PRKCD, CPTAC-1743 - 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.
Protein Sequence hover to view complete sequence
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MAPFLRIAFN | SYELGSLQAE | DEANQPFCAV | KMKEALSTER | GKTLVQKKPT |
| 60 | 70 | 80 | 90 | 100 |
| MYPEWKSTFD | AHIYEGRVIQ | IVLMRAAEEP | VSEVTVGVSV | LAERCKKNNG |
| 110 | 120 | 130 | 140 | 150 |
| KAEFWLDLQP | QAKVLMSVQY | FLEDVDCKQS | MRSEDEAKFP | TMNRRGAIKQ |
| 160 | 170 | 180 | 190 | 200 |
| AKIHYIKNHE | FIATFFGQPT | FCSVCKDFVW | GLNKQGYKCR | QCNAAIHKKC |
| 210 | 220 | 230 | 240 | 250 |
| IDKIIGRCTG | TAANSRDTIF | QKERFNIDMP | HRFKVHNYMS | PTFCDHCGSL |
| 260 | 270 | 280 | 290 | 300 |
| LWGLVKQGLK | CEDCGMNVHH | KCREKVANLC | GINQKLLAEA | LNQVTQRASR |
| 310 | 320 | 330 | 340 | 350 |
| RSDSASSEPV | GIYQGFEKKT | GVAGEDMQDN | SGTYGKIWEG | SSKCNINNFI |
| 360 | 370 | 380 | 390 | 400 |
| FHKVLGKGSF | GKVLLGELKG | RGEYFAIKAL | KKDVVLIDDD | VECTMVEKRV |
| 410 | 420 | 430 | 440 | 450 |
| LTLAAENPFL | THLICTFQTK | DHLFFVMEFL | NGGDLMYHIQ | DKGRFELYRA |
| 460 | 470 | 480 | 490 | 500 |
| TFYAAEIMCG | LQFLHSKGII | YRDLKLDNVL | LDRDGHIKIA | DFGMCKENIF |
| 510 | 520 | 530 | 540 | 550 |
| GESRASTFCG | TPDYIAPEIL | QGLKYTFSVD | WWSFGVLLYE | MLIGQSPFHG |
| 560 | 570 | 580 | 590 | 600 |
| DDEDELFESI | RVDTPHYPRW | ITKESKDILE | KLFEREPTKR | LGVTGNIKIH |
| 610 | 620 | 630 | 640 | 650 |
| PFFKTINWTL | LEKRRLEPPF | RPKVKSPRDY | SNFDQEFLNE | KARLSYSDKN |
| 660 | 670 | 676 | ||
| LIDSMDQSAF | AGFSFVNPKF | EHLLED |
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-1743 Collapse assay details
Data source: Panorama
Official Gene Symbol
PRKCD
Peptide Modified Sequence
SDSASS[+80.0]EPVGIYQGFEK
Modification Type
Phospho (ST)
Protein - Site of Modification
307
Peptide - Site of Modification
6
Peptide Start
302
Peptide End
318
CPTAC ID
CPTAC-1743
Peptide Molecular Mass
1,879.7877
Species
Homo sapiens (Human)
Assay Type
Enrichment MRM or SRM
Enrichment Method
Titanium Dioxide
Matrix
Ovarian cancer cell 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-TiO2SRM
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y4 (1+) | 13.4 | 7.6 | 7 | 17.2 | 10.8 | 10.5 | 21.8 | 13.2 | 12.6 | 15 | 15 | 15 |
| y8 (1+) | 38.8 | 27.1 | 15.1 | 30 | 33.3 | 18.3 | 49 | 42.9 | 23.7 | 15 | 15 | 15 |
| y6 (1+) | 8 | 7 | 6.2 | 11.4 | 9.5 | 6.6 | 13.9 | 11.8 | 9.1 | 15 | 15 | 15 |
| sum | 14 | 7.4 | 5.8 | 12.6 | 11.7 | 7.4 | 18.8 | 13.8 | 9.4 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-2854 Collapse assay details
Data source: Panorama
Official Gene Symbol
PRKCD
Peptide Sequence
AEFWLDLQPQAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
102
Peptide End
113
CPTAC ID
CPTAC-2854
Peptide Molecular Mass
1,444.7351
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-TiO2SRM
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 (1+) | 4.9 | 5.7 | 4.5 | 5.3 | 7.6 | 6.4 | 7.2 | 9.5 | 7.8 | 15 | 15 | 15 |
| y4 (1+) | 4.2 | 4.6 | 3.6 | 4.7 | 6.5 | 5.5 | 6.3 | 8 | 6.6 | 15 | 15 | 15 |
| y8 (1+) | 4.4 | 6.2 | 4.2 | 5.7 | 8 | 6.9 | 7.2 | 10.1 | 8.1 | 15 | 15 | 15 |
| sum | 4.1 | 5.1 | 3.8 | 4.8 | 7 | 5.9 | 6.3 | 8.7 | 7 | 15 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-2853 Collapse assay details
Data source: Panorama
Official Gene Symbol
PRKCD
Peptide Sequence
DYSNFDQEFLNEK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
629
Peptide End
641
CPTAC ID
CPTAC-2853
Peptide Molecular Mass
1,647.7053
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-TiO2SRM
Chromatograms
Data source: Panorama
Response Curves
Data source: Panorama
Retrieving Data
Repeatability
Data source: Panorama
| | 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 |
| y8 (1+) | 5.7 | 4.4 | 8 | 9.6 | 5.8 | 5.9 | 11.2 | 7.3 | 9.9 | 15 | 15 | 15 |
| y3 (1+) | 6.7 | 5 | 3.6 | 9.2 | 4.8 | 3.8 | 11.4 | 6.9 | 5.2 | 15 | 15 | 15 |
| y4 (1+) | 8.5 | 4.1 | 4.4 | 10.9 | 4.2 | 4.5 | 13.8 | 5.9 | 6.3 | 15 | 15 | 15 |
| sum | 5.2 | 4.4 | 5.1 | 7.8 | 4.6 | 4.5 | 9.4 | 6.4 | 6.8 | 15 | 15 | 15 |