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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.

MDC1

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
MDC1 KIAA0170, NFBD1
Sequence Length (AA) Molecular Weight (Da)
2089 226666
Protein Name
Mediator of DNA damage checkpoint protein 1
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MEDTQAIDWD VEEEEETEQS SESLRCNVEP VGRLHIFSGA HGPEKDFPLH
60 70 80 90 100
LGKNVVGRMP DCSVALPFPS ISKQHAEIEI LAWDKAPILR DCGSLNGTQI
110 120 130 140 150
LRPPKVLSPG VSHRLRDQEL ILFADLLCQY HRLDVSLPFV SRGPLTVEET
160 170 180 190 200
PRVQGETQPQ RLLLAEDSEE EVDFLSERRM VKKSRTTSSS VIVPESDEEG
210 220 230 240 250
HSPVLGGLGP PFAFNLNSDT DVEEGQQPAT EEASSAARRG ATVEAKQSEA
260 270 280 290 300
EVVTEIQLEK DQPLVKERDN DTKVKRGAGN GVVPAGVILE RSQPPGEDSD
310 320 330 340 350
TDVDDDSRPP GRPAEVHLER AQPFGFIDSD TDAEEERIPA TPVVIPMKKR
360 370 380 390 400
KIFHGVGTRG PGAPGLAHLQ ESQAGSDTDV EEGKAPQAVP LEKSQASMVI
410 420 430 440 450
NSDTDDEEEV SAALTLAHLK ESQPAIWNRD AEEDMPQRVV LLQRSQTTTE
460 470 480 490 500
RDSDTDVEEE ELPVENREAV LKDHTKIRAL VRAHSEKDQP PFGDSDDSVE
510 520 530 540 550
ADKSSPGIHL ERSQASTTVD INTQVEKEVP PGSAIIHIKK HQVSVEGTNQ
560 570 580 590 600
TDVKAVGGPA KLLVVSLEEA WPLHGDCETD AEEGTSLTAS VVADVRKSQL
610 620 630 640 650
PAEGDAGAEW AAAVLKQERA HEVGAQGGPP VAQVEQDLPI SRENLTDLVV
660 670 680 690 700
DTDTLGESTQ PQREGAQVPT GREREQHVGG TKDSEDNYGD SEDLDLQATQ
710 720 730 740 750
CFLENQGLEA VQSMEDEPTQ AFMLTPPQEL GPSHCSFQTT GTLDEPWEVL
760 770 780 790 800
ATQPFCLRES EDSETQPFDT HLEAYGPCLS PPRAIPGDQH PESPVHTEPM
810 820 830 840 850
GIQGRGRQTV DKVMGIPKET AERVGPERGP LERETEKLLP ERQTDVTGEE
860 870 880 890 900
ELTKGKQDRE QKQLLARDTQ RQESDKNGES ASPERDRESL KVEIETSEEI
910 920 930 940 950
QEKQVQKQTL PSKAFEREVE RPVANRECDP AELEEKVPKV ILERDTQRGE
960 970 980 990 1000
PEGGSQDQKG QASSPTPEPG VGAGDLPGPT SAPVPSGSQS GGRGSPVSPR
1010 1020 1030 1040 1050
RHQKGLLNCK MPPAEKASRI RAAEKVSRGD QESPDACLPP TVPEAPAPPQ
1060 1070 1080 1090 1100
KPLNSQSQKH LAPPPLLSPL LPSIKPTVRK TRQDGSQEAP EAPLSSELEP
1110 1120 1130 1140 1150
FHPKPKIRTR KSSRMTPFPA TSAAPEPHPS TSTAQPVTPK PTSQATRSRT
1160 1170 1180 1190 1200
NRSSVKTPEP VVPTAPELQP STSTDQPVTS EPTSQVTRGR KSRSSVKTPE
1210 1220 1230 1240 1250
TVVPTALELQ PSTSTDRPVT SEPTSQATRG RKNRSSVKTP EPVVPTAPEL
1260 1270 1280 1290 1300
QPSTSTDQPV TSEPTYQATR GRKNRSSVKT PEPVVPTAPE LRPSTSTDRP
1310 1320 1330 1340 1350
VTPKPTSRTT RSRTNMSSVK TPETVVPTAP ELQISTSTDQ PVTPKPTSRT
1360 1370 1380 1390 1400
TRSRTNMSSV KNPESTVPIA PELPPSTSTE QPVTPEPTSR ATRGRKNRSS
1410 1420 1430 1440 1450
GKTPETLVPT APKLEPSTST DQPVTPEPTS QATRGRTNRS SVKTPETVVP
1460 1470 1480 1490 1500
TAPELQPSTS TDQPVTPEPT SQATRGRTDR SSVKTPETVV PTAPELQASA
1510 1520 1530 1540 1550
STDQPVTSEP TSRTTRGRKN RSSVKTPETV VPAAPELQPS TSTDQPVTPE
1560 1570 1580 1590 1600
PTSRATRGRT NRSSVKTPES IVPIAPELQP STSRNQLVTP EPTSRATRCR
1610 1620 1630 1640 1650
TNRSSVKTPE PVVPTAPEPH PTTSTDQPVT PKLTSRATRR KTNRSSVKTP
1660 1670 1680 1690 1700
KPVEPAASDL EPFTPTDQSV TPEAIAQGGQ SKTLRSSTVR AMPVPTTPEF
1710 1720 1730 1740 1750
QSPVTTDQPI SPEPITQPSC IKRQRAAGNP GSLAAPIDHK PCSAPLEPKS
1760 1770 1780 1790 1800
QASRNQRWGA VRAAESLTAI PEPASPQLLE TPIHASQIQK VEPAGRSRFT
1810 1820 1830 1840 1850
PELQPKASQS RKRSLATMDS PPHQKQPQRG EVSQKTVIIK EEEEDTAEKP
1860 1870 1880 1890 1900
GKEEDVVTPK PGKRKRDQAE EEPNRIPSRS LRRTKLNQES TAPKVLFTGV
1910 1920 1930 1940 1950
VDARGERAVL ALGGSLAGSA AEASHLVTDR IRRTVKFLCA LGRGIPILSL
1960 1970 1980 1990 2000
DWLHQSRKAG FFLPPDEYVV TDPEQEKNFG FSLQDALSRA RERRLLEGYE
2010 2020 2030 2040 2050
IYVTPGVQPP PPQMGEIISC CGGTYLPSMP RSYKPQRVVI TCPQDFPHCS
2060 2070 2080 2089
IPLRVGLPLL SPEFLLTGVL KQEAKPEAFV LSPLEMSST

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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to view detailed assay information below
All other points link out to UniProt


Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-931 Collapse assay details

Data source: Panorama

Official Gene Symbol
MDC1
Peptide Modified Sequence
AQPFGFIDS[+80.0]DTDAEEER
Modification Type
Phospho (ST)
Protein - Site of Modification
329
Peptide - Site of Modification
9
Peptide Start
321
Peptide End
337
CPTAC ID
CPTAC-931
Peptide Molecular Mass
2,005.7942
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
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 R
LC
nanoLC-2D (Eksigent)
Column Packing
ChromXP C18-CL, 3 µm, 120 Å
Column Dimensions
75 µm x 15cm
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

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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
y14 (2+) 34.2 29.8 23.1 35.8 32.9 22 49.5 44.4 31.9 15 23 15
y15 (2+) 33.4 13.3 18.4 29.2 19.7 21.4 44.4 23.8 28.2 15 23 15
y5 (1+) 67.5 44.9 55.4 55.7 38.9 71.6 87.5 59.4 90.5 15 23 15
sum 32.2 9.7 7.7 27.2 19 12.2 42.2 21.3 14.4 15 23 15

Additional Resources and Comments

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

Assay Details for CPTAC-3234 Collapse assay details

Data source: Panorama

Official Gene Symbol
MDC1
Peptide Sequence
AQPFGFIDSDTDAEEER
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
321
Peptide End
337
CPTAC ID
CPTAC-3234
Peptide Molecular Mass
1,925.8279
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
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 R
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/min

Chromatograms

Data source: Panorama

view larger image
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Response Curves

Data source: Panorama

view larger image
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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
y10 (1+) 22.3 9.3 12.2 52.4 16.8 13.1 56.9 19.2 17.9 15 15 15
y7 (1+) 26.6 19.9 18 52.9 18.5 19.8 59.2 27.2 26.8 15 15 15
y9 (1+) 18.4 19.7 19.9 39.3 19.8 31.4 43.4 27.9 37.2 15 15 15
sum 13.8 9.3 13.2 45.7 14 14.7 47.7 16.8 19.8 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-3235 Collapse assay details

Data source: Panorama

Official Gene Symbol
MDC1
Peptide Modified Sequence
AQPFGFIDS[+80.0]DTDAEEER
Modification Type
Phospho (ST)
Protein - Site of Modification
329
Peptide - Site of Modification
9
Peptide Start
321
Peptide End
337
CPTAC ID
CPTAC-3235
Peptide Molecular Mass
2,005.7942
Species
Homo sapiens (Human)
Assay Type
Enrichment ImmunoMRM
Enrichment Method
peptide immunoaffinity
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 R
LC
Ultra NanoLC 2D+ (Eksigent)
Column Packing
ReproSil-Pur C18-AQ 3um
Column Dimensions
100 x 0.075 mm
Flow Rate
300 uL/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
y9 (1+) 32.6 10.9 12.6 67.5 19.2 21.8 75 22.1 25.2 15 15 15
y5 (1+) 30.2 12.2 17.6 70.6 20.6 16.4 76.8 23.9 24.1 15 15 15
y14 (2+) 21.7 14.5 16.1 59.4 25.9 14.7 63.2 29.7 21.8 15 15 15
y15 (2+) 18.2 5.7 11 63.3 15.5 14.3 65.9 16.5 18 15 15 15
sum 15.6 5.4 8.8 62.7 16.3 13.5 64.6 17.2 16.1 15 15 15

Additional Resources and Comments

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