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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;

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Legends
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


Apolipoprotein E

Q03247

Thr-31 (& Thr-32)

v

817.0358(3+)

m

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


Apolipoprotein E

Q03247

Thr-307

v

541.2650(3+)

v

v

m

*

LRPS(HexNAc)PTSPPSENH


Insulin-like growth factor-binding protein 5

Q05717

Thr-171

v

486.9032(3+)

v

*

m

v

FVGGAENT(HexNAc)AHPR


Collagen alpha-1(XI) chain (Fragment)

Q28083

Thr-86

v

859.8793(2+)

v

NYGTESYQT(HexNAc)EAPR


Coagulation factor V

Q28107

Ser-1151 & Thr-1154

v

759.0452(3+)

v

*

m

RS(HexNAc)PPT(HexNAc)QPSQIPNYDLR


Coagulation factor V

Q28107

Thr-1171

HCD

860.4367(2+)

v

ETD

c13

z11

c9*

c12

v

c8*

c11

b10

m

c7*

z9*

z10

AIPT(HexNAc)DVSQIFPSLE


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.


Complement component C7 neutral loss, as presented below,

Q29RQ1

Thr-696

HCD

428.2453(3+)

EAPLTPKVPK+HexNAc


The glycopeptide was identified from HCD data with a HexNAc neutral loss, as presented below,

mass differences are in ppm.

Single potential site.


Augurin neutral loss, as presented below,

Q32KM8

Thr-47

v

943.9625(2+)

v

m

EAPAPT(HexNAc)MTPVAVQESR


Complement factor I neutral loss, as presented below,

Q32PI4

Thr-57

v

747.8566(4+)

v

ETEASSEVKPT(HexNAc)STQDTSQKDFVDKK


Complement component C9 neutral loss, as presented below,

Q3MHN2

Thr-24 & Ser-26

v

911.7614(3+)

v

m

*

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


Thrombospondin-4 neutral loss, as presented below,

Q3SWW8

Thr-270 & Ser-282 & Thr-284

v

793.1561(4+)

v

m

m

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


Apolipoprotein C-IV neutral loss, as presented below,

Q3SYR5

Thr-35

1010.9789(2+)

HCD

v

ETD

y8

y13

y10

z15*

z16

m

y15

z8*

y11

m

*

y14

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


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.


Inter-alpha-trypsin inhibitor heavy chain H4 neutral loss, as presented below,

Q3T052

Q5EA67

Ser-629 & Ser-635

v

566.2913 (4+)

v

v

FGHS(HexNAc)VGDRTS(HexNAc)RKPGGGLK


Inter-alpha-trypsin inhibitor heavy chain H4 neutral loss, as presented below,

Q3T052

Q5EA67

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

v

v

m

1078.4978(3+)

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


Different colors indicate ambiguity about the site assignment: green supports Ser-686;

blue indicates sugar on Thr-688.


Inter-alpha-trypsin inhibitor heavy chain H4 assignment: green supports Ser-686;

Q3T052

Q5EA67

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

v

v

909.7225(3+)

m

*

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


Inter-alpha-trypsin inhibitor heavy chain H4 assignment: green supports Ser-686;

Q3T052

Q5EA67

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

v

604.2606(3+)

v

m

*

T(HexNAc)SGPGGAS(HexNAc)HDTDFR


Different colors indicate ambiguity about the site assignment: green supports Thr-688;

blue indicates sugar on Ser-689.


Inter-alpha-trypsin inhibitor heavy chain H4 assignment: green supports Thr-688;

Q3T052

Q5EA67

(Thr-688) & Thr-698

v

604.2604(3+)

m

v

*

T(HexNAc)SGPGGASHDT(HexNAc)DFR


Vitronectin assignment: green supports Thr-688;

Q3ZBS7

Thr-63

v

570.6102(3+)

*

m

v

m

AEC(Carbamidomethyl)KPQVT(HexNAc)RGDVF


Both ends non-tryptic! assignment: green supports Thr-688;

Precursor mass error = -0.15 ppm

Score = 26.3; E = 2.9e-4


Vitronectin assignment: green supports Thr-688;

Q3ZBS7

Thr-97 & Thr-98

v

845.4210(2+)

m

*

v

QPEST(HexNAc)T(HexNAc)LAPVLQ


both ends non-tryptic! assignment: green supports Thr-688;

Precursor mass error = -4.8 ppm

Score = 28.6; E = 4.5e-4


Vitronectin assignment: green supports Thr-688;

Q3ZBS7

Thr-107

v

680.0245(3+)

m

AQT(HexNAc)LETPVQAPVLNPEK


Vitronectin assignment: green supports Thr-688;

Q3ZBS7

Thr-142 or Ser-143

v

1054.7689(3+)

m

v

GDSEPGMGTSDLGT(HexNAc)SESPAEEETC(Carbamidomethyl)SGKPF



Peptidase inhibitor 16 may be Thr-142.

Q58D34

Thr-408

v

925.4483(2+)

v

SLSNSPSASAT(HexNAc)ANAVGGR


Fetuin B may be Thr-142.

Q58D62

Thr-19 & Thr-20

v

914.4683(2+)

v

m

*

T(HexNAc)S(HexNAc)PPQPAARPSSLL


both ends are non-tryptic may be Thr-142.

Precursor mass error = -2.3 ppm

Score = 22.1; E = 0.012


Fetuin B may be Thr-142.

Q58D62

Thr-157

v

723.9690(3+)

m

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


Fetuin B may be Thr-142.

Q58D62

Thr-173

v

723.8355(2+)

v

FM(Oxidation)ETAT(HexNAc)ESLAK


Fetuin B may be Thr-142.

Q58D62

Ser-262

v

727.8453(2+)

v

SFFNS(HexNAc)QAPTPR


Fetuin B may be Thr-142.

Q58D62

Thr-273

v

595.9606(3+)

v

v

GENAT(HexNAc)VNQRPANPSK


Fetuin B may be Thr-142.

Q58D62

(Thr-295) & Thr-299

v

777.0660(3+)

v

m

*

LQQQNTAPT(HexNAc)NSPT(HexNAc)KAVPK


Pigment epithelium-derived factor may be Thr-142.

Q95121

Thr-34

v

804.3722(3+)

v

m

AGSLTPEST(HexNAc)GAPVEEEDPFFK


This UniProt entry (recently deleted) indicated a Leu -> Val substitution at position-403 of kininogen-1, here we show ETD data confirming the mutation

F1MNV4

v

702.8290(2+)

-HexNAc

c11

v

z8*

z10

z9*

c8*

z11

z6*

z7

c6

z5*

*

TEGSTT(HexNAc)VSVPHS


This UniProt entry (recently deleted) indicated a Leu -> Val substitution at position-403 of kininogen-1, here we show HCD data confirming the mutation

F1MNV4

702.8290(2+)

HexNAc

MH+

y3

b2

b9-2xH2O

y2

y10

y5

y4

TEGSTTVSVPHS + HexNAc

All fragments are within 10 ppm


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