PARP1, CPTAC-556 - CPTAC Assay Portal (original) (raw)
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.
Protein Sequence hover to view complete sequence
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MAESSDKLYR | VEYAKSGRAS | CKKCSESIPK | DSLRMAIMVQ | SPMFDGKVPH |
| 60 | 70 | 80 | 90 | 100 |
| WYHFSCFWKV | GHSIRHPDVE | VDGFSELRWD | DQQKVKKTAE | AGGVTGKGQD |
| 110 | 120 | 130 | 140 | 150 |
| GIGSKAEKTL | GDFAAEYAKS | NRSTCKGCME | KIEKGQVRLS | KKMVDPEKPQ |
| 160 | 170 | 180 | 190 | 200 |
| LGMIDRWYHP | GCFVKNREEL | GFRPEYSASQ | LKGFSLLATE | DKEALKKQLP |
| 210 | 220 | 230 | 240 | 250 |
| GVKSEGKRKG | DEVDGVDEVA | KKKSKKEKDK | DSKLEKALKA | QNDLIWNIKD |
| 260 | 270 | 280 | 290 | 300 |
| ELKKVCSTND | LKELLIFNKQ | QVPSGESAIL | DRVADGMVFG | ALLPCEECSG |
| 310 | 320 | 330 | 340 | 350 |
| QLVFKSDAYY | CTGDVTAWTK | CMVKTQTPNR | KEWVTPKEFR | EISYLKKLKV |
| 360 | 370 | 380 | 390 | 400 |
| KKQDRIFPPE | TSASVAATPP | PSTASAPAAV | NSSASADKPL | SNMKILTLGK |
| 410 | 420 | 430 | 440 | 450 |
| LSRNKDEVKA | MIEKLGGKLT | GTANKASLCI | STKKEVEKMN | KKMEEVKEAN |
| 460 | 470 | 480 | 490 | 500 |
| IRVVSEDFLQ | DVSASTKSLQ | ELFLAHILSP | WGAEVKAEPV | EVVAPRGKSG |
| 510 | 520 | 530 | 540 | 550 |
| AALSKKSKGQ | VKEEGINKSE | KRMKLTLKGG | AAVDPDSGLE | HSAHVLEKGG |
| 560 | 570 | 580 | 590 | 600 |
| KVFSATLGLV | DIVKGTNSYY | KLQLLEDDKE | NRYWIFRSWG | RVGTVIGSNK |
| 610 | 620 | 630 | 640 | 650 |
| LEQMPSKEDA | IEHFMKLYEE | KTGNAWHSKN | FTKYPKKFYP | LEIDYGQDEE |
| 660 | 670 | 680 | 690 | 700 |
| AVKKLTVNPG | TKSKLPKPVQ | DLIKMIFDVE | SMKKAMVEYE | IDLQKMPLGK |
| 710 | 720 | 730 | 740 | 750 |
| LSKRQIQAAY | SILSEVQQAV | SQGSSDSQIL | DLSNRFYTLI | PHDFGMKKPP |
| 760 | 770 | 780 | 790 | 800 |
| LLNNADSVQA | KVEMLDNLLD | IEVAYSLLRG | GSDDSSKDPI | DVNYEKLKTD |
| 810 | 820 | 830 | 840 | 850 |
| IKVVDRDSEE | AEIIRKYVKN | THATTHNAYD | LEVIDIFKIE | REGECQRYKP |
| 860 | 870 | 880 | 890 | 900 |
| FKQLHNRRLL | WHGSRTTNFA | GILSQGLRIA | PPEAPVTGYM | FGKGIYFADM |
| 910 | 920 | 930 | 940 | 950 |
| VSKSANYCHT | SQGDPIGLIL | LGEVALGNMY | ELKHASHISK | LPKGKHSVKG |
| 960 | 970 | 980 | 990 | 1000 |
| LGKTTPDPSA | NISLDGVDVP | LGTGISSGVN | DTSLLYNEYI | VYDIAQVNLK |
| 1010 | 1014 | |||
| YLLKLKFNFK | TSLW |
Data source: UniProt
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-3240 Collapse assay details
Data source: Panorama
Official Gene Symbol
PARP1
Peptide Sequence
EELGFRPEYSASQLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
168
Peptide End
182
CPTAC ID
CPTAC-3240
Peptide Molecular Mass
1,752.8683
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
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y11 (2+) | 15 | 7.7 | 13.7 | 21.4 | 12.8 | 15.5 | 26.1 | 14.9 | 20.7 | 15 | 15 | 15 |
| y9 (1+) | 28.1 | 11.3 | 6.6 | 34.1 | 17.4 | 10.2 | 44.2 | 20.7 | 12.1 | 15 | 15 | 15 |
| y12 (2+) | 11.4 | 11.2 | 9.4 | 35.9 | 18.4 | 10.7 | 37.7 | 21.5 | 14.2 | 15 | 15 | 15 |
| y6 (1+) | 15.8 | 11.9 | 11.8 | 15.3 | 16.8 | 13.3 | 22 | 20.6 | 17.8 | 15 | 15 | 15 |
| y5 (1+) | 34.1 | 10.7 | 10.8 | 35.9 | 14.5 | 15.3 | 49.5 | 18 | 18.7 | 15 | 15 | 15 |
| sum | 10.6 | 8.1 | 8.3 | 22.5 | 13.3 | 10.5 | 24.9 | 15.6 | 13.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-3241 Collapse assay details
Data source: Panorama
Official Gene Symbol
PARP1
Peptide Modified Sequence
EELGFRPEYS[+80.0]ASQLK
Modification Type
Phospho (ST)
Protein - Site of Modification
177
Peptide - Site of Modification
10
Peptide Start
168
Peptide End
182
CPTAC ID
CPTAC-3241
Peptide Molecular Mass
1,832.8346
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
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y9-98 (2+) | 42.1 | 31.1 | 17.9 | 48.3 | 67.4 | 28.1 | 64.1 | 74.2 | 33.3 | 15 | 15 | 15 |
| y9-98 (1+) | 46.9 | 27.1 | 24.5 | 72.3 | 61.6 | 53.4 | 86.2 | 67.3 | 58.8 | 15 | 15 | 15 |
| y9 (2+) | 27.7 | 19.8 | 21.4 | 42.9 | 28.7 | 29.5 | 51.1 | 34.9 | 36.4 | 15 | 15 | 15 |
| y13 (2+) | 27.4 | 14.6 | 19.1 | 38.8 | 14.7 | 20.9 | 47.5 | 20.7 | 28.3 | 15 | 15 | 15 |
| sum | 21.8 | 11.6 | 14 | 22.6 | 16.2 | 17.6 | 31.4 | 19.9 | 22.5 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-6223 Collapse assay details
Data source: Panorama
Official Gene Symbol
PARP1
Peptide Sequence
EELGFRPEYSASQLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
7
Peptide Start
168
Peptide End
182
CPTAC ID
CPTAC-6223
Peptide Molecular Mass
1,752.8683
Species
Homo Sapiens
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
Frozen tissue
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
QTRAP 5500
Internal Standard
Extended heavy peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent
Column Packing
Reprosil C18, 3um
Column Dimensions
75µm x 15cm
Flow Rate
0.3 µL/min
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y6 (1+) | 6.6 | 3.1 | 3.1 | 10.3 | 10.6 | 6.7 | 12.2 | 11 | 7.4 | 15 | 15 | 15 |
| y5 (1+) | 4.2 | 4.2 | 2.6 | 11.6 | 5.8 | 6.3 | 12.3 | 7.2 | 6.8 | 15 | 15 | 15 |
| y11 (2+) | 6.3 | 4.5 | 2.4 | 13.1 | 6.4 | 4.8 | 14.5 | 7.8 | 5.4 | 15 | 15 | 15 |
| y12 (2+) | 5.6 | 3.2 | 3.5 | 15.5 | 6.2 | 4.7 | 16.5 | 7 | 5.9 | 15 | 15 | 15 |
| sum | 4.8 | 2.9 | 2.9 | 13.8 | 6.1 | 4.7 | 14.6 | 6.8 | 5.5 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-5899 Collapse assay details
Data source: Panorama
Official Gene Symbol
PARP1
Peptide Modified Sequence
MAIMVQS[+79.966331]PMFDGK
Modification Type
Phospho (ST)
Protein - Site of Modification
42
Peptide - Site of Modification
7
Peptide Start
35
Peptide End
47
CPTAC ID
CPTAC-5899
Peptide Molecular Mass
1,533.6431
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)
Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Cancers (Basel). 2021 Jul 30;13(15):3843. doi: 10.3390/cancers13153843. PMID: 34359745
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Sciex 5500 QTRAP
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent 425
Column Packing
Reprosil
Column Dimensions
75um x 15cm
Flow Rate
300 nL/min
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y6 (1+) | 48.6 | 24.5 | 11.2 | 74.6 | 26.3 | 18.8 | 89 | 35.9 | 21.9 | 15 | 27 | 15 |
| y4 (1+) | 48.8 | 41.3 | 16 | 61.8 | 44.5 | 13.2 | 78.7 | 60.7 | 20.7 | 15 | 27 | 15 |
| b4 (1+) | 54.4 | 31.9 | 19.5 | 57.4 | 39.1 | 20.3 | 79.1 | 50.5 | 28.1 | 15 | 27 | 15 |
| b5 (1+) | 41.3 | 28.3 | 11.6 | 37.9 | 30.5 | 25 | 56.1 | 41.6 | 27.6 | 15 | 27 | 15 |
| y10 (1+) | 73.3 | 20.4 | 13.4 | 71.8 | 24.4 | 20.1 | 102.6 | 31.8 | 24.2 | 15 | 27 | 15 |
| y9 (1+) | 66.3 | 26.6 | 18.8 | 85.4 | 29.8 | 19.5 | 108.1 | 39.9 | 27.1 | 15 | 27 | 15 |
| y7 (1+) | 71.7 | 35.5 | 9.9 | 65.2 | 37.3 | 22.2 | 96.9 | 51.5 | 24.3 | 15 | 27 | 15 |
| sum | 27.5 | 13.9 | 7.5 | 41.3 | 20 | 14.6 | 49.6 | 24.4 | 16.4 | 15 | 27 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-557 Collapse assay details
Data source: Panorama
Official Gene Symbol
PARP1
Peptide Sequence
TTNFAGILSQGLR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
866
Peptide End
878
CPTAC ID
CPTAC-557
Peptide Molecular Mass
1,376.7412
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
Publication
View Details (opens in a new window)
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y9 (1+) | 12.9 | 4.4 | 4.4 | 17.1 | 6.9 | 5.6 | 21.4 | 8.2 | 7.1 | 15 | 25 | 15 |
| y8 (1+) | 8.2 | 5.9 | 3.5 | 14.5 | 8.1 | 4.3 | 16.7 | 10 | 5.5 | 15 | 25 | 15 |
| y7 (1+) | 34.5 | 18.4 | 28.2 | 32.7 | 22.5 | 49.1 | 47.5 | 29.1 | 56.6 | 15 | 25 | 15 |
| sum | 8.3 | 5.2 | 3.2 | 12.8 | 6.8 | 4.9 | 15.3 | 8.6 | 5.9 | 15 | 25 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-556 Collapse assay details
Data source: Panorama
Official Gene Symbol
PARP1
Peptide Sequence
VVSEDFLQDVSASTK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
453
Peptide End
467
CPTAC ID
CPTAC-556
Peptide Molecular Mass
1,623.7992
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
Publication
View Details (opens in a new window)
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y11 (1+) | 26 | 10.4 | 7.4 | 25.5 | 14.9 | 10.9 | 36.4 | 18.2 | 13.2 | 15 | 25 | 15 |
| y9 (1+) | 15.9 | 7.1 | 6.9 | 20.7 | 7.8 | 10.2 | 26.1 | 10.5 | 12.3 | 15 | 25 | 15 |
| y8 (1+) | 38.1 | 9.2 | 3.8 | 36 | 10.8 | 7.3 | 52.4 | 14.2 | 8.2 | 15 | 25 | 15 |
| sum | 18.2 | 7.2 | 2.1 | 16.8 | 9.5 | 6.3 | 24.8 | 11.9 | 6.6 | 15 | 25 | 15 |