FGFR3, CPTAC-3180 - CPTAC Assay Portal | Office of Cancer Clinical Proteomics Research

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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.

Overview Data source: UniProt

Official Gene Symbol	Other Aliases
FGFR3	JTK4

Sequence Length (AA)	Molecular Weight (Da)
806	87710

Protein Name
Fibroblast growth factor receptor 3

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MGAPACALAL	CVAVAIVAGA	SSESLGTEQR	VVGRAAEVPG	PEPGQQEQLV
60	70	80	90	100
FGSGDAVELS	CPPPGGGPMG	PTVWVKDGTG	LVPSERVLVG	PQRLQVLNAS
110	120	130	140	150
HEDSGAYSCR	QRLTQRVLCH	FSVRVTDAPS	SGDDEDGEDE	AEDTGVDTGA
160	170	180	190	200
PYWTRPERMD	KKLLAVPAAN	TVRFRCPAAG	NPTPSISWLK	NGREFRGEHR
210	220	230	240	250
IGGIKLRHQQ	WSLVMESVVP	SDRGNYTCVV	ENKFGSIRQT	YTLDVLERSP
260	270	280	290	300
HRPILQAGLP	ANQTAVLGSD	VEFHCKVYSD	AQPHIQWLKH	VEVNGSKVGP
310	320	330	340	350
DGTPYVTVLK	TAGANTTDKE	LEVLSLHNVT	FEDAGEYTCL	AGNSIGFSHH
360	370	380	390	400
SAWLVVLPAE	EELVEADEAG	SVYAGILSYG	VGFFLFILVV	AAVTLCRLRS
410	420	430	440	450
PPKKGLGSPT	VHKISRFPLK	RQVSLESNAS	MSSNTPLVRI	ARLSSGEGPT
460	470	480	490	500
LANVSELELP	ADPKWELSRA	RLTLGKPLGE	GCFGQVVMAE	AIGIDKDRAA
510	520	530	540	550
KPVTVAVKML	KDDATDKDLS	DLVSEMEMMK	MIGKHKNIIN	LLGACTQGGP
560	570	580	590	600
LYVLVEYAAK	GNLREFLRAR	RPPGLDYSFD	TCKPPEEQLT	FKDLVSCAYQ
610	620	630	640	650
VARGMEYLAS	QKCIHRDLAA	RNVLVTEDNV	MKIADFGLAR	DVHNLDYYKK
660	670	680	690	700
TTNGRLPVKW	MAPEALFDRV	YTHQSDVWSF	GVLLWEIFTL	GGSPYPGIPV
710	720	730	740	750
EELFKLLKEG	HRMDKPANCT	HDLYMIMREC	WHAAPSQRPT	FKQLVEDLDR
760	770	780	790	800
VLTVTSTDEY	LDLSAPFEQY	SPGGQDTPSS	SSSGDDSVFA	HDLLPPAPPS
806
SGGSRT

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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Assay Details for CPTAC-3181 Collapse assay details

Data source: Panorama

Official Gene Symbol: FGFR3
Peptide Sequence: LLAVPAANTVR
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 163
Peptide End: 173

CPTAC ID: CPTAC-3181
Peptide Molecular Mass: 1,123.6713
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

Repeatability

Data source: Panorama

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	Average intra-assay CV (within day CV)			Average inter-assay CV (between day CV)			Total CV			n=
Fragment ion / Transition	Low	Med	High	Low	Med	High	Low	Med	High	Low	Med	High
y7 (1+)	8.9	5.8	4.3	12.1	6.3	5.1	15	8.6	6.7	15	15	15
b3 (1+)	6.8	5.9	5.6	11.7	6.1	5.8	13.5	8.5	8.1	15	15	15
y9 (1+)	7.7	6.1	4.2	14.5	6.8	5	16.4	9.1	6.5	15	15	15
sum	7.9	5.8	4.6	12	6.2	5.2	14.4	8.5	6.9	15	15	15

Additional Resources and Comments

Resources

Download SOPs

View Peptide in Panorama

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Comments

Assay Details for CPTAC-3180 Collapse assay details

Data source: Panorama

Official Gene Symbol: FGFR3
Peptide Sequence: LSSGEGPTLANVSELELPADPKWELSR
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 443
Peptide End: 469

CPTAC ID: CPTAC-3180
Peptide Molecular Mass: 2,894.4662
Species: Homo Sapiens
Assay Type: Direct PRM
Matrix: Tumor Digest
Submitting Laboratory: Washington University in St. Louis
Submitting Lab PI: Reid Townsend