CDK7, CPTAC-3036 - 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
CDK7	CAK, CAK1, CDKN7, MO15, STK1

Sequence Length (AA)	Molecular Weight (Da)
346	39038

Protein Name
Cyclin-dependent kinase 7

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MALDVKSRAK	RYEKLDFLGE	GQFATVYKAR	DKNTNQIVAI	KKIKLGHRSE
60	70	80	90	100
AKDGINRTAL	REIKLLQELS	HPNIIGLLDA	FGHKSNISLV	FDFMETDLEV
110	120	130	140	150
IIKDNSLVLT	PSHIKAYMLM	TLQGLEYLHQ	HWILHRDLKP	NNLLLDENGV
160	170	180	190	200
LKLADFGLAK	SFGSPNRAYT	HQVVTRWYRA	PELLFGARMY	GVGVDMWAVG
210	220	230	240	250
CILAELLLRV	PFLPGDSDLD	QLTRIFETLG	TPTEEQWPDM	CSLPDYVTFK
260	270	280	290	300
SFPGIPLHHI	FSAAGDDLLD	LIQGLFLFNP	CARITATQAL	KMKYFSNRPG
310	320	330	340	346
PTPGCQLPRP	NCPVETLKEQ	SNPALAIKRK	RTEALEQGGL	PKKLIF

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-5912 Collapse assay details

Data source: Panorama

Official Gene Symbol: CDK7
Peptide Modified Sequence: AYT[+79.966331]HQVVTR
Modification Type: Phospho (ST)
Protein - Site of Modification: 171
Peptide - Site of Modification: 3
Peptide Start: 168
Peptide End: 176

CPTAC ID: CPTAC-5912
Peptide Molecular Mass: 1,153.5281
Species: Homo sapiens (Human)
Assay Type: Enrichment PRM
Enrichment Method: N/A
Matrix: Cell Lysate
Submitting Laboratory: Fred Hutchinson Cancer Research Center
Submitting Lab PI: Amanda Paulovich

Publication

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Quantification of Novel Pharmacodynamic Biomarkers of ATM Kinase Inhibition. Whiteaker JR, Wang T, Zhao L, Schoenherr RM, Kennedy JJ, Voytovich U, Ivey RG, Huang D, Lin C, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Kaczmarczyk JA, Blonder J, Reading JJ, Richardson CW, Hewitt SM, Garcia-Buntley SS, Bocik W, Hiltke T, Rodriguez H, Harrington EA, Barrett JC, Lombardi B, Marco-Casanova P, Pierce AJ, Paulovich AG. Cancers (Basel). 2021 Jul 30;13(15):3843. doi: 10.3390/cancers13153843. PMID: 34359745

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: Sciex 5500 QTRAP
Internal Standard: peptide
Peptide Standard Purity: >95%
Peptide Standard Label Type: 13C and 15N at C-terminus R

LC: Eksigent 425
Column Packing: Reprosil
Column Dimensions: 75um x 15cm
Flow Rate: 300 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
y7-98 (2+)	19	9	9.4	23.3	9.6	9	30.1	13.2	13	15	27	15
y7 (2+)	37.5	18.5	12.3	38.2	16.4	13.7	53.5	24.7	18.4	15	27	15
y4 (1+)	20.6	10.6	9.3	33.4	19.2	13.1	39.2	21.9	16.1	15	27	15
y3 (1+)	14.9	11	7.3	23.2	18	9.6	27.6	21.1	12.1	15	27	15
y2 (1+)	33.1	14.7	12.4	28.6	16.9	19.6	43.7	22.4	23.2	15	27	15
y8 (2+)	28.5	24.2	12.3	33.8	20.3	20.8	44.2	31.6	24.2	15	27	15
y8-98 (2+)	19.9	10.4	8.2	19.8	13.2	7.5	28.1	16.8	11.1	15	27	15
sum	12	5.6	4.1	14.7	9.7	5.8	19	11.2	7.1	15	27	15

Additional Resources and Comments

Resources

Download SOPs

View Peptide in Panorama

View Protein in Panorama

View in CPTC Antibody Portal

Comments

Assay Details for CPTAC-3036 Collapse assay details

Data source: Panorama

Official Gene Symbol: CDK7
Peptide Sequence: LDFLGEGQFATVYK
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 15
Peptide End: 28

CPTAC ID: CPTAC-3036
Peptide Molecular Mass: 1,586.7981
Species: Homo Sapiens
Assay Type: Direct PRM
Matrix: Tumor Digest
Submitting Laboratory: Washington University in St. Louis
Submitting Lab PI: Reid Townsend