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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.

FGFR4

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
FGFR4 JTK2, TKF
Sequence Length (AA) Molecular Weight (Da)
802 87954
Protein Name
Fibroblast growth factor receptor 4
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MRLLLALLGV LLSVPGPPVL SLEASEEVEL EPCLAPSLEQ QEQELTVALG
60 70 80 90 100
QPVRLCCGRA ERGGHWYKEG SRLAPAGRVR GWRGRLEIAS FLPEDAGRYL
110 120 130 140 150
CLARGSMIVL QNLTLITGDS LTSSNDDEDP KSHRDPSNRH SYPQQAPYWT
160 170 180 190 200
HPQRMEKKLH AVPAGNTVKF RCPAAGNPTP TIRWLKDGQA FHGENRIGGI
210 220 230 240 250
RLRHQHWSLV MESVVPSDRG TYTCLVENAV GSIRYNYLLD VLERSPHRPI
260 270 280 290 300
LQAGLPANTT AVVGSDVELL CKVYSDAQPH IQWLKHIVIN GSSFGADGFP
310 320 330 340 350
YVQVLKTADI NSSEVEVLYL RNVSAEDAGE YTCLAGNSIG LSYQSAWLTV
360 370 380 390 400
LPEEDPTWTA AAPEARYTDI ILYASGSLAL AVLLLLAGLY RGQALHGRHP
410 420 430 440 450
RPPATVQKLS RFPLARQFSL ESGSSGKSSS SLVRGVRLSS SGPALLAGLV
460 470 480 490 500
SLDLPLDPLW EFPRDRLVLG KPLGEGCFGQ VVRAEAFGMD PARPDQASTV
510 520 530 540 550
AVKMLKDNAS DKDLADLVSE MEVMKLIGRH KNIINLLGVC TQEGPLYVIV
560 570 580 590 600
ECAAKGNLRE FLRARRPPGP DLSPDGPRSS EGPLSFPVLV SCAYQVARGM
610 620 630 640 650
QYLESRKCIH RDLAARNVLV TEDNVMKIAD FGLARGVHHI DYYKKTSNGR
660 670 680 690 700
LPVKWMAPEA LFDRVYTHQS DVWSFGILLW EIFTLGGSPY PGIPVEELFS
710 720 730 740 750
LLREGHRMDR PPHCPPELYG LMRECWHAAP SQRPTFKQLV EALDKVLLAV
760 770 780 790 800
SEEYLDLRLT FGPYSPSGGD ASSTCSSSDS VFSHDPLPLG SSSFPFGSGV
802
QT

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-1768 Collapse assay details

Data source: Panorama

Official Gene Symbol
FGFR4
Peptide Modified Sequence
GVHHIDYY[+80.0]K
Modification Type
Phospho (Y)
Protein - Site of Modification
643
Peptide - Site of Modification
8
Peptide Start
636
Peptide End
644
CPTAC ID
CPTAC-1768
Peptide Molecular Mass
1,210.5172
Species
Homo sapiens (Human)
Assay Type
Direct PRM
Matrix
E.coli 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
>80%
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
300nl/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
b3 (1+) 14.6 12.8 20.6 17.7 14.7 13.7 22.9 19.5 24.7 15 15 15
y2 (1+) 13.3 14.3 16.4 12.3 15.8 12.3 18.1 21.3 20.5 15 15 15
y3 (1+) 16.6 15 21.7 25.5 17.9 12.7 30.4 23.4 25.1 15 15 15
y4 (1+) 15.8 14.6 22.8 19.5 14.8 13.7 25.1 20.8 26.6 15 15 15
y5 (1+) 20 15 25 24 16.5 15.7 31.2 22.3 29.5 15 15 15
y6 (1+) 17.2 15.6 25.8 20.8 17.1 16.6 27 23.1 30.7 15 15 15
sum 15 14.1 22.4 17.8 15.8 13.9 23.3 21.2 26.4 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
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Comments

Assay Details for CPTAC-3179 Collapse assay details

Data source: Panorama

Official Gene Symbol
FGFR4
Peptide Sequence
VLLAVSEEYLDLR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
746
Peptide End
758
CPTAC ID
CPTAC-3179
Peptide Molecular Mass
1,518.8294
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

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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
y9 (1+) 6.8 4.3 11.6 11.3 10.6 16.5 13.2 11.4 20.2 15 15 15
y8 (1+) 7.3 3.8 10.7 10.5 10 15.3 12.8 10.7 18.7 15 15 15
y10 (1+) 7.7 4 11.4 11.7 10.4 16 14 11.1 19.6 15 15 15
sum 7.1 3.9 11.1 10.9 10.2 15.8 13 10.9 19.3 15 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-3178 Collapse assay details

Data source: Panorama

Official Gene Symbol
FGFR4
Peptide Sequence
YNYLLDVLER
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
235
Peptide End
244
CPTAC ID
CPTAC-3178
Peptide Molecular Mass
1,296.6714
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

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
y6 (1+) 6.1 6.1 11 8.3 12.3 14.5 10.3 13.7 18.2 15 15 15
y4 (1+) 7.8 6.3 10.6 10.9 11.2 13.4 13.4 12.9 17.1 15 15 15
y8 (1+) 7.8 6.4 11.8 11.1 13.5 15.6 13.6 14.9 19.6 15 15 15
sum 6.4 6.2 11.1 9.4 12.3 14.5 11.4 13.8 18.3 15 15 15

Additional Resources and Comments

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