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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.

TOPBP1

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
TOPBP1 KIAA0259
Sequence Length (AA) Molecular Weight (Da)
1522 170679
Protein Name
DNA topoisomerase 2-binding protein 1
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MSRNDKEPFF VKFLKSSDNS KCFFKALESI KEFQSEEYLQ IITEEEALKI
60 70 80 90 100
KENDRSLYIC DPFSGVVFDH LKKLGCRIVG PQVVIFCMHH QRCVPRAEHP
110 120 130 140 150
VYNMVMSDVT ISCTSLEKEK REEVHKYVQM MGGRVYRDLN VSVTHLIAGE
160 170 180 190 200
VGSKKYLVAA NLKKPILLPS WIKTLWEKSQ EKKITRYTDI NMEDFKCPIF
210 220 230 240 250
LGCIICVTGL CGLDRKEVQQ LTVKHGGQYM GQLKMNECTH LIVQEPKGQK
260 270 280 290 300
YECAKRWNVH CVTTQWFFDS IEKGFCQDES IYKTEPRPEA KTMPNSSTPT
310 320 330 340 350
SQINTIDSRT LSDVSNISNI NASCVSESIC NSLNSKLEPT LENLENLDVS
360 370 380 390 400
AFQAPEDLLD GCRIYLCGFS GRKLDKLRRL INSGGGVRFN QLNEDVTHVI
410 420 430 440 450
VGDYDDELKQ FWNKSAHRPH VVGAKWLLEC FSKGYMLSEE PYIHANYQPV
460 470 480 490 500
EIPVSHKPES KAALLKKKNS SFSKKDFAPS EKHEQADEDL LSQYENGSST
510 520 530 540 550
VVEAKTSEAR PFNDSTHAEP LNDSTHISLQ EENQSSVSHC VPDVSTITEE
560 570 580 590 600
GLFSQKSFLV LGFSNENESN IANIIKENAG KIMSLLSRTV ADYAVVPLLG
610 620 630 640 650
CEVEATVGEV VTNTWLVTCI DYQTLFDPKS NPLFTPVPVM TGMTPLEDCV
660 670 680 690 700
ISFSQCAGAE KESLTFLANL LGASVQEYFV RKSNAKKGMF ASTHLILKER
710 720 730 740 750
GGSKYEAAKK WNLPAVTIAW LLETARTGKR ADESHFLIEN STKEERSLET
760 770 780 790 800
EITNGINLNS DTAEHPGTRL QTHRKTVVTP LDMNRFQSKA FRAVVSQHAR
810 820 830 840 850
QVAASPAVGQ PLQKEPSLHL DTPSKFLSKD KLFKPSFDVK DALAALETPG
860 870 880 890 900
RPSQQKRKPS TPLSEVIVKN LQLALANSSR NAVALSASPQ LKEAQSEKEE
910 920 930 940 950
APKPLHKVVV CVSKKLSKKQ SELNGIAASL GADYRWSFDE TVTHFIYQGR
960 970 980 990 1000
PNDTNREYKS VKERGVHIVS EHWLLDCAQE CKHLPESLYP HTYNPKMSLD
1010 1020 1030 1040 1050
ISAVQDGRLC NSRLLSAVSS TKDDEPDPLI LEENDVDNMA TNNKESAPSN
1060 1070 1080 1090 1100
GSGKNDSKGV LTQTLEMREN FQKQLQEIMS ATSIVKPQGQ RTSLSRSGCN
1110 1120 1130 1140 1150
SASSTPDSTR SARSGRSRVL EALRQSRQTV PDVNTEPSQN EQIIWDDPTA
1160 1170 1180 1190 1200
REERARLASN LQWPSCPTQY SELQVDIQNL EDSPFQKPLH DSEIAKQAVC
1210 1220 1230 1240 1250
DPGNIRVTEA PKHPISEELE TPIKDSHLIP TPQAPSIAFP LANPPVAPHP
1260 1270 1280 1290 1300
REKIITIEET HEELKKQYIF QLSSLNPQER IDYCHLIEKL GGLVIEKQCF
1310 1320 1330 1340 1350
DPTCTHIVVG HPLRNEKYLA SVAAGKWVLH RSYLEACRTA GHFVQEEDYE
1360 1370 1380 1390 1400
WGSSSILDVL TGINVQQRRL ALAAMRWRKK IQQRQESGIV EGAFSGWKVI
1410 1420 1430 1440 1450
LHVDQSREAG FKRLLQSGGA KVLPGHSVPL FKEATHLFSD LNKLKPDDSG
1460 1470 1480 1490 1500
VNIAEAAAQN VYCLRTEYIA DYLMQESPPH VENYCLPEAI SFIQNNKELG
1510 1520 1522
TGLSQKRKAP TEKNKIKRPR VH

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-3258 Collapse assay details

Data source: Panorama

Official Gene Symbol
TOPBP1
Peptide Sequence
GVLTQTLEMR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1059
Peptide End
1068
CPTAC ID
CPTAC-3258
Peptide Molecular Mass
1,146.6067
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
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

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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
y6 (1+) 41.3 23.2 18.3 52.6 22.2 18.7 66.9 32.1 26.2 15 15 15
y8 (1+) 20.1 43.5 18.3 60.6 32.7 29.3 63.8 54.4 34.5 15 15 15
y7 (1+) 64.3 10.3 16.5 84.4 12.4 17.6 106.1 16.1 24.1 15 15 15
sum 30.6 13.1 11.9 63.5 11.1 15 70.5 17.2 19.1 15 15 15

Additional Resources and Comments

Resources
Download SOPs
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Comments

Assay Details for CPTAC-3290 Collapse assay details

Data source: Panorama

Official Gene Symbol
TOPBP1
Peptide Modified Sequence
GVLT[+80.0]QTLEMR
Modification Type
Phospho (ST)
Protein - Site of Modification
1062
Peptide - Site of Modification
4
Peptide Start
1059
Peptide End
1068
CPTAC ID
CPTAC-3290
Peptide Molecular Mass
1,226.5730
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
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
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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
y5 (1+) 28 33.1 25.3 70.2 57 41.5 75.6 65.9 48.6 15 15 15
y7-98 (1+) 17.7 29 29.2 36.4 52.1 39.7 40.5 59.6 49.3 15 15 15
y6 (1+) 27.7 25.3 21.7 37.2 39.5 31.6 46.4 46.9 38.3 15 15 15
y7 (1+) 22.2 32.3 24.6 34.1 48.8 36.6 40.7 58.5 44.1 15 15 15
y8 (1+) 30.2 34.6 30.5 49.7 55.5 38.1 58.2 65.4 48.8 15 15 15
y8-98 (1+) 32 27.4 30.2 28.6 44.1 38.1 42.9 51.9 48.6 15 15 15
sum 14.1 22.6 22.2 42.2 47.5 36.7 44.5 52.6 42.9 15 15 15

Additional Resources and Comments

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

Assay Details for CPTAC-950 Collapse assay details

Data source: Panorama

Official Gene Symbol
TOPBP1
Peptide Modified Sequence
NAVALSAS[+80.0]PQLK
Modification Type
Phospho (ST)
Protein - Site of Modification
888
Peptide - Site of Modification
8
Peptide Start
881
Peptide End
892
CPTAC ID
CPTAC-950
Peptide Molecular Mass
1,277.6381
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
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

Chromatograms

Data source: Panorama

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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
y4 (1+) 15.9 10.4 7.9 30.1 10.8 10.7 34 15 13.3 15 24 15
y7 (1+) 20.8 9 9.4 17.5 9 11.6 27.2 12.7 14.9 15 24 15
y9 (1+) 20.7 6.4 11.9 25.6 7.6 12.2 32.9 9.9 17 15 24 15
sum 16 6.5 9.3 21.5 7.3 10.1 26.8 9.8 13.7 15 24 15

Additional Resources and Comments

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

Assay Details for CPTAC-3291 Collapse assay details

Data source: Panorama

Official Gene Symbol
TOPBP1
Peptide Sequence
QTVPDVNTEPSQNEQIIWDDPTAR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1128
Peptide End
1151
CPTAC ID
CPTAC-3291
Peptide Molecular Mass
2,752.2940
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM
Enrichment Method
IMAC
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
y5 (1+) 86.4 50.6 30.8 138.1 76.1 38.6 162.9 91.4 49.4 15 15 15
y4 (1+) 54.9 45.5 36.5 117.7 60.2 43.5 129.9 75.5 56.8 15 15 15
y15 (2+) 32.9 31.3 38.5 86.7 53.1 39.5 92.7 61.6 55.2 15 15 15
y8 (1+) 33.1 39.5 29.6 61.3 50.3 38.6 69.7 64 48.6 15 15 15
y7 (1+) 53.5 25 28.6 99 33.8 45.1 112.5 42 53.4 15 15 15
y6 (1+) 36.9 20.2 39 82.3 50.1 55.2 90.2 54 67.6 15 15 15
y9 (1+) 69.6 33.9 30.7 104.9 52.9 34.1 125.9 62.8 45.9 15 15 15
sum 19.8 18.9 24.4 70 29.2 37.3 72.7 34.8 44.6 15 15 15

Additional Resources and Comments

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