PGD, CPTAC-560 - 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-2711: View additional VDDFLANEAK data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MAQADIALIG | LAVMGQNLIL | NMNDHGFVVC | AFNRTVSKVD | DFLANEAKGT |
| 60 | 70 | 80 | 90 | 100 |
| KVVGAQSLKE | MVSKLKKPRR | IILLVKAGQA | VDDFIEKLVP | LLDTGDIIID |
| 110 | 120 | 130 | 140 | 150 |
| GGNSEYRDTT | RRCRDLKAKG | ILFVGSGVSG | GEEGARYGPS | LMPGGNKEAW |
| 160 | 170 | 180 | 190 | 200 |
| PHIKTIFQGI | AAKVGTGEPC | CDWVGDEGAG | HFVKMVHNGI | EYGDMQLICE |
| 210 | 220 | 230 | 240 | 250 |
| AYHLMKDVLG | MAQDEMAQAF | EDWNKTELDS | FLIEITANIL | KFQDTDGKHL |
| 260 | 270 | 280 | 290 | 300 |
| LPKIRDSAGQ | KGTGKWTAIS | ALEYGVPVTL | IGEAVFARCL | SSLKDERIQA |
| 310 | 320 | 330 | 340 | 350 |
| SKKLKGPQKF | QFDGDKKSFL | EDIRKALYAS | KIISYAQGFM | LLRQAATEFG |
| 360 | 370 | 380 | 390 | 400 |
| WTLNYGGIAL | MWRGGCIIRS | VFLGKIKDAF | DRNPELQNLL | LDDFFKSAVE |
| 410 | 420 | 430 | 440 | 450 |
| NCQDSWRRAV | STGVQAGIPM | PCFTTALSFY | DGYRHEMLPA | SLIQAQRDYF |
| 460 | 470 | 480 | 483 | |
| GAHTYELLAK | PGQFIHTNWT | GHGGTVSSSS | YNA |
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-560 Collapse assay details
Data source: Panorama
Official Gene Symbol
PGD
Peptide Sequence
LVPLLDTGDIIIDGGNSEYR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
88
Peptide End
107
CPTAC ID
CPTAC-560
Peptide Molecular Mass
2,159.1110
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
Publication
View Details (opens in a new window)
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min
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 |
| y9 (1+) | 16.5 | 9.2 | 6.6 | 28.6 | 17.6 | 22.4 | 33 | 19.9 | 23.4 | 25 | 15 | 15 |
| y8 (1+) | 17.3 | 7.2 | 8.2 | 30.2 | 24.5 | 24.6 | 34.8 | 25.5 | 25.9 | 25 | 15 | 15 |
| y7 (1+) | 20.2 | 10.7 | 8.5 | 27.8 | 27.7 | 23.8 | 34.4 | 29.7 | 25.3 | 25 | 15 | 15 |
| sum | 12.3 | 6 | 7.9 | 27.5 | 23.5 | 23.8 | 30.1 | 24.3 | 25.1 | 25 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-561 Collapse assay details
Data source: Panorama
Official Gene Symbol
PGD
Peptide Sequence
NPELQNLLLDDFFK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
383
Peptide End
396
CPTAC ID
CPTAC-561
Peptide Molecular Mass
1,704.8723
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Seoul National University / Korea Institute of Science and Technology and FHCRC
Submitting Lab PI
Youngsoo Kim
Publication
View Details (opens in a new window)
Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins. Kennedy JJ, Abbatiello SE, Kim K, Yan P, Whiteaker JR, Lin C, Kim JS, Zhang Y, Wang X, Ivey RG, Zhao L, Min H, Lee Y, Yu MH, Yang EG, Lee C, Wang P, Rodriguez H, Kim Y, Carr SA, Paulovich AG. Nat Methods. 2014 Feb;11(2):149-55. doi: 10.1038/nmeth.2763. Epub 2013 Dec 8. PMID: 24317253
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Response curves acquired at Seoul National University / Korea Institute of Science and Technology. Repeatability data acquired at Fred Hutchinson Cancer Research Center.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C,15N
LC
nanoLC-Ultra 2D, cHiPLC-nanoflex (Eksigent)
Column Packing
ChromXP C18-CL, 3 um, 120A
Column Dimensions
150 x 0.075 mm
Flow Rate
500 nL / min
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 |
| y9 (1+) | 13 | 15.9 | 7.6 | 38.6 | 39 | 26.4 | 40.7 | 42.1 | 27.5 | 25 | 15 | 15 |
| y8 (1+) | 30.5 | 26 | 23.8 | 46.4 | 40.8 | 35.3 | 55.5 | 48.4 | 42.6 | 25 | 15 | 15 |
| y7 (1+) | 13.5 | 10.9 | 12 | 34.6 | 34.7 | 21.3 | 37.1 | 36.4 | 24.4 | 25 | 15 | 15 |
| sum | 12.2 | 11.1 | 9.6 | 37.1 | 35.9 | 24.1 | 39.1 | 37.6 | 25.9 | 25 | 15 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-2711 Collapse assay details
Data source: Panorama
Official Gene Symbol
PGD
Peptide Sequence
VDDFLANEAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
39
Peptide End
48
CPTAC ID
CPTAC-2711
Peptide Molecular Mass
1,120.5401
Species
Homo Sapiens
Assay Type
Direct MRM
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
13 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 um x 50 cm
Flow Rate
300 nL/min
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 |
| y6 (1+) | 9.5 | 4 | 4.7 | 8.7 | 4.2 | 5.2 | 12.9 | 5.8 | 7 | 15 | 15 | 15 |
| y5 (1+) | 8.3 | 4.2 | 8.2 | 9.3 | 3.1 | 10.7 | 12.5 | 5.2 | 13.5 | 15 | 15 | 15 |
| y4 (1+) | 10.3 | 5.4 | 5 | 10.6 | 4.5 | 4.8 | 14.8 | 7 | 6.9 | 15 | 15 | 15 |
| sum | 7.8 | 2.8 | 4.1 | 8.3 | 2.3 | 5.9 | 11.4 | 3.6 | 7.2 | 15 | 15 | 15 |