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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.

XRCC5

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
XRCC5 G22P2
Sequence Length (AA) Molecular Weight (Da)
732 82705
Protein Name
X-ray repair cross-complementing protein 5
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN
60 70 80 90 100
KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFDL LEDIESKIQP
110 120 130 140 150
GSQQADFLDA LIVSMDVIQH ETIGKKFEKR HIEIFTDLSS RFSKSQLDII
160 170 180 190 200
IHSLKKCDIS LQFFLPFSLG KEDGSGDRGD GPFRLGGHGP SFPLKGITEQ
210 220 230 240 250
QKEGLEIVKM VMISLEGEDG LDEIYSFSES LRKLCVFKKI ERHSIHWPCR
260 270 280 290 300
LTIGSNLSIR IAAYKSILQE RVKKTWTVVD AKTLKKEDIQ KETVYCLNDD
310 320 330 340 350
DETEVLKEDI IQGFRYGSDI VPFSKVDEEQ MKYKSEGKCF SVLGFCKSSQ
360 370 380 390 400
VQRRFFMGNQ VLKVFAARDD EAAAVALSSL IHALDDLDMV AIVRYAYDKR
410 420 430 440 450
ANPQVGVAFP HIKHNYECLV YVQLPFMEDL RQYMFSSLKN SKKYAPTEAQ
460 470 480 490 500
LNAVDALIDS MSLAKKDEKT DTLEDLFPTT KIPNPRFQRL FQCLLHRALH
510 520 530 540 550
PREPLPPIQQ HIWNMLNPPA EVTTKSQIPL SKIKTLFPLI EAKKKDQVTA
560 570 580 590 600
QEIFQDNHED GPTAKKLKTE QGGAHFSVSS LAEGSVTSVG SVNPAENFRV
610 620 630 640 650
LVKQKKASFE EASNQLINHI EQFLDTNETP YFMKSIDCIR AFREEAIKFS
660 670 680 690 700
EEQRFNNFLK ALQEKVEIKQ LNHFWEIVVQ DGITLITKEE ASGSSVTAEE
710 720 730 732
AKKFLAPKDK PSGDTAAVFE EGGDVDDLLD MI

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-6070 Collapse assay details

Data source: Panorama

Official Gene Symbol
XRCC5
Peptide Sequence
TLFPLIEAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
535
Peptide End
543
CPTAC ID
CPTAC-6070
Peptide Molecular Mass
1,030.6063
Species
Human
Assay Type
Enrichment MRM
Enrichment Method
N/A
Matrix
FFPE lung tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Lundeen RA, Voytovich U, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Chowdhury S, Vandermeer J, Smith SD, Gopal AK, Ramchurren N, Fling SP, Wang P, Paulovich AG. A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials. Front Oncol. 2023 May 2;13:1168710. doi: 10.3389/fonc.2023.1168710. PMID: 37205196; PMCID: PMC10185886.

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.075 mm
Flow Rate
0.3 µL/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
b3 (1+) 15.3 7.3 8 18.8 5.7 7.1 24.2 9.3 10.7 15 15 15
y3 (1+) 29.9 9.5 8.7 31.7 8.1 8.4 43.6 12.5 12.1 15 15 15
y4 (1+) 28.5 10.1 9 29.9 6.6 9 41.3 12.1 12.7 15 15 15
y5 (1+) 16.7 7.5 8.9 19.8 6.3 9.6 25.9 9.8 13.1 15 15 15
y6 (1+) 15.3 8.4 7.1 18.9 6.6 6.9 24.3 10.7 9.9 15 15 15
sum 15.5 8.2 7.2 18.5 6.2 7.1 24.1 10.3 10.1 15 15 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-606 Collapse assay details

Data source: Panorama

Official Gene Symbol
XRCC5
Peptide Sequence
LTIGSNLSIR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
251
Peptide End
260
CPTAC ID
CPTAC-606
Peptide Molecular Mass
1,072.6241
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 and 15N at C-terminus R
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

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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
y8 (1+) 9.4 11.7 8.1 15.2 22.3 16.4 17.9 25.2 18.3 15 25 15
y7 (1+) 11.7 8.9 6.7 17.6 17.6 16.2 21.1 19.7 17.5 15 25 15
y8 (2+) 28.5 15.8 17 26.5 25.2 23.5 38.9 29.7 29 15 25 15
sum 11.4 9.2 7.3 13.4 18.4 16.5 17.6 20.6 18 15 25 15

Additional Resources and Comments

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

Assay Details for CPTAC-607 Collapse assay details

Data source: Panorama

Official Gene Symbol
XRCC5
Peptide Sequence
TDTLEDLFPTTK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
470
Peptide End
481
CPTAC ID
CPTAC-607
Peptide Molecular Mass
1,379.6820
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

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
y8 (1+) 9.7 5.9 4.7 21.1 7.9 9.5 23.2 9.9 10.6 15 25 15
y7 (1+) 16.7 7.5 4.2 27.9 8.8 6.2 32.5 11.6 7.5 15 25 15
y6 (1+) 37.4 9.6 6.5 45.4 12.1 9.9 58.8 15.4 11.8 15 25 15
sum 15.7 5.8 3.9 22.9 7.3 6.5 27.8 9.3 7.6 15 25 15

Additional Resources and Comments

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