APEX1, CPTAC-24 - CPTAC Assay Portal | Office of Cancer Clinical Proteomics Research

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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

Official Gene Symbol	Other Aliases
APEX1	APE, APE1, APEX, APX, HAP1, REF1

Sequence Length (AA)	Molecular Weight (Da)
318	35555

Protein Name
DNA-(apurinic or apyrimidinic site) lyase

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MPKRGKKGAV	AEDGDELRTE	PEAKKSKTAA	KKNDKEAAGE	GPALYEDPPD
60	70	80	90	100
QKTSPSGKPA	TLKICSWNVD	GLRAWIKKKG	LDWVKEEAPD	ILCLQETKCS
110	120	130	140	150
ENKLPAELQE	LPGLSHQYWS	APSDKEGYSG	VGLLSRQCPL	KVSYGIGDEE
160	170	180	190	200
HDQEGRVIVA	EFDSFVLVTA	YVPNAGRGLV	RLEYRQRWDE	AFRKFLKGLA
210	220	230	240	250
SRKPLVLCGD	LNVAHEEIDL	RNPKGNKKNA	GFTPQERQGF	GELLQAVPLA
260	270	280	290	300
DSFRHLYPNT	PYAYTFWTYM	MNARSKNVGW	RLDYFLLSHS	LLPALCDSKI
310	318
RSKALGSDHC	PITLYLAL

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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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

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Response Curves

Data source: Panorama

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Retrieving Data

Repeatability

Data source: Panorama

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	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

Resources

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View Peptide in Panorama

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