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Please include the following statement when referencing the CPTAC Assay Portal
We would like to acknowledge the National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) Assay Portal (assays.cancer.gov) for developing assays and establishing criteria for the assays described in this publication.

EPHB4

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
EPHB4 HTK, MYK1, TYRO11
Sequence Length (AA) Molecular Weight (Da)
987 108270
Protein Name
Ephrin type-B receptor 4
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MELRVLLCWA SLAAALEETL LNTKLETADL KWVTFPQVDG QWEELSGLDE
60 70 80 90 100
EQHSVRTYEV CDVQRAPGQA HWLRTGWVPR RGAVHVYATL RFTMLECLSL
110 120 130 140 150
PRAGRSCKET FTVFYYESDA DTATALTPAW MENPYIKVDT VAAEHLTRKR
160 170 180 190 200
PGAEATGKVN VKTLRLGPLS KAGFYLAFQD QGACMALLSL HLFYKKCAQL
210 220 230 240 250
TVNLTRFPET VPRELVVPVA GSCVVDAVPA PGPSPSLYCR EDGQWAEQPV
260 270 280 290 300
TGCSCAPGFE AAEGNTKCRA CAQGTFKPLS GEGSCQPCPA NSHSNTIGSA
310 320 330 340 350
VCQCRVGYFR ARTDPRGAPC TTPPSAPRSV VSRLNGSSLH LEWSAPLESG
360 370 380 390 400
GREDLTYALR CRECRPGGSC APCGGDLTFD PGPRDLVEPW VVVRGLRPDF
410 420 430 440 450
TYTFEVTALN GVSSLATGPV PFEPVNVTTD REVPPAVSDI RVTRSSPSSL
460 470 480 490 500
SLAWAVPRAP SGAVLDYEVK YHEKGAEGPS SVRFLKTSEN RAELRGLKRG
510 520 530 540 550
ASYLVQVRAR SEAGYGPFGQ EHHSQTQLDE SEGWREQLAL IAGTAVVGVV
560 570 580 590 600
LVLVVIVVAV LCLRKQSNGR EAEYSDKHGQ YLIGHGTKVY IDPFTYEDPN
610 620 630 640 650
EAVREFAKEI DVSYVKIEEV IGAGEFGEVC RGRLKAPGKK ESCVAIKTLK
660 670 680 690 700
GGYTERQRRE FLSEASIMGQ FEHPNIIRLE GVVTNSMPVM ILTEFMENGA
710 720 730 740 750
LDSFLRLNDG QFTVIQLVGM LRGIASGMRY LAEMSYVHRD LAARNILVNS
760 770 780 790 800
NLVCKVSDFG LSRFLEENSS DPTYTSSLGG KIPIRWTAPE AIAFRKFTSA
810 820 830 840 850
SDAWSYGIVM WEVMSFGERP YWDMSNQDVI NAIEQDYRLP PPPDCPTSLH
860 870 880 890 900
QLMLDCWQKD RNARPRFPQV VSALDKMIRN PASLKIVARE NGGASHPLLD
910 920 930 940 950
QRQPHYSAFG SVGEWLRAIK MGRYEESFAA AGFGSFELVS QISAEDLLRI
960 970 980 987
GVTLAGHQKK ILASVQHMKS QAKPGTPGGT GGPAPQY

Data source: UniProt

Protein Map Collapse protein map

Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

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Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-2788 Collapse assay details

Data source: Panorama

Official Gene Symbol
EPHB4
Peptide Modified Sequence
EAEY[+80.0]SDKHGQYLIGHGTK
Modification Type
Phospho (Y)
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
571
Peptide End
588
CPTAC ID
CPTAC-2788
Peptide Molecular Mass
2,111.9314
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
Mammalian Cell Lysate
Submitting Laboratory
Johns Hopkins University / Pandey
Submitting Lab PI
Akhilesh Pandey

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
Orbitrap Fusion Lumos
Internal Standard
100fmol
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Easy nLC 1200 System
Column Packing
C18 2um 100A
Column Dimensions
75um i.d. x 50cm
Flow Rate
250nl/min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

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Repeatability

Data source: Panorama

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  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y11 (1+) 26.3 11 7.8 28.3 10.5 8.4 38.6 15.2 11.5 14 15 15
y10 (1+) 30.3 7.6 6.4 35.1 8.6 8.5 46.4 11.5 10.6 15 15 15
y6 (1+) 40.7 6.6 7.1 36.5 7.7 8.7 54.7 10.1 11.2 14 15 15
y5 (1+) 28.3 4.3 3.9 34.3 4.8 5.3 44.5 6.4 6.6 15 15 15
y3 (1+) 24.9 13.4 7.6 31.5 11.8 10.6 40.2 17.9 13 14 15 15
sum 26.8 3.3 4.7 33.5 3.4 6 42.9 4.7 7.6 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
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Comments

Assay Details for CPTAC-2919 Collapse assay details

Data source: Panorama

Official Gene Symbol
EPHB4
Peptide Sequence
DLVEPWVVVR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
385
Peptide End
394
CPTAC ID
CPTAC-2919
Peptide Molecular Mass
1,210.6710
Species
Homo Sapiens
Assay Type
Direct PRM
Matrix
Tumor Digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
ThermoFisher, Q-Exactive
Internal Standard
25 fmol on column
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
Easy-nLC 1000 Thermo Scientific
Column Packing
C18
Column Dimensions
75 µm x 50 cm
Flow Rate
300 nL/min

Chromatograms

Data source: Panorama

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Response Curves

Data source: Panorama

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Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y8 (1+) 9 4.5 8.4 8.3 14.5 13.4 12.2 15.2 15.8 15 15 15
y6 (1+) 4.1 3.8 6.7 5.1 14.1 11.7 6.5 14.6 13.5 15 15 15
y7 (1+) 5.2 3.9 6.9 7 14.2 12.2 8.7 14.7 14 15 15 15
sum 4.6 3.9 6.9 5.6 14.1 12 7.2 14.6 13.8 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments

Assay Details for CPTAC-2841 Collapse assay details

Data source: Panorama

Official Gene Symbol
EPHB4
Peptide Sequence
FPQVVSALDK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
867
Peptide End
876
CPTAC ID
CPTAC-2841
Peptide Molecular Mass
1,102.6023
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
Tumor Digest
Submitting Laboratory
Washington University in St. Louis
Submitting Lab PI
Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
ThermoFisher, Q-Exactive™
Internal Standard
25 fmol on column
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
EASY-nLC™ 1000 Thermo Scientific
Column Packing
C18
Column Dimensions
75 µm x 50 cm
Flow Rate
300 nl/min

Chromatograms

Data source: Panorama

view larger image
view larger image
view larger image

Response Curves

Data source: Panorama

view larger image
view larger image
view larger image

Retrieving Data

Loader

Repeatability

Data source: Panorama

view larger image
  Average intra-assay CV
(within day CV)		 Average inter-assay CV
(between day CV)		 Total CV
equation		 n=
Fragment ion / Transition Low Med High Low Med High Low Med High Low Med High
y8 (1+) 29.8 3.9 2.5 31.5 13.6 7.3 43.4 14.1 7.7 15 15 15
y7 (1+) 8.9 4 1.7 25.8 12.1 4.6 27.3 12.7 4.9 15 15 15
y6 (1+) 20.1 4.6 2.4 30.4 11.7 7.4 36.4 12.6 7.8 15 15 15
sum 12.2 3.6 1.5 16.2 12.2 5.9 20.3 12.7 6.1 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
Comments