MSH6, CPTAC-544 - 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

CPTAC-6060: View additional LANLPEEVIQK data

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-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

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 | | 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

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

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 | | 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