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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.

MSH6

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Available Assays

Overview Data source: UniProt

Official Gene Symbol Other Aliases
MSH6 GTBP
Sequence Length (AA) Molecular Weight (Da)
1360 152786
Protein Name
DNA mismatch repair protein Msh6
Sources
UniProt
PhosphoSitePlus ®
GeneCards 		Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MSRQSTLYSF FPKSPALSDA NKASARASRE GGRAAAAPGA SPSPGGDAAW
60 70 80 90 100
SEAGPGPRPL ARSASPPKAK NLNGGLRRSV APAAPTSCDF SPGDLVWAKM
110 120 130 140 150
EGYPWWPCLV YNHPFDGTFI REKGKSVRVH VQFFDDSPTR GWVSKRLLKP
160 170 180 190 200
YTGSKSKEAQ KGGHFYSAKP EILRAMQRAD EALNKDKIKR LELAVCDEPS
210 220 230 240 250
EPEEEEEMEV GTTYVTDKSE EDNEIESEEE VQPKTQGSRR SSRQIKKRRV
260 270 280 290 300
ISDSESDIGG SDVEFKPDTK EEGSSDEISS GVGDSESEGL NSPVKVARKR
310 320 330 340 350
KRMVTGNGSL KRKSSRKETP SATKQATSIS SETKNTLRAF SAPQNSESQA
360 370 380 390 400
HVSGGGDDSS RPTVWYHETL EWLKEEKRRD EHRRRPDHPD FDASTLYVPE
410 420 430 440 450
DFLNSCTPGM RKWWQIKSQN FDLVICYKVG KFYELYHMDA LIGVSELGLV
460 470 480 490 500
FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA
510 520 530 540 550
HISKYDRVVR REICRIITKG TQTYSVLEGD PSENYSKYLL SLKEKEEDSS
560 570 580 590 600
GHTRAYGVCF VDTSLGKFFI GQFSDDRHCS RFRTLVAHYP PVQVLFEKGN
610 620 630 640 650
LSKETKTILK SSLSCSLQEG LIPGSQFWDA SKTLRTLLEE EYFREKLSDG
660 670 680 690 700
IGVMLPQVLK GMTSESDSIG LTPGEKSELA LSALGGCVFY LKKCLIDQEL
710 720 730 740 750
LSMANFEEYI PLDSDTVSTT RSGAIFTKAY QRMVLDAVTL NNLEIFLNGT
760 770 780 790 800
NGSTEGTLLE RVDTCHTPFG KRLLKQWLCA PLCNHYAIND RLDAIEDLMV
810 820 830 840 850
VPDKISEVVE LLKKLPDLER LLSKIHNVGS PLKSQNHPDS RAIMYEETTY
860 870 880 890 900
SKKKIIDFLS ALEGFKVMCK IIGIMEEVAD GFKSKILKQV ISLQTKNPEG
910 920 930 940 950
RFPDLTVELN RWDTAFDHEK ARKTGLITPK AGFDSDYDQA LADIRENEQS
960 970 980 990 1000
LLEYLEKQRN RIGCRTIVYW GIGRNRYQLE IPENFTTRNL PEEYELKSTK
1010 1020 1030 1040 1050
KGCKRYWTKT IEKKLANLIN AEERRDVSLK DCMRRLFYNF DKNYKDWQSA
1060 1070 1080 1090 1100
VECIAVLDVL LCLANYSRGG DGPMCRPVIL LPEDTPPFLE LKGSRHPCIT
1110 1120 1130 1140 1150
KTFFGDDFIP NDILIGCEEE EQENGKAYCV LVTGPNMGGK STLMRQAGLL
1160 1170 1180 1190 1200
AVMAQMGCYV PAEVCRLTPI DRVFTRLGAS DRIMSGESTF FVELSETASI
1210 1220 1230 1240 1250
LMHATAHSLV LVDELGRGTA TFDGTAIANA VVKELAETIK CRTLFSTHYH
1260 1270 1280 1290 1300
SLVEDYSQNV AVRLGHMACM VENECEDPSQ ETITFLYKFI KGACPKSYGF
1310 1320 1330 1340 1350
NAARLANLPE EVIQKGHRKA REFEKMNQSL RLFREVCLAS ERSTVDAEAV
1360
HKLLTLIKEL

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-6060 Collapse assay details

Data source: Panorama

Official Gene Symbol
MSH6
Peptide Sequence
LANLPEEVIQK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
1305
Peptide End
1315
CPTAC ID
CPTAC-6060
Peptide Molecular Mass
1,252.7027
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
b4 (1+) 15.9 8.1 9 20.4 8.5 11.5 25.9 11.7 14.6 15 15 15
b8 (1+) 28.6 14.3 18 30.7 11.5 22.3 42 18.4 28.7 15 15 15
y3 (1+) 10.9 16.2 11.3 13.8 12.5 13.6 17.6 20.5 17.7 15 15 15
y4 (1+) 31.8 9.8 10.2 30.2 10.7 11.2 43.9 14.5 15.1 15 15 15
y6 (1+) 20 10.8 9.5 18.6 12.3 14.6 27.3 16.4 17.4 15 15 15
y7 (1+) 17.8 11 4.8 18.7 9 8.3 25.8 14.2 9.6 15 15 15
y8 (1+) 31.9 13.7 9.5 52.7 13.4 28.1 61.6 19.2 29.7 15 15 15
sum 16.2 10 5.1 17.8 8.7 8.8 24.1 13.3 10.2 15 15 15

Additional Resources and Comments

Resources
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Assay Details for CPTAC-544 Collapse assay details

Data source: Panorama

Official Gene Symbol
MSH6
Peptide Modified Sequence
SVAPAAPTSC[+57.0]DFSPGDLVWAK
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
88
Peptide - Site of Modification
10
Peptide Start
79
Peptide End
99
CPTAC ID
CPTAC-544
Peptide Molecular Mass
2,175.0307
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

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view larger image
view larger image

Response Curves

Data source: Panorama

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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
y10 (1+) 32 31.4 52 32.5 33.3 45.3 45.6 45.8 69 15 25 15
y18 (2+) 15.4 13.9 14.1 18 15.7 20.3 23.7 21 24.7 15 25 15
y15 (2+) 12.2 14.5 22.5 13 20.7 22.2 17.8 25.3 31.6 15 25 15
sum 9.8 11.7 15.7 13.9 15.4 19.7 17 19.3 25.2 15 25 15

Additional Resources and Comments

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