DSP, CPTAC-498 - 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-498: View additional YGDGIQLTR data

non-CPTAC-3703: View additional AITGFDDPFSGK 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-499 Collapse assay details

Data source: Panorama

Official Gene Symbol

DSP

Peptide Sequence

GFFDPNTEENLTYLQLK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

2414

Peptide End

2430

CPTAC ID

CPTAC-499

Peptide Molecular Mass

2,027.9840

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+) | 20.9 | 14.7 | 8.9 | 24.9 | 28.3 | 21.6 | 32.5 | 31.9 | 23.4 | 15 | 25 | 15 | | y6 (1+) | 12.4 | 11.8 | 7.3 | 20.2 | 24.8 | 17.5 | 23.7 | 27.5 | 19 | 15 | 25 | 15 | | y13 (2+) | 23.3 | 8.2 | 5.4 | 27 | 19.2 | 14.6 | 35.7 | 20.9 | 15.6 | 15 | 25 | 15 | | sum | 8.6 | 8.6 | 5.2 | 12.9 | 21.7 | 15.7 | 15.5 | 23.3 | 16.5 | 15 | 25 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-498 Collapse assay details

Data source: Panorama

Official Gene Symbol

DSP

Peptide Sequence

YGDGIQLTR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

95

Peptide End

103

CPTAC ID

CPTAC-498

Peptide Molecular Mass

1,021.5193

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

Additional Resources and Comments

Assay Details for non-CPTAC-3703 Collapse assay details

Data source: Panorama

Official Gene Symbol

Dsp

Peptide Sequence

AITGFDDPFSGK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

2104

Peptide End

2115

CPTAC ID

non-CPTAC-3703

Peptide Molecular Mass

1,253.5928

Species

Mus musculus (Mouse)

Assay Type

Direct MRM

Matrix

Plasma

Submitting Laboratory

UVic-Genome BC Proteomics Centre

Submitting Lab PI

Christoph Borchers

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

Agilent 6490/6495 QQQ

Internal Standard

synthetic peptide

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus K

LC

1290 LC (Agilent)

Column Packing

Zorbax Eclipse Plus C18, 1.8 µm

Column Dimensions

2.1 x 150 mm

Flow Rate

400 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 | | y10 (2+) | 10.9 | 3.6 | 2.2 | 12.2 | 6.2 | 8 | 16.4 | 7.2 | 8.3 | 15 | 15 | 15 | | y3 (1+) | 14.8 | 9.6 | 8.5 | 14 | 11.8 | 8.5 | 20.4 | 15.2 | 12 | 15 | 15 | 15 | | y7 (1+) | 16 | 6.5 | 4.4 | 23.3 | 6.6 | 7.7 | 28.3 | 9.3 | 8.9 | 15 | 15 | 15 | | y9 (1+) | 11.4 | 3.7 | 6.6 | 14.6 | 2.7 | 7.9 | 18.5 | 4.6 | 10.3 | 15 | 15 | 15 | | y10 (1+) | 7.7 | 5.2 | 4.3 | 10.2 | 6.1 | 7.2 | 12.8 | 8 | 8.4 | 15 | 15 | 15 | | sum | 6.5 | 2.4 | 1.7 | 8.2 | 4.9 | 6.5 | 10.5 | 5.5 | 6.7 | 15 | 15 | 15 |

Additional Resources and Comments