APEX1, CPTAC-23 - 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.

Overview Data source: UniProt

Protein Sequence hover to view complete sequence

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-23 Collapse assay details

Data source: Panorama

Official Gene Symbol

APEX1

Peptide Sequence

EGYSGVGLLSR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

126

Peptide End

136

CPTAC ID

CPTAC-23

Peptide Molecular Mass

1,136.5826

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

cell line lysate pool

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich

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

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 | | y8 (1+) | 31.4 | 6.6 | 8.7 | 27.5 | 16.5 | 14.7 | 41.7 | 17.8 | 17.1 | 15 | 25 | 15 | | y7 (1+) | 18.9 | 6.9 | 9.6 | 30.3 | 16.8 | 11.7 | 35.7 | 18.2 | 15.1 | 15 | 25 | 15 | | y6 (1+) | 30 | 14.2 | 10.3 | 35.8 | 20.4 | 19.2 | 46.7 | 24.9 | 21.8 | 15 | 25 | 15 | | sum | 19.1 | 5.2 | 7.1 | 26.3 | 15.5 | 11.5 | 32.5 | 16.3 | 13.5 | 15 | 25 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-24 Collapse assay details

Data source: Panorama

Official Gene Symbol

APEX1

Peptide Sequence

VSYGIGDEEHDQEGR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

142

Peptide End

156

CPTAC ID

CPTAC-24

Peptide Molecular Mass

1,689.7231

Species

Homo sapiens (Human)

Assay Type

Direct MRM

Matrix

cell line lysate pool

Submitting Laboratory

Fred Hutchinson Cancer Research Center

Submitting Lab PI

Amanda Paulovich

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

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 | | y13 (2+) | 10.8 | 7.8 | 2.2 | 17 | 11.3 | 3.9 | 20.1 | 13.7 | 4.5 | 15 | 25 | 15 | | y12 (2+) | 10 | 15.2 | 6.3 | 23.4 | 19 | 6.4 | 25.4 | 24.3 | 9 | 15 | 25 | 15 | | y10 (2+) | 14.3 | 7.1 | 4.9 | 11.6 | 8.3 | 8.2 | 18.4 | 10.9 | 9.6 | 15 | 25 | 15 | | sum | 9 | 9.4 | 3.2 | 23.1 | 10.5 | 3.4 | 24.8 | 14.1 | 4.7 | 15 | 25 | 15 |

Additional Resources and Comments