CDK9, CPTAC-2942 - 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
CDK9	CDC2L4, TAK

Sequence Length (AA)	Molecular Weight (Da)
372	42778

Protein Name
Cyclin-dependent kinase 9

Sources
UniProt PhosphoSitePlus ® GeneCards	Human Protein Atlas

Protein Sequence hover to view complete sequence

10	20	30	40	50
MAKQYDSVEC	PFCDEVSKYE	KLAKIGQGTF	GEVFKARHRK	TGQKVALKKV
60	70	80	90	100
LMENEKEGFP	ITALREIKIL	QLLKHENVVN	LIEICRTKAS	PYNRCKGSIY
110	120	130	140	150
LVFDFCEHDL	AGLLSNVLVK	FTLSEIKRVM	QMLLNGLYYI	HRNKILHRDM
160	170	180	190	200
KAANVLITRD	GVLKLADFGL	ARAFSLAKNS	QPNRYTNRVV	TLWYRPPELL
210	220	230	240	250
LGERDYGPPI	DLWGAGCIMA	EMWTRSPIMQ	GNTEQHQLAL	ISQLCGSITP
260	270	280	290	300
EVWPNVDNYE	LYEKLELVKG	QKRKVKDRLK	AYVRDPYALD	LIDKLLVLDP
310	320	330	340	350
AQRIDSDDAL	NHDFFWSDPM	PSDLKGMLST	HLTSMFEYLA	PPRRKGSQIT
360	370	372
QQSTNQSRNP	ATTNQTEFER	VF

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-1602 Collapse assay details

Data source: Panorama

Official Gene Symbol: CDK9
Peptide Sequence: IGQGTFGEVFK
Modification Type: unmodified
Protein - Site of Modification: N/A
Peptide - Site of Modification: N/A
Peptide Start: 25
Peptide End: 35

CPTAC ID: CPTAC-1602
Peptide Molecular Mass: 1,181.6081
Species: Homo sapiens (Human)
Assay Type: Direct PRM
Matrix: Ovarian cancer tumor tissue lysate
Submitting Laboratory: Pacific Northwest National Laboratory
Submitting Lab PI: Tao Liu

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument: TSQ Vantage
Internal Standard: peptide
Peptide Standard Purity: >95%
Peptide Standard Label Type: 13C and 15N at C-terminus K

LC: Waters nanoACQUITY (Part Number 176016000)
Column Packing: Waters BEH C18, 1.7 um 130 Å (Part Number 186007485)
Column Dimensions: 100 um x 100 mm
Flow Rate: 0.5 uL/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
y6 (1+)	6.8	2.7	4.7	19.8	3.2	7.7	20.9	4.2	9	15	15	15
y8 (1+)	5.9	0.6	1.9	12.1	3.9	5.6	13.5	3.9	5.9	15	15	15
y10 (1+)	10.8	2.9	3.4	10.1	3.4	5.5	14.8	4.5	6.5	15	15	15
sum	3.8	1.3	1.8	10.4	3.1	5.7	11.1	3.4	6	15	15	15

Additional Resources and Comments

Resources

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View Peptide in Panorama

View Protein in Panorama

Comments

Assay Details for CPTAC-2942 Collapse assay details

Data source: Panorama

Official Gene Symbol: CDK9
Peptide Modified Sequence: HENVVNLIEIC[+57.0]R
Modification Type: Carbamidomethyl (C)
Protein - Site of Modification: 86
Peptide - Site of Modification: 11
Peptide Start: 75
Peptide End: 86

CPTAC ID: CPTAC-2942
Peptide Molecular Mass: 1,494.7613
Species: Homo Sapiens
Assay Type: Direct PRM
Matrix: Tumor Digest
Submitting Laboratory: Washington University in St. Louis
Submitting Lab PI: Reid Townsend