CDK9, CPTAC-1602 - 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-1602: View additional IGQGTFGEVFK data

CPTAC-2941: View additional LLVLDPAQR data

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

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-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 MRM or SRM

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

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | 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

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 MRM or SRM

Matrix

Tumor Digest

Submitting Laboratory

Washington University in St. Louis

Submitting Lab PI

Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

ThermoFisher, Q-Exactive

Internal Standard

25 fmol on column

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Easy-nLC 1000 Thermo Scientific

Column Packing

C18

Column Dimensions

75 µm x 50 cm

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | b4 (1+) | 5.6 | 12.5 | 9 | 7.7 | 10.9 | 9.1 | 9.5 | 16.6 | 12.8 | 15 | 15 | 15 | | b6 (1+) | 6.1 | 10.7 | 11.1 | 11.7 | 15.6 | 12.5 | 13.2 | 18.9 | 16.7 | 15 | 15 | 15 | | y4 (1+) | 4.3 | 11.9 | 10.1 | 6.8 | 10.5 | 9.3 | 8 | 15.9 | 13.7 | 15 | 15 | 15 | | sum | 4.4 | 11.7 | 9.8 | 6.9 | 11.4 | 9.2 | 8.2 | 16.3 | 13.4 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-2941 Collapse assay details

Data source: Panorama

Official Gene Symbol

CDK9

Peptide Sequence

LLVLDPAQR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

295

Peptide End

303

CPTAC ID

CPTAC-2941

Peptide Molecular Mass

1,023.6077

Species

Homo Sapiens

Assay Type

Direct MRM or SRM

Matrix

Tumor Digest

Submitting Laboratory

Washington University in St. Louis

Submitting Lab PI

Reid Townsend

Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument

ThermoFisher, Q-Exactive

Internal Standard

25 fmol on column

Peptide Standard Purity

>95%

Peptide Standard Label Type

13C and 15N at C-terminus R

LC

Easy-nLC 1000 Thermo Scientific

Column Packing

C18

Column Dimensions

75 µm x 50 cm

Flow Rate

300 nL/min

Assay Multiplexing Expand assay panel

Pacific Northwest National Laboratory-DirectSRM3

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

Loader

Repeatability

Data source: Panorama

| | Average intra-assay CV(within day CV) | Average inter-assay CV(between day CV) | Total CVequation | n= | | | | | | | | | | | ---------------------------------------- | -------------------------------------- | --------------------------------------------------------------------------------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | ------- | ------- | -------- | | Fragment ion / Transition | Low | Med | High | Low | Med | High | Low | Med | High | Low | Med | High | | y7 (1+) | 7.9 | 5.6 | 8.4 | 10 | 6.5 | 9 | 12.7 | 8.6 | 12.3 | 15 | 15 | 15 | | y6 (1+) | 8.8 | 5.4 | 7.6 | 10.6 | 6.7 | 9 | 13.8 | 8.6 | 11.8 | 15 | 15 | 15 | | y4 (1+) | 7.6 | 5.8 | 7.4 | 8.9 | 6.5 | 8.2 | 11.7 | 8.7 | 11 | 15 | 15 | 15 | | sum | 7.7 | 5.5 | 7.5 | 9.2 | 6.4 | 8.3 | 12 | 8.4 | 11.2 | 15 | 15 | 15 |

Additional Resources and Comments