PIK3CD, CPTAC-1213 - CPTAC Assay Portal (original) (raw)

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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.

PIK3CD

Overview Data source: UniProt

Official Gene Symbol Other Aliases
PIK3CD N/A
Sequence Length (AA) Molecular Weight (Da)
1044 119479
Protein Name
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform
Sources
UniProt PhosphoSitePlus ® GeneCards Human Protein Atlas

Protein Sequence hover to view complete sequence

CPTAC-1213: View additional GELLNPTGTVR data

10 20 30 40 50
MPPGVDCPME FWTKEENQSV VVDFLLPTGV YLNFPVSRNA NLSTIKQLLW
60 70 80 90 100
HRAQYEPLFH MLSGPEAYVF TCINQTAEQQ ELEDEQRRLC DVQPFLPVLR
110 120 130 140 150
LVAREGDRVK KLINSQISLL IGKGLHEFDS LCDPEVNDFR AKMCQFCEEA
160 170 180 190 200
AARRQQLGWE AWLQYSFPLQ LEPSAQTWGP GTLRLPNRAL LVNVKFEGSE
210 220 230 240 250
ESFTFQVSTK DVPLALMACA LRKKATVFRQ PLVEQPEDYT LQVNGRHEYL
260 270 280 290 300
YGSYPLCQFQ YICSCLHSGL TPHLTMVHSS SILAMRDEQS NPAPQVQKPR
310 320 330 340 350
AKPPPIPAKK PSSVSLWSLE QPFRIELIQG SKVNADERMK LVVQAGLFHG
360 370 380 390 400
NEMLCKTVSS SEVSVCSEPV WKQRLEFDIN ICDLPRMARL CFALYAVIEK
410 420 430 440 450
AKKARSTKKK SKKADCPIAW ANLMLFDYKD QLKTGERCLY MWPSVPDEKG
460 470 480 490 500
ELLNPTGTVR SNPNTDSAAA LLICLPEVAP HPVYYPALEK ILELGRHSEC
510 520 530 540 550
VHVTEEEQLQ LREILERRGS GELYEHEKDL VWKLRHEVQE HFPEALARLL
560 570 580 590 600
LVTKWNKHED VAQMLYLLCS WPELPVLSAL ELLDFSFPDC HVGSFAIKSL
610 620 630 640 650
RKLTDDELFQ YLLQLVQVLK YESYLDCELT KFLLDRALAN RKIGHFLFWH
660 670 680 690 700
LRSEMHVPSV ALRFGLILEA YCRGSTHHMK VLMKQGEALS KLKALNDFVK
710 720 730 740 750
LSSQKTPKPQ TKELMHLCMR QEAYLEALSH LQSPLDPSTL LAEVCVEQCT
760 770 780 790 800
FMDSKMKPLW IMYSNEEAGS GGSVGIIFKN GDDLRQDMLT LQMIQLMDVL
810 820 830 840 850
WKQEGLDLRM TPYGCLPTGD RTGLIEVVLR SDTIANIQLN KSNMAATAAF
860 870 880 890 900
NKDALLNWLK SKNPGEALDR AIEEFTLSCA GYCVATYVLG IGDRHSDNIM
910 920 930 940 950
IRESGQLFHI DFGHFLGNFK TKFGINRERV PFILTYDFVH VIQQGKTNNS
960 970 980 990 1000
EKFERFRGYC ERAYTILRRH GLLFLHLFAL MRAAGLPELS CSKDIQYLKD
1010 1020 1030 1040 1044
SLALGKTEEE ALKHFRVKFN EALRESWKTK VNWLAHNVSK DNRQ

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-1213 Collapse assay details

Data source: Panorama

Official Gene Symbol

PIK3CD

Peptide Sequence

GELLNPTGTVR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

450

Peptide End

460

CPTAC ID

CPTAC-1213

Peptide Molecular Mass

1,155.6248

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 R

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-DirectMRM

Chromatograms

Data source: Panorama

Response Curves

Data source: Panorama

Retrieving Data

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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+) | 14.5 | 4.1 | 3.3 | 13.9 | 5.7 | 5.3 | 20.1 | 7 | 6.2 | 15 | 15 | 15 | | y7 (1+) | 18.3 | 5.6 | 3.3 | 17.3 | 8.5 | 4.3 | 25.2 | 10.2 | 5.4 | 15 | 15 | 15 | | y8 (1+) | 36.7 | 7.3 | 5.9 | 23.6 | 8.9 | 7.5 | 43.6 | 11.5 | 9.5 | 15 | 15 | 15 | | sum | 10.3 | 4.1 | 2.3 | 10.6 | 5.8 | 4.4 | 14.8 | 7.1 | 5 | 15 | 15 | 15 |

Selectivity

Data source: Panorama

Slope of Curve Fit for cell line
fragment_ion 1 2 3 4 5 6
y8 (1+) 1.66 1.5 1.97 1.73 1.79 2.41
y7 (1+) 1.57 1.54 2.35 1.65 1.67 1.89
y6 (1+) 1.58 1.55 2.25 1.71 1.57 1.86
sum 1.58 1.54 2.25 1.69 1.62 1.91

Stability

Data source: Panorama

Fragment ion / Transition control_intra_CV actual_temp_intra_CV frozen_intra_CV FTx1_intra_CV FTx2_intra_CV
y6 (1+) 3.4 4.7 2 1.5 2.9
y7 (1+) 6.8 3.7 3.7 2.3 7.1
y8 (1+) 14.4 5.1 8.4 4.6 9.1
sum 3.5 1.5 1.3 1 2
Fragment ion / Transition all_intra_CV all_inter_CV
y6 (1+) 3.2 4.1
y7 (1+) 4.6 5.1
y8 (1+) 7.8 10.9
sum 1.8 3.4

Endogenous

Data source: Panorama

Fragment ion / Transition intra_CV inter_CV total_CV
y7 (1+) 38 52.9 65.1
y6 (1+) 44.8 42.7 61.9
y8 (1+) 45.4 43 62.5
sum 33.9 45.2 56.5

Additional Resources and Comments

Comments

Assay Details for CPTAC-3075 Collapse assay details

Data source: Panorama

Official Gene Symbol

PIK3CD

Peptide Sequence

KPSSVSLWSLEQPFR

Modification Type

unmodified

Protein - Site of Modification

N/A

Peptide - Site of Modification

N/A

Peptide Start

310

Peptide End

324

CPTAC ID

CPTAC-3075

Peptide Molecular Mass

1,759.9257

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-DirectMRM

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+) | 12.9 | 10.3 | 11.9 | 9.1 | 15.8 | 13.9 | 15.8 | 18.9 | 18.3 | 15 | 15 | 15 | | y5 (1+) | 11.8 | 10.9 | 12.1 | 9.3 | 15.9 | 13.3 | 15 | 19.3 | 18 | 15 | 15 | 15 | | y3 (1+) | 12.6 | 9.3 | 11.7 | 8.5 | 14.8 | 13 | 15.2 | 17.5 | 17.5 | 15 | 15 | 15 | | sum | 12.2 | 10.2 | 11.9 | 8.6 | 15.5 | 13.4 | 14.9 | 18.6 | 17.9 | 15 | 15 | 15 |

Additional Resources and Comments

Comments