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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.

Overview Data source: UniProt

Official Gene Symbol Other Aliases
GAPDH GAPD
Sequence Length (AA) Molecular Weight (Da)
335 36053
Protein Name
Glyceraldehyde-3-phosphate dehydrogenase
Sources
UniProt
PhosphoSitePlus ®
GeneCards
Human Protein Atlas

Protein Sequence hover to view complete sequence

10 20 30 40 50
MGKVKVGVNG FGRIGRLVTR AAFNSGKVDI VAINDPFIDL NYMVYMFQYD
60 70 80 90 100
STHGKFHGTV KAENGKLVIN GNPITIFQER DPSKIKWGDA GAEYVVESTG
110 120 130 140 150
VFTTMEKAGA HLQGGAKRVI ISAPSADAPM FVMGVNHEKY DNSLKIISNA
160 170 180 190 200
SCTTNCLAPL AKVIHDNFGI VEGLMTTVHA ITATQKTVDG PSGKLWRDGR
210 220 230 240 250
GALQNIIPAS TGAAKAVGKV IPELNGKLTG MAFRVPTANV SVVDLTCRLE
260 270 280 290 300
KPAKYDDIKK VVKQASEGPL KGILGYTEHQ VVSSDFNSDT HSSTFDAGAG
310 320 330 335
IALNDHFVKL ISWYDNEFGY SNRVVDLMAH MASKE

Data source: UniProt


Position of Targeted Peptide Analytes Relative to SNPs, Isoforms, and PTMs

Uniprot Database Entry PhosphoSitePlus ®

Click a point on a node
to view detailed assay information below
All other points link out to UniProt



Phosphorylation Acetylation Ubiquitylation Other

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Assay Details for CPTAC-5855 Collapse assay details

Data source: Panorama

Official Gene Symbol
GAPDH
Peptide Sequence
GALQNIIPASTGAAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
201
Peptide End
215
CPTAC ID
CPTAC-5855
Peptide Molecular Mass
1,410.7831
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
Matrix
Frozen breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/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+) 19.9 7.5 4.4 24.5 11 5.3 31.6 13.3 6.9 15 17 15
y10 (1+) 36.8 12 5.7 39.8 19.4 6.5 54.2 22.8 8.6 15 17 15
y11 (1+) 19 13.2 4 22.6 18.3 5.6 29.5 22.6 6.9 15 17 15
sum 16.4 7.6 2.9 20.8 12.2 4.4 26.5 14.4 5.3 15 17 15


Additional Resources and Comments


Assay Details for CPTAC-5880 Collapse assay details

Data source: Panorama

Official Gene Symbol
GAPDH
Peptide Sequence
GALQNIIPASTGAAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
201
Peptide End
215
CPTAC ID
CPTAC-5880
Peptide Molecular Mass
1,410.7831
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
Matrix
FFPE breast cancer tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues. Kennedy JJ, Whiteaker JR, Kennedy LC, Bosch DE, Lerch ML, Schoenherr RM, Zhao L, Lin C, Chowdhury S, Kilgore MR, Allison KH, Wang P, Hoofnagle AN, Baird GS, Paulovich AG. Clin Chem. 2021 Jun 17:hvab047. doi: 10.1093/clinchem/hvab047. Online ahead of print. PMID: 34136904


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 6500
Internal Standard
peptide
Peptide Standard Purity
Crude
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
10.0 µL/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+) 16.1 7.8 6.8 12.9 8.8 7.4 20.6 11.8 10 12 12 12
y10 (1+) 26.9 15 5.3 22.3 14.8 6.2 34.9 21.1 8.2 12 12 12
y11 (1+) 30.9 9.7 6 25.5 11.1 6.5 40.1 14.7 8.8 12 12 12
sum 14.7 5.3 5.2 13.2 7.7 5.9 19.8 9.3 7.9 12 12 12


Additional Resources and Comments


Assay Details for CPTAC-5942 Collapse assay details

Data source: Panorama

Official Gene Symbol
GAPDH
Peptide Sequence
GALQNIIPASTGAAK
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
4
Peptide Start
201
Peptide End
215
CPTAC ID
CPTAC-5942
Peptide Molecular Mass
1,410.7831
Species
Homo sapiens (Human)
Assay Type
Enrichment PRM
Enrichment Method
N/A
Matrix
FFPE tumor tissue lysate pool
Submitting Laboratory
Fred Hutchinson Cancer Research Center
Submitting Lab PI
Amanda Paulovich

Publication

View Details (opens in a new window)

Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Lundeen RA, Voytovich U, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Chowdhury S, Vandermeer J, Smith SD, Gopal AK, Ramchurren N, Fling SP, Wang P, Paulovich AG. A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials. Front Oncol. 2023 May 2;13:1168710. doi: 10.3389/fonc.2023.1168710. PMID: 37205196; PMCID: PMC10185886.

View Details (opens in a new window)

Targeted Mass Spectrometry Enables Multiplexed Quantification of Immunomodulatory Proteins in Clinical Biospecimens.Whiteaker JR, Lundeen RA, Zhao L, Schoenherr RM, Burian A, Huang D, Voytovich U, Wang T, Kennedy JJ, Ivey RG, Lin C, Murillo OD, Lorentzen TD, Thiagarajan M, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Kaczmarczyk JA, Richardson CW, Garcia-Buntley SS, Bocik W, Hewitt SM, Murray KE, Do N, Brophy M, Wilz SW, Yu H, Ajjarapu S, Boja E, Hiltke T, Rodriguez H, Paulovich AG.Front Immunol. 2021 Nov 11;12:765898. doi: 10.3389/fimmu.2021.765898. eCollection 2021.PMID: 34858420


Assay Parameters Collapse assay parameters

Data source: Panorama

Instrument
QTRAP 5500
Internal Standard
peptide
Peptide Standard Purity
>95%
Peptide Standard Label Type
13C and 15N at C-terminus K
LC
Eksigent nanoLC 425
Column Packing
3 µm ChromXP C18EP, 120 Å
Column Dimensions
150 x 0.3 mm
Flow Rate
0.3 µL/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
y11 (1+) 5.1 5.9 4.2 8.6 10.5 10 10 12 10.8 13 25 14
y10 (1+) 9.2 6.6 4.6 18.4 9.7 13.2 20.6 11.7 14 13 25 14
y9 (1+) 6.2 5.7 3.6 5.9 8.3 9.5 8.6 10.1 10.2 13 25 14
sum 4.8 4.7 1.6 4.9 8 9.7 6.9 9.3 9.8 13 25 14


Additional Resources and Comments


Assay Details for CPTAC-2733 Collapse assay details

Data source: Panorama

Official Gene Symbol
GAPDH
Peptide Sequence
LVINGNPITIFQER
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
67
Peptide End
80
CPTAC ID
CPTAC-2733
Peptide Molecular Mass
1,612.8937
Species
Homo Sapiens
Assay Type
Direct PRM
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 R
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

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
y4 (1+) 6.8 5 4.9 10.7 6.4 5.6 12.7 8.1 7.4 15 15 15
y10 (1+) 11.9 5.5 5.9 16.1 7.7 6.5 20 9.5 8.8 15 15 15
y11 (1+) 7.5 4.3 5.8 8.9 5.3 6.4 11.6 6.8 8.6 15 15 15
sum 7.6 4.1 5.1 9.7 5.9 5.7 12.3 7.2 7.6 15 15 15


Additional Resources and Comments