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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.

PDGFRA

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PDGFRA PDGFR2, RHEPDGFRA
Sequence Length (AA) Molecular Weight (Da)
1089 122670
Protein Name
Platelet-derived growth factor receptor alpha
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MGTSHPAFLV LGCLLTGLSL ILCQLSLPSI LPNENEKVVQ LNSSFSLRCF
60 70 80 90 100
GESEVSWQYP MSEEESSDVE IRNEENNSGL FVTVLEVSSA SAAHTGLYTC
110 120 130 140 150
YYNHTQTEEN ELEGRHIYIY VPDPDVAFVP LGMTDYLVIV EDDDSAIIPC
160 170 180 190 200
RTTDPETPVT LHNSEGVVPA SYDSRQGFNG TFTVGPYICE ATVKGKKFQT
210 220 230 240 250
IPFNVYALKA TSELDLEMEA LKTVYKSGET IVVTCAVFNN EVVDLQWTYP
260 270 280 290 300
GEVKGKGITM LEEIKVPSIK LVYTLTVPEA TVKDSGDYEC AARQATREVK
310 320 330 340 350
EMKKVTISVH EKGFIEIKPT FSQLEAVNLH EVKHFVVEVR AYPPPRISWL
360 370 380 390 400
KNNLTLIENL TEITTDVEKI QEIRYRSKLK LIRAKEEDSG HYTIVAQNED
410 420 430 440 450
AVKSYTFELL TQVPSSILDL VDDHHGSTGG QTVRCTAEGT PLPDIEWMIC
460 470 480 490 500
KDIKKCNNET SWTILANNVS NIITEIHSRD RSTVEGRVTF AKVEETIAVR
510 520 530 540 550
CLAKNLLGAE NRELKLVAPT LRSELTVAAA VLVLLVIVII SLIVLVVIWK
560 570 580 590 600
QKPRYEIRWR VIESISPDGH EYIYVDPMQL PYDSRWEFPR DGLVLGRVLG
610 620 630 640 650
SGAFGKVVEG TAYGLSRSQP VMKVAVKMLK PTARSSEKQA LMSELKIMTH
660 670 680 690 700
LGPHLNIVNL LGACTKSGPI YIITEYCFYG DLVNYLHKNR DSFLSHHPEK
710 720 730 740 750
PKKELDIFGL NPADESTRSY VILSFENNGD YMDMKQADTT QYVPMLERKE
760 770 780 790 800
VSKYSDIQRS LYDRPASYKK KSMLDSEVKN LLSDDNSEGL TLLDLLSFTY
810 820 830 840 850
QVARGMEFLA SKNCVHRDLA ARNVLLAQGK IVKICDFGLA RDIMHDSNYV
860 870 880 890 900
SKGSTFLPVK WMAPESIFDN LYTTLSDVWS YGILLWEIFS LGGTPYPGMM
910 920 930 940 950
VDSTFYNKIK SGYRMAKPDH ATSEVYEIMV KCWNSEPEKR PSFYHLSEIV
960 970 980 990 1000
ENLLPGQYKK SYEKIHLDFL KSDHPAVARM RVDSDNAYIG VTYKNEEDKL
1010 1020 1030 1040 1050
KDWEGGLDEQ RLSADSGYII PLPDIDPVPE EEDLGKRNRH SSQTSEESAI
1060 1070 1080 1089
ETGSSSSTFI KREDETIEDI DMMDDIGIDS SDLVEDSFL

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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All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-1767 Collapse assay details

Data source: Panorama

Official Gene Symbol
PDGFRA
Peptide Modified Sequence
DIMHDSNY[+80.0]VSK
Modification Type
Phospho (Y)
Protein - Site of Modification
849
Peptide - Site of Modification
8
Peptide Start
842
Peptide End
852
CPTAC ID
CPTAC-1767
Peptide Molecular Mass
1,387.5479
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
b8 (1+) 7.5 7 10.9 9.9 8 10.1 12.4 10.6 14.9 15 15 15
b2 (1+) 7.6 6 8.7 9.7 5.1 8.8 12.3 7.9 12.4 15 15 15
y2 (1+) 6.9 6 7 9.5 5.4 7.4 11.7 8.1 10.2 15 15 15
y5 (1+) NA NA NA NA NA NA NA NA NA 0 0 0
y6 (1+) 4.4 5.6 9.6 8.4 5.1 8.6 9.5 7.6 12.9 15 15 15
y7 (1+) 7.2 7.4 10.3 9.7 6.4 9.4 12.1 9.8 13.9 15 15 15
y8 (1+) 5 7.7 13 9.1 7.2 12.3 10.4 10.5 17.9 15 15 15
b6 (1+) NA NA NA NA NA NA NA NA NA 0 0 0
sum 5.9 6.5 9.4 8.9 5.8 8.9 10.7 8.7 12.9 15 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-3116 Collapse assay details

Data source: Panorama

Official Gene Symbol
PDGFRA
Peptide Sequence
LVYTLTVPEATVK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
271
Peptide End
283
CPTAC ID
CPTAC-3116
Peptide Molecular Mass
1,432.8177
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 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

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Response Curves

Data source: Panorama

view larger image
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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+) 5.7 5 3.7 10.1 6.2 4.8 11.6 8 6.1 15 15 15
y7 (1+) 5.9 4.2 4.3 10.1 6.3 5.1 11.7 7.6 6.7 15 15 15
y8 (1+) 4.9 5.8 3.6 11.7 6.8 4.2 12.7 8.9 5.5 15 15 15
sum 5.1 5 3.7 10.4 6.3 4.5 11.6 8 5.8 15 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-3115 Collapse assay details

Data source: Panorama

Official Gene Symbol
PDGFRA
Peptide Sequence
NVLLAQGK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
823
Peptide End
830
CPTAC ID
CPTAC-3115
Peptide Molecular Mass
841.5022
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 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
y5 (1+) 4.4 10.8 5.2 5.1 12.9 4.4 6.7 16.8 6.8 15 15 15
y4 (1+) 5.2 11.3 3.2 5.7 12.1 3.7 7.7 16.6 4.9 15 15 15
y6 (1+) 3.2 11.7 3.2 2.9 13.1 3.5 4.3 17.6 4.7 15 15 15
sum 3.5 11.2 3.5 3.5 12.5 3.3 4.9 16.8 4.8 15 15 15

Additional Resources and Comments

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