PRKCA, CPTAC-1615 - 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-1615: View additional GTEELYAIK data

CPTAC-3173: View additional LSVEIWDWDR data

10 20 30 40 50
MADVFPGNDS TASQDVANRF ARKGALRQKN VHEVKDHKFI ARFFKQPTFC
60 70 80 90 100
SHCTDFIWGF GKQGFQCQVC CFVVHKRCHE FVTFSCPGAD KGPDTDDPRS
110 120 130 140 150
KHKFKIHTYG SPTFCDHCGS LLYGLIHQGM KCDTCDMNVH KQCVINVPSL
160 170 180 190 200
CGMDHTEKRG RIYLKAEVAD EKLHVTVRDA KNLIPMDPNG LSDPYVKLKL
210 220 230 240 250
IPDPKNESKQ KTKTIRSTLN PQWNESFTFK LKPSDKDRRL SVEIWDWDRT
260 270 280 290 300
TRNDFMGSLS FGVSELMKMP ASGWYKLLNQ EEGEYYNVPI PEGDEEGNME
310 320 330 340 350
LRQKFEKAKL GPAGNKVISP SEDRKQPSNN LDRVKLTDFN FLMVLGKGSF
360 370 380 390 400
GKVMLADRKG TEELYAIKIL KKDVVIQDDD VECTMVEKRV LALLDKPPFL
410 420 430 440 450
TQLHSCFQTV DRLYFVMEYV NGGDLMYHIQ QVGKFKEPQA VFYAAEISIG
460 470 480 490 500
LFFLHKRGII YRDLKLDNVM LDSEGHIKIA DFGMCKEHMM DGVTTRTFCG
510 520 530 540 550
TPDYIAPEII AYQPYGKSVD WWAYGVLLYE MLAGQPPFDG EDEDELFQSI
560 570 580 590 600
MEHNVSYPKS LSKEAVSVCK GLMTKHPAKR LGCGPEGERD VREHAFFRRI
610 620 630 640 650
DWEKLENREI QPPFKPKVCG KGAENFDKFF TRGQPVLTPP DQLVIANIDQ
660 670 672
SDFEGFSYVN PQFVHPILQS AV

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-1615 Collapse assay details

Data source: Panorama

Official Gene Symbol

PRKCA

Peptide Sequence

GTEELYAIK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

360

Peptide End

368

CPTAC ID

CPTAC-1615

Peptide Molecular Mass

1,022.5284

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 | | y4 (1+) | 9 | 6.4 | 5.4 | 14 | 7.6 | 6.7 | 16.6 | 9.9 | 8.6 | 15 | 15 | 15 | | y6 (1+) | 9.9 | 3.4 | 3.4 | 14.4 | 5.9 | 7.5 | 17.5 | 6.8 | 8.2 | 15 | 15 | 15 | | y7 (1+) | 4.7 | 3.3 | 2.2 | 11.1 | 5.8 | 3.2 | 12.1 | 6.7 | 3.9 | 15 | 15 | 15 | | sum | 3.9 | 1.9 | 1.9 | 12 | 5.1 | 4.9 | 12.6 | 5.4 | 5.3 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-3173 Collapse assay details

Data source: Panorama

Official Gene Symbol

PRKCA

Peptide Sequence

LSVEIWDWDR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

240

Peptide End

249

CPTAC ID

CPTAC-3173

Peptide Molecular Mass

1,317.6354

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+) | 6.1 | 5.4 | 5.9 | 6.7 | 15 | 19.2 | 9.1 | 15.9 | 20.1 | 15 | 15 | 15 | | y5 (1+) | 5.3 | 4.8 | 5.5 | 5.6 | 13.9 | 18 | 7.7 | 14.7 | 18.8 | 15 | 15 | 15 | | y3 (1+) | 4.3 | 4.3 | 4.7 | 5.6 | 12.1 | 15.5 | 7.1 | 12.8 | 16.2 | 15 | 15 | 15 | | sum | 5.1 | 4.8 | 5.3 | 5.7 | 13.7 | 17.7 | 7.6 | 14.5 | 18.5 | 15 | 15 | 15 |

Additional Resources and Comments

Assay Details for CPTAC-3172 Collapse assay details

Data source: Panorama

Official Gene Symbol

PRKCA

Peptide Sequence

STLNPQWNESFTFK

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

217

Peptide End

230

CPTAC ID

CPTAC-3172

Peptide Molecular Mass

1,697.8049

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 K

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 | | y5 (1+) | 19.9 | 6.5 | 4.2 | 23.4 | 5.2 | 4.3 | 30.7 | 8.3 | 6 | 15 | 15 | 15 | | y7 (1+) | 14.4 | 5 | 4.7 | 13.7 | 4.8 | 5.5 | 19.9 | 6.9 | 7.2 | 15 | 15 | 15 | | y8 (1+) | 8.8 | 4.2 | 5.2 | 10.1 | 3.7 | 5.4 | 13.4 | 5.6 | 7.5 | 15 | 15 | 15 | | sum | 11.4 | 4.8 | 4.3 | 11.8 | 3.9 | 4.8 | 16.4 | 6.2 | 6.4 | 15 | 15 | 15 |

Additional Resources and Comments