Overview Data source: UniProt

Official Gene Symbol Other Aliases
PGD PGDH
Sequence Length (AA) Molecular Weight (Da)
483 53140
Protein Name
6-phosphogluconate dehydrogenase, decarboxylating
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

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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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.


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

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Repeatability

Data source: Panorama

  Average intra-assay CV
(within day CV)
Average inter-assay CV
(between day CV)
Total CV
equation
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.


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

Loader

Repeatability

Data source: Panorama

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