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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.

BRCA1

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
BRCA1 RNF53
Sequence Length (AA) Molecular Weight (Da)
1863 207721
Protein Name
Breast cancer type 1 susceptibility protein
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MDLSALRVEE VQNVINAMQK ILECPICLEL IKEPVSTKCD HIFCKFCMLK
60 70 80 90 100
LLNQKKGPSQ CPLCKNDITK RSLQESTRFS QLVEELLKII CAFQLDTGLE
110 120 130 140 150
YANSYNFAKK ENNSPEHLKD EVSIIQSMGY RNRAKRLLQS EPENPSLQET
160 170 180 190 200
SLSVQLSNLG TVRTLRTKQR IQPQKTSVYI ELGSDSSEDT VNKATYCSVG
210 220 230 240 250
DQELLQITPQ GTRDEISLDS AKKAACEFSE TDVTNTEHHQ PSNNDLNTTE
260 270 280 290 300
KRAAERHPEK YQGSSVSNLH VEPCGTNTHA SSLQHENSSL LLTKDRMNVE
310 320 330 340 350
KAEFCNKSKQ PGLARSQHNR WAGSKETCND RRTPSTEKKV DLNADPLCER
360 370 380 390 400
KEWNKQKLPC SENPRDTEDV PWITLNSSIQ KVNEWFSRSD ELLGSDDSHD
410 420 430 440 450
GESESNAKVA DVLDVLNEVD EYSGSSEKID LLASDPHEAL ICKSERVHSK
460 470 480 490 500
SVESNIEDKI FGKTYRKKAS LPNLSHVTEN LIIGAFVTEP QIIQERPLTN
510 520 530 540 550
KLKRKRRPTS GLHPEDFIKK ADLAVQKTPE MINQGTNQTE QNGQVMNITN
560 570 580 590 600
SGHENKTKGD SIQNEKNPNP IESLEKESAF KTKAEPISSS ISNMELELNI
610 620 630 640 650
HNSKAPKKNR LRRKSSTRHI HALELVVSRN LSPPNCTELQ IDSCSSSEEI
660 670 680 690 700
KKKKYNQMPV RHSRNLQLME GKEPATGAKK SNKPNEQTSK RHDSDTFPEL
710 720 730 740 750
KLTNAPGSFT KCSNTSELKE FVNPSLPREE KEEKLETVKV SNNAEDPKDL
760 770 780 790 800
MLSGERVLQT ERSVESSSIS LVPGTDYGTQ ESISLLEVST LGKAKTEPNK
810 820 830 840 850
CVSQCAAFEN PKGLIHGCSK DNRNDTEGFK YPLGHEVNHS RETSIEMEES
860 870 880 890 900
ELDAQYLQNT FKVSKRQSFA PFSNPGNAEE ECATFSAHSG SLKKQSPKVT
910 920 930 940 950
FECEQKEENQ GKNESNIKPV QTVNITAGFP VVGQKDKPVD NAKCSIKGGS
960 970 980 990 1000
RFCLSSQFRG NETGLITPNK HGLLQNPYRI PPLFPIKSFV KTKCKKNLLE
1010 1020 1030 1040 1050
ENFEEHSMSP EREMGNENIP STVSTISRNN IRENVFKEAS SSNINEVGSS
1060 1070 1080 1090 1100
TNEVGSSINE IGSSDENIQA ELGRNRGPKL NAMLRLGVLQ PEVYKQSLPG
1110 1120 1130 1140 1150
SNCKHPEIKK QEYEEVVQTV NTDFSPYLIS DNLEQPMGSS HASQVCSETP
1160 1170 1180 1190 1200
DDLLDDGEIK EDTSFAENDI KESSAVFSKS VQKGELSRSP SPFTHTHLAQ
1210 1220 1230 1240 1250
GYRRGAKKLE SSEENLSSED EELPCFQHLL FGKVNNIPSQ STRHSTVATE
1260 1270 1280 1290 1300
CLSKNTEENL LSLKNSLNDC SNQVILAKAS QEHHLSEETK CSASLFSSQC
1310 1320 1330 1340 1350
SELEDLTANT NTQDPFLIGS SKQMRHQSES QGVGLSDKEL VSDDEERGTG
1360 1370 1380 1390 1400
LEENNQEEQS MDSNLGEAAS GCESETSVSE DCSGLSSQSD ILTTQQRDTM
1410 1420 1430 1440 1450
QHNLIKLQQE MAELEAVLEQ HGSQPSNSYP SIISDSSALE DLRNPEQSTS
1460 1470 1480 1490 1500
EKAVLTSQKS SEYPISQNPE GLSADKFEVS ADSSTSKNKE PGVERSSPSK
1510 1520 1530 1540 1550
CPSLDDRWYM HSCSGSLQNR NYPSQEELIK VVDVEEQQLE ESGPHDLTET
1560 1570 1580 1590 1600
SYLPRQDLEG TPYLESGISL FSDDPESDPS EDRAPESARV GNIPSSTSAL
1610 1620 1630 1640 1650
KVPQLKVAES AQSPAAAHTT DTAGYNAMEE SVSREKPELT ASTERVNKRM
1660 1670 1680 1690 1700
SMVVSGLTPE EFMLVYKFAR KHHITLTNLI TEETTHVVMK TDAEFVCERT
1710 1720 1730 1740 1750
LKYFLGIAGG KWVVSYFWVT QSIKERKMLN EHDFEVRGDV VNGRNHQGPK
1760 1770 1780 1790 1800
RARESQDRKI FRGLEICCYG PFTNMPTDQL EWMVQLCGAS VVKELSSFTL
1810 1820 1830 1840 1850
GTGVHPIVVV QPDAWTEDNG FHAIGQMCEA PVVTREWVLD SVALYQCQEL
1860 1863
DTYLIPQIPH SHY

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-916 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRCA1
Peptide Modified Sequence
NYPS[+80.0]QEELIK
Modification Type
Phospho (ST)
Protein - Site of Modification
1524
Peptide - Site of Modification
4
Peptide Start
1521
Peptide End
1530
CPTAC ID
CPTAC-916
Peptide Molecular Mass
1,299.5748
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich U, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized metal affinity chromatography coupled to multiple reaction monitoring enables reproducible quantification of phospho-signaling. Molecular and Cellular Proteomics. mcp.O115.054940

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTrap 5500 (Sciex)
Internal Standard
Peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
nanoLC-2D (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
75 µm x 15cm
Flow Rate
300 nL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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
y8 (2+) 21.8 7.9 8 18.7 8.4 8.9 28.7 11.5 12 15 24 15
y8-98 (1+) 20.3 6.1 8.4 14.7 8.6 9.6 25.1 10.5 12.8 15 24 15
y8 (1+) 25 10.3 11.1 20.8 11.4 11.3 32.5 15.4 15.8 15 24 15
sum 20.2 6.3 6.7 16.2 7.7 6.6 25.9 9.9 9.4 15 24 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-3218 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRCA1
Peptide Sequence
NYPSQEELIK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1521
Peptide End
1530
CPTAC ID
CPTAC-3218
Peptide Molecular Mass
1,219.6085
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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+) 12.1 5.1 6.8 15.5 5.3 10.4 19.7 7.4 12.4 15 15 15
y7 (1+) 17.3 8.8 11.8 24.2 16.6 8.9 29.7 18.8 14.8 15 15 15
y8 (2+) 11.2 10.1 9 10.4 13.4 11.8 15.3 16.8 14.8 15 15 15
sum 9.8 4.1 5.3 10.3 7.7 6.6 14.2 8.7 8.5 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
View Protein in Panorama
View in CPTC Antibody Portal
Comments

Assay Details for CPTAC-3219 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRCA1
Peptide Modified Sequence
NYPS[+80.0]QEELIK
Modification Type
Phospho (ST)
Protein - Site of Modification
1524
Peptide - Site of Modification
4
Peptide Start
1521
Peptide End
1530
CPTAC ID
CPTAC-3219
Peptide Molecular Mass
1,299.5748
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
cell lysate
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. Radiat Res. 2018 Feb 23. doi: 10.1667/RR14963.1. [Epub ahead of print]

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
6500 QTRAP (Sciex)
Internal Standard
synthetic peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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
y8 (1+) 17.1 6.1 6.9 41.2 9 7.7 44.6 10.9 10.3 15 15 15
y8-98 (1+) 16.8 6.4 5.5 31 7.1 5.4 35.3 9.6 7.7 15 15 15
y7 (1+) 28.8 10.2 13.8 52.7 13.5 17.9 60.1 16.9 22.6 15 15 15
y8 (2+) 13.4 4 4.4 37.3 7.5 4.7 39.6 8.5 6.4 15 15 15
sum 7.8 3.5 3.7 35.7 6.7 4.7 36.5 7.6 6 15 15 15

Additional Resources and Comments

Resources
Download SOPs
View Peptide in Panorama
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Assay Details for CPTAC-2611 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRCA1
Peptide Sequence
SVESNIEDK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
450
Peptide End
459
CPTAC ID
CPTAC-2611
Peptide Molecular Mass
1,019.4771
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tumor tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TSQ Vantage
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Accela 1250 Quaternary Low Pump
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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
y7 (1+) 7 3.6 3.8 5.3 7.3 4.7 8.8 8.1 6 15 15 15
y6 (1+) 26.2 4.6 4.6 18.9 8.8 6.6 32.3 9.9 8 15 15 15
y5 (1+) 66.9 16.5 11.4 65.7 16.7 11.1 93.8 23.5 15.9 15 15 15
sum 8.6 3.5 3.6 5 7.3 4.3 9.9 8.1 5.6 15 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-2610 Collapse assay details

Data source: Panorama

Official Gene Symbol
BRCA1
Peptide Sequence
TSVYIELGSDSSEDTVNK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
175
Peptide End
193
CPTAC ID
CPTAC-2610
Peptide Molecular Mass
1,942.9007
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
Human ovarian tumor tissue digest
Submitting Laboratory
Johns Hopkins University
Submitting Lab PI
Daniel Chan, Hui Zhang, Zhen Zhang

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
TSQ Vantage
Internal Standard
Stable isotope-labeled peptides
Peptide Standard Purity
Crude (~60%)
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Accela 1250 Quaternary Low Pump
Column Packing
C18, 3 µm, 300 Å
Column Dimensions
1.0 mm I.D. x 15 cm
Flow Rate
50 µL/min

Assay Multiplexing Expand assay panel

Johns Hopkins University-I

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
y11 (1+) 17.1 15.6 12.2 15.7 20.1 15.5 23.2 25.4 19.7 15 15 15
y10 (1+) 35.2 21 16.3 33.2 25.6 17.6 48.4 33.1 24 15 15 15
y9 (1+) 38.8 21.6 20.4 50.4 30.2 18.1 63.6 37.1 27.3 15 15 15
sum 11.6 14.8 11 12.3 21 13 16.9 25.7 17 15 15 15

Additional Resources and Comments

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