Overview Data source: UniProt

Official Gene Symbol Other Aliases
PHGDH PGDH3
Sequence Length (AA) Molecular Weight (Da)
533 56651
Protein Name
D-3-phosphoglycerate dehydrogenase
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MAFANLRKVL ISDSLDPCCR KILQDGGLQV VEKQNLSKEE LIAELQDCEG
60 70 80 90 100
LIVRSATKVT ADVINAAEKL QVVGRAGTGV DNVDLEAATR KGILVMNTPN
110 120 130 140 150
GNSLSAAELT CGMIMCLARQ IPQATASMKD GKWERKKFMG TELNGKTLGI
160 170 180 190 200
LGLGRIGREV ATRMQSFGMK TIGYDPIISP EVSASFGVQQ LPLEEIWPLC
210 220 230 240 250
DFITVHTPLL PSTTGLLNDN TFAQCKKGVR VVNCARGGIV DEGALLRALQ
260 270 280 290 300
SGQCAGAALD VFTEEPPRDR ALVDHENVIS CPHLGASTKE AQSRCGEEIA
310 320 330 340 350
VQFVDMVKGK SLTGVVNAQA LTSAFSPHTK PWIGLAEALG TLMRAWAGSP
360 370 380 390 400
KGTIQVITQG TSLKNAGNCL SPAVIVGLLK EASKQADVNL VNAKLLVKEA
410 420 430 440 450
GLNVTTSHSP AAPGEQGFGE CLLAVALAGA PYQAVGLVQG TTPVLQGLNG
460 470 480 490 500
AVFRPEVPLR RDLPLLLFRT QTSDPAMLPT MIGLLAEAGV RLLSYQTSLV
510 520 530 533
SDGETWHVMG ISSLLPSLEA WKQHVTEAFQ FHF

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-109 Collapse assay details

Data source: Panorama

Official Gene Symbol
PHGDH
Peptide Sequence
AGTGVDNVDLEAATR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
76
Peptide End
90
CPTAC ID
CPTAC-109
Peptide Molecular Mass
1,487.7216
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

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


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus R
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
y10 (1+) 10.6 8.7 3.3 10.1 9.1 7.7 14.6 12.6 8.4 15 25 15
y9 (1+) 14.6 8.3 6.6 19.4 10.3 6.7 24.3 13.2 9.4 15 25 15
y7 (1+) 7.3 5.7 4 8.4 6.8 5 11.1 8.9 6.4 15 25 15
sum 6.9 5.9 2.7 7 7 5.1 9.8 9.2 5.8 15 25 15

Additional Resources and Comments


Assay Details for CPTAC-110 Collapse assay details

Data source: Panorama

Official Gene Symbol
PHGDH
Peptide Sequence
GTIQVITQGTSLK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
352
Peptide End
364
CPTAC ID
CPTAC-110
Peptide Molecular Mass
1,344.7613
Species
Homo sapiens (Human)
Assay Type
Direct MRM
Matrix
cell line lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

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


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
5500 QTRAP (ABSCIEX)
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
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+) 10 6.2 5.2 20.4 15.4 5.5 22.7 16.6 7.6 15 25 15
y8 (1+) 4.6 5 5.1 17.4 15.3 5.3 18 16.1 7.4 15 25 15
y7 (1+) 8.2 5.5 4.1 14.1 13.3 5.9 16.3 14.4 7.2 15 25 15
sum 4.5 4.7 3 15.8 14.6 4 16.4 15.3 5 15 25 15

Additional Resources and Comments