400

600

800

1000

m/z (zoom)

1200

1400

Intensity

600

Relative Abundance

80

800

y₈

b₆²⁺ 416.18

y₂-H₂O 258.14

Scan number

25322

Raw file


Method

ITMS; CID

Pepti...

242.91

GlyGly Site Id 25

y₁₃²⁺

y₁₂

-H₂O y₁₁

y₁₀

-NH₃ y₉

-H₂O y₈

y₇

T

F

E

I

E

E

K

y₆

y₅

y₄

y₃

E

E

S

F

gl

_

N

b₃ -H₂O

b₄ -H₂O

b₅ -H₂O

b₆

-NH₃

b₉

b₁₀

b₁₁ -H₂O

-H₂O

L

b₁₂ -H₂O

b₁₃ -NH₃

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800 1200

120

400

1000

100

y₁₃²⁺ 871.93

y₉

1252.61

y₈

1123.56

y₇

y₁₀

1365.69

y₆

752.38

b₅

605.29

y₈-NH₃ 1106.54

b₅-H₂O 587.28

b₃-NH₃ 346.14

y₅

623.34

b₆

734.34

y₈-H₂O 1105.55

b₇-NH₃ 846.35

y₁₁-H₂O 1476.72

b₁₂

1597.7

y₁₂

1641.8

b₄-H₂O 474.2 b₁₀

b₈-H₂O 1087.51

b₁₁

1363.6

b₁₂-NH₃ 1580.68

1450.63

200

y₁₀²⁺ 683.35

20

b₁₃-NH₃ 1693.76

b₉

1234.56

b₄-NH₃ 475.18

b₃

y₁₁

1494.73

b₅-NH₃ 588.27 363.17

y₉-NH₃ 1235.58 400

40

y₄ 494.3

b₄

b₃-H₂O 345.16

492.21

y₃

407.27

y₁₁-NH₃ 1477.71

b₁₂-H₂O 1579.69

b₁₃

1710.79

0

b₁₁-H₂O 1432.62

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

Intensity

60

994.52

600

Relative Abundance

800

80

y₁₂²⁺ 821.4

Scan number

16519

Raw file

nak_UBX7LSAX6_20Jan11_6

Method

ITMS; CID

Pepti...

173.36

GlyGly Site Id 26

-NH₃ y₁₅²⁺

y₁₄²⁺

y₁₃

y₁₂²⁺

y₁₁²⁺

y₁₀

y₉

y₈

y₇²⁺

y₆

y₅

E

E

G

N

N

V

Y

E

I

Q

D

y₃

y₂

E

K

gl

_

M

L

b₂

b₃

b₈

b₉²⁺ -H₂O

-H₂O

b₁₀ -NH₃

b₁₁

b₁₃ -H₂O

L

b₁₄²⁺ -NH₃

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000 2500

120

200

100

y₁₅²⁺ 975.46

1500

60

Intensity

40

1000

y₁₃²⁺ 846.42 b₉-NH₃ 1033.43 b₁₄²⁺ 824.88 b₉-H₂O 1032.45 y₉²⁺ 654.33

y₇²⁺ 508.28 a₂

b₂

217.14 245.13

b₃

374.17

y₂

417.26

y₃

546.3

b₄-H₂O 485.21

y₅

774.41

b₈

b₁₀-NH₃ 1162.47

887.39

y₆

y₁₀²⁺ 703.87

y₁₁²⁺ 760.89

y₈

y₁₂²⁺ 817.91

1144.6

b₁₀

1179.5

b₁₁

1292.58

y₁₃

b₁₃

1691.83

1535.67

y₉

1307.66

902.47

y₁₀

1406.73

b₁₃-H₂O 1517.66

500

20

b₉²⁺ 525.73

y₁₅-NH₃ 1932.89

b₁₄-NH₃ 1631.73

0

Relative Abundance

80

2000

y₁₄²⁺ 910.94

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Scan number

17246

Raw file

nak_UBX3LSAX3_28jan11_21

Method

ITMS; CID

Pepti...

158.11

GlyGly Site Id 27

y₁₂²⁺

y₁₁²⁺

y₁₀²⁺

y₉²⁺

y₈

y₇

y₆²⁺

y₅

-H₂O y₄

y₃

y₂

N

D

D

Q

E

D

I

V

F

T

K

y₁

gl

_

L

b₂ -NH₃

b₃

b₄

b₇

b₈ -H₂O

b₉ -NH₃

b₁₀ -NH₃

R

b₁₂

_

-NH₃

m/z (full) 400

600

800

1000

1200

1400

1600

120

200

y₄

100

679.41

60 40

y₃

532.34

y₁₂²⁺ 804.4

20

y₆²⁺ 446.28

a₂

778.48

b₈-NH₃ 926.37

y₂

431.29

y₁

b₂

y₉²⁺ 632.35

b₄

458.19

b₃

343.16

b₈-H₂O 925.39

b₉-NH₃ 1025.44

y₇

1006.59

b₁₀-NH₃ 1172.51

y₈

b₁₁-NH₃ 1273.56

1135.63

b₁₂

1540.74

0

181.14 228.13

1189.54

b₇

830.32

y₄-H₂O 661.4

200.14

b₁₀

1042.47

y₅

2000

b₉

y₁₀²⁺ 689.86

b₂-NH₃ 211.11

b₈

943.4

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

Intensity

4000

Relative Abundance

80

6000

y₁₁²⁺ 747.37

Scan number

28889

Raw file


Method

ITMS; CID

Pepti...

73.45

y₁₇²⁺

y₁₆²⁺

I b₇

A b₈

GlyGly Site Id 28 & 29

y₁₅

y₁₃

y₉

y₈²⁺

G

Q b₁₆²⁺

y₄

y₃

y₂

A

G

K

gl

_

L

R

E b₃

E

I b₅

F b₆

N b₉²⁺

E b₁₀²⁺

G

V

H

T

F b₁₇²⁺

I b₁₈²⁺

Y

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

5000

100

b₁₇²⁺ 971.49

60 40

2000

y₁₇²⁺ 974.01

b₁₆²⁺ 897.96

y₈²⁺ 534.8

b₇

901.51

y₄

b₃

517.31

399.24

y₁₅²⁺ 881.95

20

b₅

641.36

y₁₃²⁺ 760.4

y₂

389.25

1000

y₃

446.27

b₈

972.55

b₆

788.43

b₁₀²⁺ 608.32 b₃-H₂O 381.22

y₉

y₁₅

y₁₃

1125.61

1762.89

0

1519.8

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

3000

Relative Abundance

80

4000

b₁₈²⁺ 1028.04

y₁₆²⁺ 917.47

b₉²⁺ 543.8

Scan number

10694

Raw file


Method

ITMS; CID

Pepti...

228.19

GlyGly Site Id 30

y₁₇²⁺

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

y₁₃

y₁₂²⁺

-H₂O y₁₁²⁺

-H₂O y₁₀

y₉

y₈

G

L

S

H

D

H

T

H

D

E

-NH₃ y₇

-NH₃ y₆

y₅

y₄

D

T

-NH₃ y₂

gl

_

Y

b₂

b₅

b₉

b₁₀

b₁₁ -H₂O

I b₁₂

K

b₁₄

V b₁₆²⁺

V

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

y₄

100

480.32

80

y₁₀²⁺ 670.36

y₇-NH₃ 941.56

y₁₄²⁺ 915.46

300

y₆

845.5

y₈

1087.63

y₆-NH₃ 828.48 b₁₄²⁺ 885.9

b₁₁²⁺ 646.77

y₁₂²⁺ 789.41

60

y₁₅²⁺ 958.97 y₇

958.59

b₁₂²⁺ 703.31

b₉

y₅

1048.46

595.35

40

y₁₇²⁺ 1044.03

y₁₁-H₂O 1422.75

b₁₀²⁺ 582.25 y₉

y₁₆²⁺ 1015.52

y₁₀-H₂O 1321.7

b₅

558.27

20

y₇²⁺ 479.8

1202.66

y₂-NH₃ 263.18

100

y₂

280.21

b₁₀

1163.49

y₆²⁺ 423.25

b₁₁

1292.53

y₁₀

1339.72

b₁₂

y₁₃

1405.61

1692.85

b₁₄

1770.79

b₁₁-H₂O 1274.52

b₂

0

221.09

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

y₁₁²⁺ 720.89

200

Relative Abundance

b₁₆²⁺ 985.96

y₁₃²⁺ 846.93

Scan number

11997

Raw file


Method

ITMS; CID

Pepti...

95.36

_

M


-H₂O y₈

y₇ ox

ox

I

M

M

b₂

-NH₃ y₆

-NH₃ y₂

y₁

Q

K

gl

S

N

gl

K

b₆

b₈ -H₂O

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

1200

1300

120

200

3000

b₈

2000

40

60

Intensity 1000

b₈-H₂O 1092.46

20

y₇²⁺ 563.75 y₈²⁺ 620.29

y₁

261.16

a₂

b₆

740.28

b₂

217.14 245.13

y₈

1126.5

1239.58

b₈-NH₃ 1093.45

b₈²⁺ 555.74

y₂

389.21

y₇

y₆

979.46

y₅-NH₃ 815.4

y₆-NH₃ 962.44

y₈-H₂O 1221.57

0

Relative Abundance

80

100

1110.47

0

200

300

400

500

600

700

m/z (zoom)

800

900

1000

1100

1200

1300

Scan number

26266

Raw file

nak_cdc48UbconjugatecontrolSAX3_22may10_12

Method

ITMS; CID

Pepti...

98.57

y₁₆²⁺

y₁₅²⁺

D

S

GlyGly Site Id 33

y₁₃²⁺

y₁₂²⁺

y₁₁²⁺

y₁₀

y₉²⁺

-H₂O y₈²⁺

A

L

T

Y

D

R

y₅

gl

_

T

L

b₂

S

K

b₄

T

T

b₆²⁺

S

b₁₀

b₁₁²⁺ -H₂O

-NH₃

-H₂O

-NH₃

b₁₅²⁺ -H₂O

L

b₁₆

E

b₁₇²⁺

F b₁₈²⁺

A b₁₉²⁺

T

I

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

100

120

200

3000

y₁₂²⁺ 749.41

y₁₁²⁺ 692.86 60

y₈-H₂O 987.57

40

b₁₁²⁺ 610.31

b₄

544.31

y₉²⁺ 560.81

b₁₂-H₂O 1302.65

b₁₈²⁺ 1072.53

b₁₅²⁺ 877.93

y₈²⁺ 503.3

20

b₁₉²⁺ 1108.05

b₈-NH₃ 931.44

y₅

607.36

b₁₆²⁺ 934.47

y₁₀

1283.67

b₁₇²⁺ 998.99 a₂

b₂

y₁₅²⁺ 871.96

y₁₆²⁺ 929.47

b₁₀

1106.53

b₆²⁺ 373.71

b₁₄-NH₃ 1581.73

b₁₁-H₂O 1201.61

b₁₅-H₂O 1736.84

b₁₆

1867.94

0

187.14 215.14

1000

b₁₀²⁺ 553.77

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

2000

Relative Abundance

80

y₁₃²⁺ 784.93

Scan number

20635

Raw file


Method

ITMS; CID

Pepti...

179.79

GlyGly Site Id 34

y₁₀

y₈

y₇

-H₂O y₆

-NH₃ y₅

y₄

y₃

A

V

S

Q

G

K

y₂

gl

_

S

L

R

b₂ -H₂O

P

b₃

S

F

D

E

b₇

b₈

b₉

b₁₀

-H₂O

b₁₁ -H₂O

b₁₂

b₁₃

b₁₄²⁺

F b₁₅²⁺

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

1600

1800

120

200

1.4

y₆

836.44

y₄

100

621.35

80

1.2

60

b₉²⁺ 502.25 0.6

y₅

40

749.41

b₁₁²⁺ 595.3 b₁₃²⁺ 687.84

b₁₄²⁺ 808.9

b₈

0.4

y₇²⁺ 468.26

932.45

y₃

564.33

20

y₆²⁺ 418.72 b₂

201.12

y₂

b₆-H₂O 670.37

b₈²⁺ 466.73

322.19

b₇ 803.4

b₁₀

b₁₅²⁺ 882.44

1102.55

y₇

935.51

b₁₂²⁺ 659.33

y₅-NH₃ 732.38

y₆-H₂O 818.43

b₁₁-NH₃ 1172.56 y₈

1006.54

b₁₁-H₂O 1171.57

y₁₀

1250.61

b₁₂

1317.64

b₁₃

1374.66

0

b₂-H₂O 183.11

0.2

b₃

357.22

b₁₁

1189.58

0

200

400

600

800

1000

m/z (zoom)

1200

1400

Intensity [10e4]

b₉

1003.48

0.8

Relative Abundance

1

b₁₀²⁺ 551.78

Scan number

27217

Raw file


Method

ITMS; CID

Pepti...

157.98

y₁₆²⁺

-NH₃ y₁₄

-NH₃ y₁₃

y₁₂

S

E

K

GlyGly Site Id 35

y₁₁

y₁₀

y₉

y₈

S

W

S

P

y₆

y₅

y₄

y₃

G

L

E

D

gl

_

L

F

N

b₃

b₆

b₇

b₈

-H₂O

b₉ -NH₃

V

b₁₁ -H₂O

b₁₂

b₁₄

b₁₅ -H₂O

A

K

b₁₆

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

1200

y₈

100

828.45

1000

y₉

800

60

b₉

1193.56

40

y₆

632.32

b₈

y₁₆²⁺ 954.46

20

b₁₁

1106.53

1389.68

y₁₂

1430.73

y₁₄²⁺ 823.9

y₁₀

b₇

b₅-NH₃ 574.25

1101.56

920.45

b₉-NH₃ 1176.53

y₃

b₁₁-H₂O 1371.67

y₄

462.22

y₁₃

1559.77

b₁₂

y₁₃-NH₃ 1542.74

1446.7

y₁₄

1646.8

b₁₄

1688.83

y₁₄-NH₃ 1629.78

b₁₅

1803.85

b₁₆

1874.89

b₁₅-H₂O 1785.84

0

333.18

b₃

b₁₁-NH₃ 1372.65

200

b₅-H₂O 573.27 375.2

400

b₆

833.42

y₅

575.3

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

y₁₁

1188.59

600

Relative Abundance

80

915.48

Scan number

18398

Raw file

nak_UBX7LSAX2_20Jan11_2

Method

ITMS; CID

Pepti...

188.27


-H₂O y₁₇²⁺

y₁₆²⁺

Q

K

ac

gl

_

S

D

F

b₃

b₄

-H₂O

y₁₅²⁺

y₁₃

y₁₂

y₁₁²⁺

V

E

E

y₉

-NH₃ y₈

-NH₃ y₇

-NH₃ y₆

-NH₃ y₅

-NH₃ y₄

y₃

E

Q

Q

Q

Q

Q

I

y₂

gl

E

b₅

K

b₈

b₉

Q

b₁₀ -H₂O

b₁₁

b₁₃²⁺

b₁₅²⁺

I b₁₉²⁺

b₁₈²⁺

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

b₁₈²⁺ 1251.08 b₈

b₁₉²⁺ 1307.62

300

100

y₁₆²⁺ 1121.08

1232.59

y₇

80

885.52

y₈

y₆

757.46

b₉

60

1361.63

y₇-NH₃ 868.49 y₉

y₁₅²⁺ 1000.01 y₆-NH₃ 740.43

y₃

40

373.28

y₈-NH₃ 996.55

y₅

629.4

y₄

b₁₀

1490.68

b₁₃²⁺ 938.42

y₅-NH₃ 612.37

20

y₄-NH₃ 484.31

100

b₃

y₁₇²⁺ 1185.11

y₁₁²⁺ 700.36

501.34

392.15

1142.62

b₅

762.34

y₁₀-H₂O 1252.66

b₁₀-NH₃ 1473.65

b₁₅²⁺ 1066.48

y₁₃

1627.83

b₄

b₁₀-H₂O 1472.67

520.2

y₂

260.2

y₁₂

1528.76

b₁₁

y₁₄-H₂O 1851.96

0

1618.73

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

200

Relative Abundance

1013.57

Scan number

31937

Raw file


Method

ITMS; CID

Pepti...

199.31

GlyGly Site Id 38

y₁₂

y₁₁²⁺

-H₂O y₁₀

y₉

y₈

-NH₃ y₇

D

L

A

S

G

K

y₆

y₅

y₄

y₃

I

T

D

F

gl

_

I

b₂

b₃

b₄

b₅ -H₂O

b₇

b₈ -H₂O

b₉

b₁₀ -H₂O

I b₁₂ -H₂O

b₁₁ -H₂O

K

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1500

120

200

y₉

100

1500

1122.62

y₁₁²⁺ 653.87

y₈

y₁₂²⁺ 711.39 1000

60

Intensity

y₅

623.34

y₆

40

736.42

y₁₀²⁺ 597.33 y₄

522.29

b₈

912.51

20

b₃

342.2

b₂

b₅-H₂O 482.26

b₇

799.43

b₅

b₈-H₂O 894.5

500.27

y₇-NH₃ 961.54

b₄

413.24

229.12

b₁₂

1388.74

b₁₀

y₃

b₁₁

1275.66

y₇

978.56 1128.59

407.27

500

y₇²⁺ 489.78

y₁₀

1193.65

y₉²⁺ 561.81

b₉

1013.56

b₁₀-H₂O 1110.58

b₁₁-H₂O 1257.65 y₁₀-H₂O 1175.64

b₁₂-H₂O 1370.73 y₁₂

1421.76

0

Relative Abundance

80

1035.58

0

200

300

400

500

600

700

800

900

m/z (zoom)

1000

1100

1200

1300

1400

1500

Scan number

33510

Raw file

nak_UBX3HSAX3_28jan11_29

Method

ITMS; CID

Pepti...

89.62

GlyGly Site Id 39

-NH₃ y₁₇²⁺

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

y₁₃²⁺

y₁₁

y₁₀

y₈

y₄

y₃

D b₁₅²⁺

A

gl

_

I

D b₂

L

A

S

G

K

I

T b₉²⁺

D b₁₀²⁺

F b₁₁²⁺

I

K

F

G

K

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

1200

1300

1400

120

200

400

100

y₁₅²⁺ 856.45

300

y₁₃²⁺ 777.42 b₁₁²⁺ 581.31 40

y₁₇²⁺ 970.51 y₁₀²⁺ 628.32

b₁₅²⁺ 889.97 100

y₄

20

390.2

a₂

b₂

229.12

b₉²⁺ 450.26

y₃

275.17

201.12

b₁₀²⁺ 507.78

y₈

1039.56

y₄-NH₃ 373.17

y₁₀

1255.63

y₁₁

0

1368.72

0

200

300

400

500

600

700

800

m/z (zoom)

900

1000

1100

1200

1300

1400

Intensity

60

y₁₆²⁺ 913

200

Relative Abundance

80

y₁₄²⁺ 820.94

Scan number

36803

Raw file


Method

ITMS; CID

Pepti...

134.76

GlyGly Site Id 40

-H₂O

-NH₃ y₁₀

y₁₂

y₈²⁺

y₇

y₆

y₅

y₄

I b₁₀ -NH₃

P

L b₁₂²⁺

S

E

y₃

-NH₃ y₂

gl

_

T

D

E

K

C

b₅

F

I

b₆ -H₂O

G

b₇

N

b₈

b₉ -H₂O

F b₁₅ -NH₃

S b₁₆²⁺

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

5000

b₁₀²⁺ 646.8

y₇

100

835.43

60 40

2000

b₁₀-NH₃ 1275.57

b₁₂²⁺ 751.87

20

y₂

262.15

y₃

409.22

y₄

895.36

b₁₆²⁺ 976.96

b₁₅

y₁₃-NH₃ 1522.74

b₁₀

1292.59

1865.87

b₇

b₉²⁺ 590.26

1008.45

b₆-H₂O 877.35

y₆

538.26

b₉

1179.51

738.38

b₁₅²⁺ 933.44

b₈

1065.47

y₁₀

1119.58

b₉-H₂O 1161.5

y₁₂

1379.73

b₁₅-NH₃ 1848.85

y₁₃-H₂O 1521.75

0

y₂-NH₃ 245.12

y₈²⁺ 474.76

b₆

b₅

748.29

1000

y₁₀-NH₃ 1102.55

y₅

625.29

b₇²⁺ 504.73

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

3000

Relative Abundance

80

4000

y₇²⁺ 418.22

Scan number

36246

Raw file

nak_UBX3LSAX1_28jan11_19

Method

ITMS; CID

Pepti...

168.69

-NH₃

-NH₃ y₁₇²⁺

GlyGly Site Id 41

-H₂O y₁₃²⁺

y₁₂

y₁₁

y₁₀

G

L

L

Q

-H₂O y₈

y₉

-H₂O y₆

y₅

A

N

-H₂O y₃

-NH₃ y₂

gl

_

S

V

K

F

b₃ -NH₃

V

Q

b₆

b₇

b₈

b₉

N b₁₁²⁺ -H₂O

b₁₀

A

A b₁₃²⁺

A b₁₆²⁺

E b₁₇²⁺

A b₁₈²⁺

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

2500

y₉

y₆

603.31

60

b₁₃²⁺ 735.91 b₁₈²⁺ 964.01

y₇-H₂O 656.34

y₁₇²⁺ 944.01

y₁₀

y₁₃²⁺ 635.84

987.49

y₈

b₉²⁺ 543.82

745.38

b₇

860.46

1000

40

y₁₁²⁺ 550.79

b₆

803.44

b₁₇²⁺ 928.49

y₇-NH₃ 657.32 y₃

347.19

b₃

y₅

532.27

b₁₀²⁺ 607.85

b₈

973.55

y₈-H₂O 727.37

b₉

1086.63

429.25

20

y₂

218.15

y₃-H₂O 329.18

y₁₂

b₃-NH₃ 412.22

y₁₈-NH₃ 1969.05

y₁₄-H₂O 1380.72

1213.65

y₁₁

1100.57

b₁₀

1214.69

y₁₇-NH₃ 1869.98 b₁₁-H₂O 1310.72

0

y₂-NH₃ 201.12

500

b₁₆²⁺ 863.97

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

b₁₁²⁺ 664.87

1500

Relative Abundance

2000

80

100

859.43

Scan number

23306

Raw file


Method

ITMS; CID

Pepti...

156.36

y₁₂²⁺

y₁₁²⁺

y₁₀²⁺

F

N

K

GlyGly Site Id 42

y₉

-H₂O y₈

y₇

y₆

y₅

y₄

-H₂O y₃

W

S

F

E

E

V

E

y₂

gl

_

L

b₂

b₄

b₅

b₆

b₇ -NH₃

-NH₃

V b₁₂²⁺

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

1600

1800

1600

120

200

100

1400

y₁₁²⁺ 762.89

b₄

y₈²⁺ 487.75

y₇²⁺ 444.23

y₄

20

482.31

y₂

254.2

898.47

b₁₂²⁺ 815.9 y₇

887.46

b₇²⁺ 523.27

b₅

811.43

y₈

y₃-H₂O 365.23

974.49

b₂

y₈-H₂O 956.48

b₇-NH₃ 1028.51

y₉

1160.57

b₉-NH₃ 1286.59

b₁₁-H₂O 1513.72

0

233.16 261.16

b₇

1045.53

200

a₂

b₆

y₁₀²⁺ 705.87

400

y₃

383.24

y₅

611.35

y₁₂²⁺ 836.42 600

40

625.35

0

200

400

600

800

1000

m/z (zoom)

1200

1400

Intensity

800

60

1000

Relative Abundance

80

1200

y₆

740.39

Scan number

32480

Raw file


Method

ITMS; CID

Pepti...

114.96

GlyGly Site Id 43

-H₂O y₁₈²⁺

y₁₇²⁺

N

T

-NH₃ y₁₅²⁺

y₁₂

y₁₁

S

P

y₉

y₈

y₇

G

L

E

y₄

y₃

y₂

Q

L

P

gl

_

L

F

b₂

E

K

b₅ -H₂O

b₆²⁺ -H₂O

S

W

b₉ -H₂O

V

b₁₁

b₁₄ -NH₃

D

V

b₁₇²⁺

b₁₈²⁺

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

100

1200

y₁₁²⁺ 597.84

800

y₁₈²⁺ 1071.05

y₁₅²⁺ 898.98

40

y₁₂²⁺ 641.36

y₁₁

1194.67

b₆-H₂O 829.42

y₁₇²⁺ 1014.03

605.29

y₇

828.45

b₁₇²⁺ 1023 y₁₀-NH₃ 1080.59 400

b₅

b₉

1207.57

y₁₆-H₂O 1907.99

y₈

941.53

20

b₅-H₂O 587.28 b₁₆-H₂O 1898.93

y₂

1702.84

b₂

261.16

a₂

200

b₁₄

244.17

y₃

b₆²⁺ 424.22

b₉-H₂O 1189.56

y₄

485.31

y₁₂

1281.7

357.25

b₁₁

1403.7

b₁₄-NH₃ 1685.82

0

233.16

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

60

b₁₈²⁺ 1079.54

600

Relative Abundance

80

1000

y₉

998.55

Scan number

24973

Raw file


Method

ITMS; CID

Pepti...

90.42

y₁₇²⁺

y₁₆²⁺

-NH₃ y₁₅

I

V

G

GlyGly Site Id 44

-H₂O y₁₃²⁺

y₁₂²⁺

y₁₁

y₁₀

D

V

H

N

-H₂O y₈²⁺

y₄

y₂

gl

_

T

G

V

b₃

b₄

b₅

E

b₁₀²⁺

b₁₁

L

F

b₁₃

T

b₁₄

Y

b₁₅

A

K

E

H

K

_

-NH₃

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

600

100

120

200

y₁₆²⁺ 1009.01

60 40

y₁₇²⁺ 1065.55

b₁₁

1121.56

200

y₁₀²⁺ 690.87

b₁₁²⁺ 561.28

y₁₃²⁺ 866.44

20

y₃-H₂O 403.22

y₄

b₁₀²⁺ 504.26

b₄

671.38

371.23

b₃

258.14

b₅

y₂

470.3

y₈²⁺ 577.3

y₁₂²⁺ 808.93 b₁₂-NH₃ 1217.62

b₁₃

y₁₅

1381.71

y₁₀

1380.72

1917.94

b₁₄

1482.76

y₁₁

1517.78

y₁₅-NH₃ 1900.92

b₁₅

1645.82

0

292.19

y₉-H₂O 1248.67

b₁₄²⁺ 741.88

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

400

Relative Abundance

80

y₁₅²⁺ 959.47

Scan number

30507

Raw file


Method

ITMS; CID

Pepti...

56.77

GlyGly Site Id 45

-H₂O y₂₃²⁺

-H₂O

-NH₃

y₁₅

-H₂O

-NH₃

y₇

y₆

y₅

y₄

y₃

T

A

Q

T

P

gl

_

V

K

P

I

E

V

D

P

N b₉²⁺

L

S

E

A

E

K

V b₁₆²⁺

A

I b₁₈²⁺

I b₁₉²⁺

L

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1800

2000

120

200

600

100

b₁₈²⁺ 1024.06

300

40

y₉-NH₃ 967.58 200

y₅

586.36

y₆

657.39

y₉-H₂O 966.6 20

y₅-H₂O 568.35 y₇²⁺ 379.72 y₄

100

b₁₆²⁺ 932 458.3

y₃

y₈-NH₃ 854.5 y₁₅

b₉²⁺ 553.8

1611.93

b₁₉²⁺ 1080.6

357.25

y₂₃²⁺ 1240.19

y₁₅-H₂O 1593.92

0

y₂-NH₃ 243.17

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

Intensity

60

400

Relative Abundance

80

500

y₇

758.44

Scan number

17678

Raw file


Method

ITMS; CID

Pepti...

135.68

GlyGly Site Id 46

-H₂O y₁₅²⁺

y₁₄²⁺

y₁₂

-H₂O y₈

y₁₀

y₇

y₆

-H₂O y₅

-H₂O y₂

gl

_

M

L

N

H

P

S

Q

G

S

D b₁₀²⁺

D b₁₁²⁺

A b₁₂

Q b₁₃ -H₂O

D b₁₄

E b₁₅ -NH₃

K b₁₆²⁺

Q b₁₇²⁺

G

D b₁₉²⁺

F b₂₀²⁺

P

V b₂₂²⁺

I b₂₃²⁺

E

E

E

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

1800

2000

120

200

y₇

100

843.45

Intensity

60

3000

y₈-H₂O 972.5 y₇²⁺ 422.23 40

b₁₄²⁺ 748.81

b₂₀²⁺ 1157.99

b₁₆²⁺ 934.4

y₅

2000

647.32

b₁₀²⁺ 534.23

b₁₂²⁺ 627.26

y₁₄²⁺ 888.92

b₁₃²⁺ 691.29

y₁₅²⁺ 952.95

20

y₈

b₂₂²⁺ 1256.05

990.51

y₈²⁺ 495.76

y₂

276.16

y₅-H₂O 629.31 b₁₁²⁺ 591.75

y₁₃-H₂O 1643.79 1000

y₆

746.39

b₁₃-H₂O 1363.57

b₁₇²⁺ 998.43

b₁₅-NH₃ 1608.62

y₁₀

1162.56

b₁₅²⁺ 813.33

b₁₂

1253.52

b₂₃²⁺ 1312.59

y₂-H₂O 258.14

b₁₃

1381.58

b₁₄

1496.61

y₁₂

b₁₅

1625.65

1532.76

0

Relative Abundance

80

4000

b₁₉²⁺ 1084.45

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

Scan number

28720

Raw file


Method

ITMS; CID

Pepti...

256.67

y₂₀²⁺

y₁₉²⁺

y₁₈²⁺

y₁₇²⁺

I

F

A

G

GlyGly Site Id 47

-NH₃ y₁₅

-H₂O y₁₄

-H₂O y₁₃

Q

L

E

-H₂O y₁₂

-H₂O y₁₁

-NH₃ y₉

y₇

y₆

-NH₃ y₃

y₅

gl

_

L

b₅

K

b₆

b₇ -NH₃

b₈

D b₁₀ -H₂O

G

R b₁₂

T b₁₃

L b₁₄

S b₁₅ -H₂O

D b₁₆ -H₂O

Y b₁₇²⁺

N

I b₁₉²⁺

Q b₂₀²⁺

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

y₁₁

b₁₆

1858.97

b₁₀

1229.65

Intensity

60

1500

b₁₀-H₂O 1211.64 y₂₀²⁺ 1205.62 b₁₅-H₂O 1725.93

b₁₃

40

1543.82

y₉

1081.55

y₁₉²⁺ 1149.08

y₅

y₁₇²⁺ 1040.03

b₇

20

y₇

b₅

b₆

744.44

y₆

780.39

y₄-NH₃ 485.27

b₇-NH₃ 855.47

b₁₅

1743.94

b₁₆-H₂O 1840.96

y₁₄

1651.83

y₁₃-H₂O 1520.73

b₁₄

1656.91

y₁₅-NH₃ 1762.86 b₁₆-NH₃ 1841.94

y₁₈²⁺ 1075.55 y₁₁-H₂O 1276.66

b₁₆²⁺ 929.99

y₁₂-H₂O 1391.69

b₁₂

1442.78

y₁₃-NH₃ 1521.72 y₁₄-H₂O 1633.82

b₁₅-NH₃ 1726.91

y₁₅

1779.89

0

y₃-NH₃ 371.23

y₁₂-NH₃ 1392.68

b₈

b₁₇²⁺ 1011.52

y₁₄-NH₃ 1634.8

b₂₀²⁺ 1189.11

985.58

867.42

502.3

1538.74

1409.7

500

y₃

388.26

b₁₉²⁺ 1125.08

y₁₃

y₁₂

665.36 872.5

1000

Relative Abundance

80

2000

100

1294.67

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Scan number

28985

Raw file


Method

ITMS; CID

Pepti...

262.36

GlyGly Site Id 48

y₁₆²⁺

y₁₅²⁺

y₁₄²⁺

-NH₃ y₁₃

y₁₂

-H₂O y₁₁

y₁₀

S

D

Y

N

I

Q

K

y₉

-H₂O y₈

y₇

y₆

y₅

y₄

y₃

E

S

T

L

H

L

V

gl

_

T

L

b₅

-H₂O

b₇ -H₂O

b₉ -H₂O

b₁₀ -NH₃

b₁₁ -H₂O

b₁₂

b₁₃ -H₂O

b₁₄ -H₂O

b₁₅

b₁₆ -NH₃

L

R

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

4000

y₉

y₁₀

1323.79

60

y₁₁

1451.85

y₈

944.6

y₅

643.43

b₁₃-NH₃ 1598.78

y₁₁-NH₃ 1434.83

b₁₄

b₇-NH₃ 790.36

1752.86

40

y₁₆²⁺ 1022.55 b₇-H₂O 789.38

y₄

506.38

b₁₃-H₂O 1597.79

y₁₁-H₂O 1433.84

1564.94

y₁₅²⁺ 979.04 y₆

b₉

y₁₃-NH₃ 1661.95

1185.6

y₁₃²⁺ 839.99

b₁₄-NH₃ 1735.84

20

756.52

y₃

b₉²⁺ 593.3

393.29

b₆-H₂O 676.29

b₇

807.39

y₈-H₂O 926.59

b₉-NH₃ 1168.57

b₁₀

1314.64

b₁₁

1401.67

b₁₂

b₁₃

b₁₆-NH₃ 1947.99

y₁₃

b₅

b₉-H₂O 1167.59

b₁₀-NH₃ 1297.62

b₁₁-H₂O 1383.66

0

580.26

b₁₆

1965.02

1615.81

1502.72 1678.98

y₆²⁺ 378.76

b₁₅

1865.95

1000

b₆-NH₃ 677.28

b₁₄-H₂O 1734.85

y₁₂

y₇

857.57

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

y₁₄²⁺ 921.52

2000

Relative Abundance

3000

80

100

1073.64

Scan number

22153

Raw file

nak_cdc48UbconjugatesSAX2_21may13

Method

ITMS; CID

Pepti...

117.52

GlyGly Site Id 49

y₁₀²⁺

y₉²⁺

-H₂O y₈

-H₂O y₇

y₆²⁺

Q

I

F

V

K

y₅

y₄

y₃

-NH₃ y₂

-NH₃ y₁

T

L

T

G

K

gl

_

M

b₂ -NH₃

b₅

b₆

_

m/z (full) 200

300

400

500

600

700

800

900

1000

1100

y₅

519.31

60

y₃

305.18

y₆²⁺ 381.23 y₁₀²⁺ 624.87

40

b₂

y₉²⁺ 560.84

260.11

b₅

619.33

y₄

418.27

1000

y₈²⁺ 504.3

b₂-NH₃ 243.08 20

y₇²⁺ 430.76 y₁

147.11

y₇

y₈-NH₃ 990.56

860.52

y₇-H₂O 842.51

y₂-NH₃ 187.11

b₆

861.47

y₈

1007.59

y₈-H₂O 989.58

0

y₁-NH₃ 130.09

y₂

204.13

0

100

200

300

400

500

600

m/z (zoom)

700

800

900

1000

1100

Intensity

2000

Relative Abundance

80

3000

100

120

100

Scan number

25324

Raw file


Method

ITMS; CID

Pepti...

316.66

y₁₉²⁺

y₁₈²⁺

T

G

GlyGly Site Id 50

-H₂O y₁₆

-H₂O y₁₅

-H₂O y₁₄

-NH₃ y₁₃

-H₂O y₁₂

y₁₁

-H₂O y₁₀

y₉

y₈

-NH₃ y₇

-H₂O y₆

y₅

-NH₃ y₄

y₃

T

I

T

L

E

V

E

S

S

D

T

I

D

N

gl

_

T

L

K

b₅ -H₂O

b₆ -H₂O

b₇ -H₂O

b₈ -H₂O

b₉ -H₂O

-H₂O

b₁₁ -H₂O

b₁₂ -H₂O

b₁₃

b₁₄

b₁₅ -H₂O

b₁₆ -NH₃

b₁₇ -H₂O

V b₂₀²⁺

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

1200

y₁₄

100

1549.76

1000

y₁₂

800

b₁₀-NH₃ 1155.63 60

b₁₆-NH₃ 1773.88 b₇

b₉

829.48

b₁₀-H₂O 1154.64

y₁₃

1448.71

y₁₂-H₂O 1317.62

1043.61

b₁₅-NH₃ 1672.83 y₁₀

40

b₇-H₂O 811.47 b₆-H₂O 698.38

y₄

475.25

b₅-H₂O 597.34

b₈-H₂O 912.51 y₆

689.38

y₈

y₄-NH₃ 458.22

y₃

y₅

y₆-H₂O 671.37

b₆

716.39

588.34

b₈

930.53

b₁₅-H₂O 1671.84 b₁₂

1400.76

y₁₁

y₁₅

1662.84

b₉-H₂O 1025.6

b₁₁

b₁₃

1271.72

b₁₅

1689.85

b₁₇-H₂O 1885.98

y₁₄-H₂O 1531.75

1487.8

b₂₀²⁺ 1116.57

b₁₆

1790.9

b₁₁-H₂O 1253.71

y₇

y₁₂-NH₃ 1318.6

y₁₃-NH₃ 1431.68

y₁₅-H₂O 1644.83

b₁₇-NH₃ 1886.96 y₁₆-H₂O 1745.88

0

804.41

1903.99

b₁₄

y₁₈²⁺ 1032.03 y₁₉²⁺ 1082.55

b₁₇

y₁₆

1763.89

1574.83

1206.58

y₇-NH₃ 787.38 891.44

360.22

y₁₀-H₂O 1089.51

b₁₂-H₂O 1382.75

200

20

615.35

b₁₁-NH₃ 1254.69

y₁₄-NH₃ 1532.73 400

b₅

1107.52

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

y₉

978.47

600

Relative Abundance

80

1335.63

Scan number

5907

Raw file

nak_cdc48UbconjugatecontrolSAX1_22may10_10

Method

ITMS; CID

Pepti...

275.83

y₁₄²⁺

y₁₃

-NH₃ y₁₂

-H₂O y₁₁

y₁₀

-H₂O y₉

I

Q

D

K

E

GlyGly Site Id 51

y₇

-H₂O y₆

I

P

y₅

-NH₃ y₄

-NH₃ y₃

D

Q

gl

_

S

K

b₂

b₃ -NH₃

b₄ -NH₃

b₅ -H₂O

b₆ -H₂O

G

b₇

b₈

b₉ -H₂O

P b₁₁²⁺

b₁₀ -NH₃

b₁₂

Q

b₁₃

b₁₄ -H₂O

R

_

m/z (full) 600

800

1000

1200

1400

1600

1800

120

400

y₆

100

740.37

60 40

y₆-NH₃ 723.34

y₁₀²⁺ 584.31

y₅

20

y₄ 546.26 b₂

b₃

443.26

y₄-NH₃ 529.24

b₄

571.32

y₁₀

1167.61

b₈

1000.51

b₁₁²⁺ 654.35

y₆-H₂O 722.36

b₆

814.44

y₇

1422.72

b₇

y₉

1039.52

b₉-H₂O 1095.58

y₉-H₂O 1021.51

853.45 943.48

y₁₁-NH₃ 1265.61

y₁₂

1410.7

b₁₃

1550.78

b₁₄

1678.84

b₁₀-NH₃ 1193.62

b₁₀

1210.64

y₁₁

1282.64

y₁₂-NH₃ 1393.67

y₁₃

1523.78

b₁₄-H₂O 1660.83

0

y₃-NH₃ 414.21

b₅-H₂O 668.34

b₁₂

b₉-NH₃ 1096.56

b₆-H₂O 796.43

643.32

0.5

b₃-NH₃ 426.23

y₁₁-H₂O 1264.63

y₉-NH₃ 1022.49

686.35

b₄-NH₃ 554.29

330.18

y₁₄²⁺ 883.46

b₅

y₃

431.24

0

400

600

800

1000

m/z (zoom)

1200

1400

1600

1800

Intensity [10e4]

1

Relative Abundance

80

1.5

b₉

1113.59

Scan number

24624

Raw file


Method

ITMS; CID

Pepti...

289.98

GlyGly Site Id 52

-H₂O y₁₆

y₁₅

-H₂O y₁₄

-H₂O y₁₃

-H₂O y₁₂

-H₂O y₁₁

-H₂O y₁₀

-H₂O y₉

T

L

E

V

E

S

S

D

y₈

y₇

-H₂O y₆

y₅

-H₂O y₄

-H₂O y₃

I

D

N

V

K

gl

_

T

I

b₄

-H₂O

b₆ -H₂O

T b₁₁

b₁₀ -H₂O

-H₂O

b₁₃ -H₂O

b₁₄ -NH₃

b₁₅ -H₂O

b₁₆ -NH₃

S

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

y₁₁

100

1307.64

y₆

804.42

60

b₁₅-NH₃ 1600.76

y₁₀

1220.61

y₈

1018.55

y₁₃

y₁₆-NH₃ 1861.9

1535.75

y₉

1133.58

y₃

y₆-NH₃ 787.39

40

y₁₂-H₂O 1418.68

y₁₀-NH₃ 1203.59

476.28

b₅-H₂O 540.3

b₆

657.38

y₆-H₂O 786.41

y₉-H₂O 1115.57

y₇

y₁₀-H₂O 1202.6

y₁₁-H₂O 1289.63

b₁₆

b₁₀

y₁₃-H₂O 1517.74

1075.52

20

b₁₅

1617.79 1859.92

y₄

b₁₁

1176.56

y₁₃²⁺ 768.38 y₄-H₂O 557.34

b₁₄

1518.72

917.51

575.35

y₃-H₂O 458.27

y₁₆-H₂O 1860.92

b₈-H₂O 855.45

b₁₆²⁺ 930.47

y₁₂-NH₃ 1419.66

200

b₆-H₂O 639.37

y₁₄-H₂O 1646.79

y₁₆²⁺ 939.97

b₁₅-H₂O 1599.77

b₁₃

b₁₆-NH₃ 1842.9

1404.67

y₁₆

1878.93

y₁₄

1664.8

b₁₀-H₂O 1057.5 b₁₃-H₂O 1386.66

b₄

429.27

b₁₄-NH₃ 1501.69 y₁₅

0

1777.88

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

y₅

689.39

400

Relative Abundance

80

600

y₁₂

1436.69

Scan number

14106

Raw file


Method

ITMS; CID

Pepti...

86.62

GlyGly Site Id 53

-NH₃ y₇

y₆²⁺

I

S

y₄

y₃

ac

gl

_

S

A

G

-H₂O

D

-H₂O

A

I

N b₉²⁺ -NH₃

b₈

-H₂O

I b₁₀ -NH₃

K

_

m/z (full) 200

300

400

500

600

700

800

900

1000

120

100

160 140

100

b₈²⁺ 379.19

80

40

60

b₇-H₂O 626.28

y₄

b₈

y₁-NH₃ 244.13

b₁₀ 984.5

y₇

757.37

872.52

b₉²⁺ 436.21 b₁₀-NH₃ 967.47

b₉-NH₃ 854.39

0

b₃-H₂O 240.1

20

b₂-H₂O 183.08

40

20

601.37

0

100

200

300

400

500

600

m/z (zoom)

700

800

900

1000

Intensity

60

100

Relative Abundance

80

120

y₃

488.28

y₆²⁺ 380.22

Scan number

19256

Raw file


Method

ITMS; CID

Pepti...

195.96

-H₂O y₂₂²⁺

y₂₁²⁺

y₂₀²⁺

y₁₉²⁺

y₁₈²⁺

y₁₇²⁺

L

A

E

E

T

A

GlyGly Site Id 54

-NH₃ y₁₅²⁺

y₁₄

y₁₃

y₁₂²⁺

y₁₁

y₁₀²⁺

Y

E

G

N

E

N

-H₂O y₈

-H₂O y₇

A

E

-H₂O y₅

y₄

-NH₃

E

D

y₂

gl

_

I

b₃

b₄

b₅

b₆ -H₂O

A

b₇ -H₂O

b₈

b₉

b₁₀

b₁₃ -H₂O

b₁₄ -H₂O

E

b₁₇²⁺

K

A

L

K

_

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

60

y₇-H₂O 928.47 y₂₁²⁺ 1213.04 y₁₅²⁺ 926.91 y₁₇²⁺ 997.95

40

y₁₃²⁺ 780.86

y₁₈²⁺ 1048.47

b₆-H₂O 639.33

b₇

20

728.38

y₅-H₂O 557.29

y₃-NH₃ 314.21

y₂

b₃

298.21

y₁₉²⁺ 1113 b₈

799.42

b₁₃

1391.63

y₁₄²⁺ 845.38 y₈

b₆

1017.52

657.35

b₇-H₂O 710.37 b₄

427.26

y₄

446.26

b₅

556.3

y₅

575.3

y₁₀²⁺ 630.81

y₁₁²⁺ 695.33

b₁₇²⁺ 917.9

y₁₁

y₂₀²⁺ 1177.52

1389.65

b₁₄

1505.68

y₁₆-H₂O 1905.85

y₂₂²⁺ 1269.58 y₇

946.48

y₈-H₂O 999.51

b₁₀

1091.53

b₁₃-H₂O 1373.62

b₁₄-H₂O 1487.66

y₁₃

1560.71

y₁₄

1689.76

y₁₅-NH₃ 1835.79

0

260.2

2

y₁₂²⁺ 752.35

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity [10e4]

4

Relative Abundance

80

100

6

b₉

962.48

Scan number

18410

Raw file


Method

ITMS; CID

Pepti...

146.78

GlyGly Site Id 55

y₂₂²⁺

y₂₁²⁺

y₂₀²⁺

y₁₉²⁺

y₁₈²⁺

y₁₇²⁺

y₁₆

y₁₅

-H₂O y₁₄²⁺

y₁₃

y₁₂

y₁₁

y₁₀

L

A

E

E

T

A

A

Y

E

G

N

E

N

y₈

y₅

y₁ gl

_

I

b₄ -H₂O

b₅

-H₂O

b₇ -H₂O

b₉ -H₂O

b₁₂²⁺

b₁₄ -H₂O

E

A

E

K

b₁₇

E

D

b₂₀²⁺

A

L

K

_

-NH₃

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

120

400

4000

b₉

40

962.48

y₁₈²⁺ 1048.47 y₁₇²⁺ 997.95

20

b₇-H₂O 710.37 b₄ 427.26

y₁

b₄-H₂O 409.24

y₈²⁺ 509.26

b₅

556.3

b₁₂²⁺ 631.8

y₅

689.35

b₁₄

b₂₀²⁺ 1103.98

b₁₈-NH₃ 1945.87

y₂₀²⁺ 1177.52

b₉-H₂O 944.47

y₁₂

y₈

b₇

1017.52

728.38

y₁₅

1503.69

y₁₀

1260.61

y₁₁

1389.65

b₁₄-H₂O 1487.66

1852.82

y₁₃

1560.71

y₁₄-H₂O 1671.75

b₁₇

1834.8

y₁₆

1923.86

0

261.16

y₁₄²⁺ 845.38

y₂₂²⁺ 1269.58 1505.68

y₁₃²⁺ 780.86

b₆-H₂O 639.33

y₁₉²⁺ 1113

2000

y₁₅²⁺ 926.91

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

60

6000

Relative Abundance

80

100

8000

y₂₁²⁺ 1213.04

Scan number

22448

Raw file


Method

ITMS; CID

Pepti...

208.56

GlyGly Site Id 56

y₈

-H₂O y₇

y₆

y₅

y₄

y₃

V

E

Y

F

A

K

-H₂O y₂

gl

_

F

N

b₂ -NH₃

b₃ -NH₃

b₄ -NH₃

b₅ -H₂O

b₆ -H₂O

b₇ -NH₃

E

b₈ -H₂O

K

b₉ -H₂O

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1300

1400

120

200

1400

y₆

100

915.49

y₇

1044.53

1200

y₅

1000

y₄

b₅

653.29

y₃

40

600

534.32

y₈

1143.6

b₅-NH₃ 636.27

b₂

262.12

b₉

b₃

1250.59

361.19

b₇

871.4

490.23

b₃-NH₃ 344.16

20

b₅-H₂O 635.28

b₄

b₆-NH₃ 783.33

b₂-NH₃ 245.09

b₇-NH₃ 854.37

y₈²⁺ 572.3

y₇-H₂O 1026.52

b₈

1121.55

b₉-NH₃ 1233.57 200

b₄-NH₃ 473.2 a₂

400

y₂

284.17

b₆

800.36

b₆-H₂O 782.35

y₂-H₂O 266.16

b₈-H₂O 1103.54

b₉-H₂O 1232.58

0

234.12

0

200

300

400

500

600

700

800

m/z (zoom)

900

1000

1100

1200

Intensity

60

605.36

800

Relative Abundance

80

752.43

Scan number

37234

Raw file


Method

ITMS; CID

Pepti...

178.14

GlyGly Site Id 57

-NH₃ y₁₆

y₁₂²⁺

y₁₁

V

K

-H₂O y₉

y₈

A

G

y₆

y₅

y₄

-NH₃ y₂

y₃

gl

_

G

F

T

b₂

L

b₃ -H₂O

b₄

A

E b₆²⁺ -H₂O

b₅

b₇

A

b₈

b₉

b₁₀

L b₁₂

b₁₁

T b₁₃²⁺

A

b₁₄

A b₁₅²⁺

Y b₁₆²⁺

A

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

120

200

y₄

100

480.26

y₅

551.29

y₃

b₇

b₁₅²⁺ 758.41

718.38

y₆

40

652.34

b₅

b₁₃²⁺ 687.37

b₆-H₂O 601.3

b₁₆²⁺ 839.94

y₉-H₂O 875.47

490.27

y₁₁²⁺ 603.83

500

b₈²⁺ 480.76

y₂

246.16

20

y₈

822.45

b₁₀²⁺ 551.8

b₆²⁺ 310.16

y₁₂²⁺ 653.37

b₃

306.14

y₂-NH₃ 229.13 b₃-H₂O 288.13

b₈

960.51

b₄

y₉

419.23

893.48

y₁₄-NH₃ 1488.78 b₉

1031.55

b₁₀

1102.59

b₂

b₁₁

1159.61

y₁₁

1206.66

b₁₂

1272.69

y₁₆

1719.94

b₁₄

1444.78

0

205.1

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

1800

Intensity

60

409.22

1000

Relative Abundance

80

1500

b₁₄²⁺ 722.89

Scan number

29163

Raw file


Method

ITMS; CID

Pepti...

107.03

GlyGly Site Id 58

-NH₃ y₁₀²⁺

y₉²⁺

y₆

y₃

y₂

-NH₃ y₁

E

R

gl

_

A

I

K

b₂

S

L

E

S

b₆ -H₂O

b₇ -H₂O

F

L b₉²⁺

b₈ -H₂O

F b₁₀²⁺

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

1200

1300

1400

1200

1300

1400

120

200

500

y₃

100

451.23

60 40

200

y₁₀²⁺ 685.36

b₉²⁺ 552.31

b₆

756.43

b₆-H₂O 738.41

y₆²⁺ 399.71 y₁-NH₃ 158.09 y₂

304.16

a₂

y₁

b₈

b₆²⁺ 378.72

990.53

b₇

b₂

843.46

185.13

b₈-H₂O 972.51

y₈-NH₃ 1023.51

0

157.13 175.12

y₆

798.41

b₁₀²⁺ 625.84

100

20

b₇-H₂O 825.45

0

200

300

400

500

600

700

800

m/z (zoom)

900

1000

1100

Intensity

300

Relative Abundance

80

400

y₉²⁺ 564.29

Scan number

29413

Raw file


Method

ITMS; CID

Pepti...

148.85

GlyGly Site Id 59

-H₂O y₂₁²⁺

y₁₉²⁺

y₁₈²⁺

y₁₇²⁺

y₁₆²⁺

y₁₅²⁺

A

V

T

I

I

y₁₃

y₁₁

y₉²⁺

y₈

y₇

y₆

-H₂O y₅

y₄

E

P

I

L

A

P

gl

_

A

L

P

D

b₆ -H₂O

b₇ -H₂O

b₈ -H₂O

b₉

E

b₁₀

P

K

b₁₂ -NH₃

E

E

b₁₄

b₁₅

b₁₈²⁺

b₁₉²⁺

S

V

K

_

-NH₃

m/z (full) 400

600

800

1000

1200

1400

1600

1800

2000

120

200

100

4

60 40 20

y₄

438.28

y₈²⁺ 416.77

y₉²⁺ 481.29

b₆

b₇

668.36

567.31

y₆

622.4

b₆-H₂O 549.3

b₉

894.53

y₇

y₁₇²⁺ 1012.07

y₂₁²⁺ 1203.16 b₁₉²⁺ 1076.59 b₁₂

735.49

b₇-H₂O 650.35

b₈

781.45

1370.78

y₈

832.54

y₁₆²⁺ 961.54 b₁₅²⁺ 879.46

b₁₀

1023.57

y₁₈²⁺ 1061.6

y₁₁

1219.67

b₁₂-NH₃ 1353.75

y₁₂-H₂O 1451.81

y₁₃

1566.87

b₁₄

1628.86

b₁₇-NH₃ 1951.01

b₁₅

1757.9

0

b₆²⁺ 284.16

y₅

509.32

b₁₈²⁺ 1041.07

b₈-H₂O 763.43

1

y₅-H₂O 491.31

y₁₉²⁺ 1097.12

0

200

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity [10e4]

2

Relative Abundance

80

3

y₁₅²⁺ 905

y₁₃²⁺ 783.94

Scan number

16298

Raw file


Method

ITMS; CID

Pepti...

172.94

GlyGly Site Id 60

y₇

-H₂O y₆

y₅

-NH₃ y₄

y₃

-NH₃ y₂

-NH₃ y₁

N

E

E

Y

L

I

K

gl

_

L

b₂ -NH₃

-H₂O

b₅ -NH₃

-H₂O

b₆ -NH₃

b₇ -NH₃

_

m/z (full) 300

400

500

600

700

800

900

1000

1100

120

200

800

y₆

100

908.47

60

y₅

779.43

y₃

487.32

b₂

40

228.13

y₆-H₂O 890.46

y₂

374.24

y₁

b₆-NH₃ 745.34

261.16

b₇-NH₃ 858.42

y₂-NH₃ 357.21

200

y₄-NH₃ 633.36

b₃-NH₃ 340.15

b₄-NH₃ 469.19

20

b₆

762.37

b₂-NH₃ 211.11

y₁-NH₃ 244.13

b₄-H₂O 468.21

b₅-NH₃ 632.26

y₇²⁺ 511.76

b₃-H₂O 339.17

y₇

1022.52

b₇

875.45

b₅

649.28

a₂

0

200.14

0

200

300

400

500

600

m/z (zoom)

700

800

900

1000

1100

Intensity

400

Relative Abundance

80

600

y₄

650.39

Scan number

5910

Raw file

nak_UBX7HSAX2_20Jan11_2

Method

ITMS; CID

Pepti...

81.9

GlyGly Site Id 61

-H₂O y₈

y₇

-H₂O y₆

-NH₃ y₅

y₄

S

E

E

Q

D

y₂ gl

_

H

G

N

Y

T

b₄

V

b₆ -H₂O

b₇ -H₂O

b₈

b₁₀

K

-NH₃

V b₁₃²⁺

K

_

-H₂O

m/z (full) 400

600

800

1000

1200

1400

1600

1800

1600

1800

120

200

100

60

y₅

731.4

50

y₈

40

60

b₆

672.31

b₄

472.19

b₈

888.38

b₇-H₂O 741.33 b₁₃²⁺ 801.36

40

b₆-H₂O 654.3

y₇

20

y₅-NH₃ 714.38

y₆

860.45

989.49

y₄

603.35

y₂

y₈-H₂O 1058.51

b₆²⁺ 336.66

b₁₀

1145.49

b₁₁-NH₃ 1243.49

20

246.18

b₁₂-H₂O 1484.64

0

10 0

200

400

600

800

1000

m/z (zoom)

1200

1400

Intensity

y₆-H₂O 842.44 b₇

759.34

30

Relative Abundance

80

1076.52

Scan number

20584

Raw file

nak_cdc48UbconjugatesSAX2_21may13

Method

ITMS; CID

Pepti...

131.17

GlyGly Site Id 62

-H₂O y₁₂ ac

-NH₃ y₄

-NH₃ y₃

R

G

y₂

gl

_

I

K

F

T

N

E

N

b₆ -NH₃

L

b₇ -H₂O

I

b₈

b₉ -H₂O

b₁₁ -H₂O

I b₁₂

R

_

m/z (full) 400

600

800

1000

1200

1400

1600

120

200

y₄

100

501.33

400

b₉

b₇²⁺ 502.25 300

Intensity

60

y₄-NH₃ 484.3 y₁₂-NH₃ 1557.85

b₉-NH₃ 1212.63 40

200

y₁₂-H₂O 1556.87

y₃

345.22

y₁₂

1574.88

b₇

1003.48

b₆

b₁₁

y₂

288.2

b₇-H₂O 985.47

1442.78

100

20

b₇-NH₃ 986.46 b₆-NH₃ 872.41

b₁₂

1555.86

889.44

y₃-NH₃ 328.2

b₉-H₂O 1211.64 b₈

1116.57

b₁₁-H₂O 1424.76

0

Relative Abundance

80

1229.65

0

200

400

600

800

1000

m/z (zoom)

1200

1400

1600

Scan number

41746

Raw file


Method

ITMS; CID

Pepti...

114.63

GlyGly Site Id 63

-NH₃ y₃₁²⁺

y₂₈²⁺ y₂₇²⁺ y₂₆²⁺ y₂₅²⁺

y₂₃²⁺

y₁₇

y₁₆

y₁₅

L

G

G

y₁₃

-NH₃ -NH₃ -H₂O y₁₂ y₁₀

y₉

y₈

y₇

y₆

L

E

M

A

-NH₃ -NH₃ y₅ y₄

y₃

gl

_

S

T

A

T

G

P

S

E

A

V

W

b₁₀ b₁₁ -H₂O -H₂O -H₂O

Y

G

b₁₃ -H₂O

P

P

K

A

A

b₁₇

N

V

A

V

S

G

b₂₈²⁺

Q

N

b₃₂²⁺ b₃₃²⁺ S

Q R b₃₅²⁺

_

-H₂O -H₂O

m/z (full) 600

800

1000

1200

1400

1600

1800

2000

y₂₅²⁺ 1315.16 60

y₂₆²⁺ 1408.2 y₁₃

1390.67

y₂₃²⁺ 1205.12

b₁₃

40

1307.59

b₂₈²⁺ 1377.2 y₂₈²⁺ 1493.25

y₁₁-NH₃ 1203.54 y₈ 963.43

y₇

y₆

834.39

20

y₄

504.25

y₃

y₄-NH₃ 487.23

y₅

b₁₁-H₂O 1069.49

632.31

y₅-NH₃ 615.28

y₁₃²⁺ 695.84

b₃₂²⁺ 1606.79

b₁₇

1814.87

b₁₃-H₂O 1289.58 y₁₀-H₂O 1115.53

y₂₀-NH₃ 1955.96

y₁₂

1319.64

y₁₅

1546.76

b₉-H₂O 784.35

y₁₆

1603.79

y₃₁²⁺ 1649.82

y₁₇

1716.87

b₃₅²⁺ 1771.35 b₁₈-H₂O 1867.9

0

390.21

y₉

1076.52

b₁₀-H₂O 883.42

b₁₉-H₂O 1981.94

y₂₇²⁺ 1457.74

y₁₀

1133.54 703.35

b₃₃²⁺ 1663.81

y₁₂-NH₃ 1302.61

b₁₁ 1087.51

100

b₁₀ 901.43

0

400

600

800

1000

1200

m/z (zoom)

1400

1600

1800

2000

Intensity

200

Relative Abundance

80

300

100

120

400

Scan number

8817

Raw file


Method

ITMS; CID

Pepti...

168.89

GlyGly Site Id 64

-NH₃ y₁₃²⁺

y₁₁²⁺

y₁₀

V

Y

-H₂O y₈

-H₂O y₇

y₆

L

E

K

-NH₃ y₅

y₄

y₃

-H₂O y₂

D

S

S

gl

_

K

S

D

D

b₅

b₆ -H₂O

b₇ -H₂O

b₈

N b₁₀²⁺

b₉

K

_

m/z (full) 400

600

800

1000

1200

1400

1600

1800

1400

1600

1800

2000

120

200

100

y₈²⁺ 525.77

60

b₆

716.33

y₆

808.41

y₅

40

558.26

y₇

937.46

b₆²⁺ 358.67

20

y₁₁²⁺ 714.35 y₇-H₂O 919.45

y₇²⁺ 469.23 y₆²⁺ 404.71

b₅

y₁₀²⁺ 664.82

601.31

y₂

b₈

958.46

b₇

829.42

b₇-H₂O 811.41

242.16

y₄

b₆-H₂O 698.32

444.22

y₅-NH₃ 541.23

500

y₃

329.19

b₉²⁺ 604.81

y₇-NH₃ 920.43

y₈

1050.54

b₁₀²⁺ 661.83

y₂-H₂O 224.15

y₉-NH₃ 1148.54

b₉

y₁₀

1328.63

1208.61

0

y₈-H₂O 1032.53

0

200

400

600

800

1000

m/z (zoom)

1200

Intensity

1000

Relative Abundance

80

1500

y₁₃²⁺ 815.38

Scan number

7530

Raw file

nak_ubx5H_SAX1_17Sep1

Method

ITMS; CID

Pepti...

111.94

GlyGly Site Id 65

y₁₀²⁺

y₉²⁺

-H₂O y₈

y₇

y₆

-H₂O

L

H

F

D

T

-NH₃ y₃

y₁

gl

_

T

K

b₄ -H₂O

b₅

b₆²⁺ -H₂O

A

b₇

E

b₈ -H₂O

P

b₉

b₁₀²⁺

V

K

b₁₁

_

m/z (full) 400

600

800

1000

1200

1400

120

200

60

b₁₁²⁺ 681.35 0.6

b₄

40

602.35

b₁₀²⁺ 631.82

0.4

b₄-H₂O 584.34 y₄-H₂O 462.28

y₆

652.38

y₈

914.47

y₇

767.4

y₃

20

351.25

y₁

y₉²⁺ 526.27

b₈

b₇

1036.53

965.49

749.42

b₆-H₂O 846.43

y₂-NH₃ 237.17

y₈-NH₃ 897.44

b₈-H₂O 1018.52

b₉

1165.57

b₁₁

1361.69

0

155.13

y₈-H₂O 896.46 b₅

0.2

b₆²⁺ 432.73

0

200

400

600

800

m/z (zoom)

1000

1200

1400

Intensity [10e4]

0.8

Relative Abundance

1

80

1.2

100

1.4

y₁₀²⁺ 582.81

Scan number

12204

Raw file


Method

ITMS; CID

Pepti...

126.71

-NH₃ y₁₁

y₁₀

A

K

GlyGly Site Id 66

y₉

y₈

y₇

y₆

E

G

Y

G

y₄

y₃

y₂

F

E

D

gl

_

S

V

b₄ -NH₃

b₅ -H₂O

b₇

Y

b₉ -H₂O

b₁₀

b₁₁

b₁₂

R

_

m/z (full) 600

800

1000

1200

1400

1600

120

400

y₆

100

120

786.34

y₈

1006.43

y₄

80

y₁₁²⁺ 724.83

40

y₁₀²⁺ 689.31 b₅

629.33

b₁₂

1460.63

b₉

1069.49

40

y₇

949.41

20

b₅-H₂O 611.31 y₂

290.15

b₇

y₁₁

b₉-H₂O 1051.48

849.41

1448.64

b₁₁²⁺ 673.31

b₄

500.28

b₁₀

b₄-NH₃ 483.26

b₁₁

1345.61

y₁₀

1377.61

0

1216.56

20

y₁₁-NH₃ 1431.62

y₉²⁺ 568.24

y₃

419.19

0

400

600

800

1000

m/z (zoom)

1200

1400

1600

Intensity

60

566.26

60

Relative Abundance

80

100

y₉

1135.47