VCP, CPTAC-295 - 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
non-CPTAC-4013: View additional LAGESESNLR data
| 10 | 20 | 30 | 40 | 50 |
|---|---|---|---|---|
| MASGADSKGD | DLSTAILKQK | NRPNRLIVDE | AINEDNSVVS | LSQPKMDELQ |
| 60 | 70 | 80 | 90 | 100 |
| LFRGDTVLLK | GKKRREAVCI | VLSDDTCSDE | KIRMNRVVRN | NLRVRLGDVI |
| 110 | 120 | 130 | 140 | 150 |
| SIQPCPDVKY | GKRIHVLPID | DTVEGITGNL | FEVYLKPYFL | EAYRPIRKGD |
| 160 | 170 | 180 | 190 | 200 |
| IFLVRGGMRA | VEFKVVETDP | SPYCIVAPDT | VIHCEGEPIK | REDEEESLNE |
| 210 | 220 | 230 | 240 | 250 |
| VGYDDIGGCR | KQLAQIKEMV | ELPLRHPALF | KAIGVKPPRG | ILLYGPPGTG |
| 260 | 270 | 280 | 290 | 300 |
| KTLIARAVAN | ETGAFFFLIN | GPEIMSKLAG | ESESNLRKAF | EEAEKNAPAI |
| 310 | 320 | 330 | 340 | 350 |
| IFIDELDAIA | PKREKTHGEV | ERRIVSQLLT | LMDGLKQRAH | VIVMAATNRP |
| 360 | 370 | 380 | 390 | 400 |
| NSIDPALRRF | GRFDREVDIG | IPDATGRLEI | LQIHTKNMKL | ADDVDLEQVA |
| 410 | 420 | 430 | 440 | 450 |
| NETHGHVGAD | LAALCSEAAL | QAIRKKMDLI | DLEDETIDAE | VMNSLAVTMD |
| 460 | 470 | 480 | 490 | 500 |
| DFRWALSQSN | PSALRETVVE | VPQVTWEDIG | GLEDVKRELQ | ELVQYPVEHP |
| 510 | 520 | 530 | 540 | 550 |
| DKFLKFGMTP | SKGVLFYGPP | GCGKTLLAKA | IANECQANFI | SIKGPELLTM |
| 560 | 570 | 580 | 590 | 600 |
| WFGESEANVR | EIFDKARQAA | PCVLFFDELD | SIAKARGGNI | GDGGGAADRV |
| 610 | 620 | 630 | 640 | 650 |
| INQILTEMDG | MSTKKNVFII | GATNRPDIID | PAILRPGRLD | QLIYIPLPDE |
| 660 | 670 | 680 | 690 | 700 |
| KSRVAILKAN | LRKSPVAKDV | DLEFLAKMTN | GFSGADLTEI | CQRACKLAIR |
| 710 | 720 | 730 | 740 | 750 |
| ESIESEIRRE | RERQTNPSAM | EVEEDDPVPE | IRRDHFEEAM | RFARRSVSDN |
| 760 | 770 | 780 | 790 | 800 |
| DIRKYEMFAQ | TLQQSRGFGS | FRFPSGNQGG | AGPSQGSGGG | TGGSVYTEDN |
| 806 | ||||
| DDDLYG |
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-295 Collapse assay details
Data source: Panorama
Official Gene Symbol
VCP
Peptide Modified Sequence
LGDVISIQPC[+57.0]PDVK
Modification Type
Carbamidomethyl Cysteine
Protein - Site of Modification
105
Peptide - Site of Modification
10
Peptide Start
96
Peptide End
109
CPTAC ID
CPTAC-295
Peptide Molecular Mass
1,539.7967
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,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 |
| y10 (1+) | 7.1 | 6.8 | 8.8 | 11.2 | 9 | 7.4 | 13.3 | 11.3 | 11.5 | 15 | 25 | 15 |
| y9 (1+) | 4.8 | 5.9 | 9.5 | 10.1 | 8.1 | 9.4 | 11.2 | 10 | 13.4 | 15 | 25 | 15 |
| y7 (1+) | 16.8 | 7.7 | 8.2 | 16.1 | 8.5 | 9 | 23.3 | 11.5 | 12.2 | 15 | 25 | 15 |
| sum | 5.3 | 6.2 | 8.9 | 9.2 | 8.1 | 8.6 | 10.6 | 10.2 | 12.4 | 15 | 25 | 15 |
Additional Resources and Comments
Assay Details for CPTAC-296 Collapse assay details
Data source: Panorama
Official Gene Symbol
VCP
Peptide Sequence
WALSQSNPSALR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
454
Peptide End
465
CPTAC ID
CPTAC-296
Peptide Molecular Mass
1,328.6837
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,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 |
| y10 (1+) | 5.8 | 5.7 | 5.2 | 8.9 | 9.9 | 8.3 | 10.6 | 11.4 | 9.8 | 15 | 25 | 15 |
| y9 (1+) | 7.7 | 6.2 | 4.4 | 8.2 | 8.1 | 7.9 | 11.2 | 10.2 | 9 | 15 | 25 | 15 |
| y7 (1+) | 8.5 | 7.1 | 4.1 | 9.1 | 9.4 | 7.8 | 12.5 | 11.8 | 8.8 | 15 | 25 | 15 |
| sum | 4.9 | 4.9 | 4.1 | 6.4 | 8.3 | 7.8 | 8.1 | 9.6 | 8.8 | 15 | 25 | 15 |
Additional Resources and Comments
Assay Details for non-CPTAC-4013 Collapse assay details
Data source: Panorama
Official Gene Symbol
Vcp
Peptide Sequence
LAGESESNLR
Modification Type
unmodified
Protein - Site of Modification
N/A
Peptide - Site of Modification
N/A
Peptide Start
278
Peptide End
287
CPTAC ID
non-CPTAC-4013
Peptide Molecular Mass
1,074.5306
Species
Mus musculus (Mouse)
Assay Type
Direct MRM
Matrix
Plasma
Submitting Laboratory
UVic-Genome BC Proteomics Centre
Submitting Lab PI
Christoph Borchers
Publication
View Details (opens in a new window)
Molecular phenotyping of laboratory mouse strains using 500 multiple reaction monitoring mass spectrometry plasma assays. Michaud SA, Sinclair NJ, Petrošová H, Palmer AL, Pistawka AJ, Zhang S, Hardie DB, Mohammed Y Eshghi A1, Richard VR, Sickmann A, Borchers CH. Commun Biol. 2018 Jun 27;1:78. doi: 10.1038/s42003-018-0087-6. eCollection 2018.
Assay Parameters Collapse assay parameters
Data source: Panorama
Instrument
Agilent 6490/6495 QQQ
Internal Standard
synthetic peptide
Peptide Standard Purity
>80%
Peptide Standard Label Type
13C and 15N at C-terminus R
LC
1290 LC (Agilent)
Column Packing
Zorbax Eclipse Plus C18, 1.8 µm
Column Dimensions
2.1 x 150 mm
Flow Rate
400 µL/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 |
| b3 (1+) | 28.5 | 5.9 | 10.2 | 27.7 | 9.6 | 10.5 | 39.7 | 11.3 | 14.6 | 15 | 15 | 15 |
| y4 (1+) | 21.2 | 6.8 | 8.3 | 23.8 | 7.9 | 9.7 | 31.9 | 10.4 | 12.8 | 15 | 15 | 15 |
| y6 (1+) | 15.6 | 7.1 | 7 | 15.5 | 6.9 | 7.4 | 22 | 9.9 | 10.2 | 15 | 15 | 15 |
| y8 (1+) | 7.6 | 6.5 | 4.9 | 13.2 | 9.9 | 6.2 | 15.2 | 11.8 | 7.9 | 15 | 15 | 15 |
| y9 (1+) | 22.8 | 8.1 | 7.2 | 32.5 | 10.2 | 10 | 39.7 | 13 | 12.3 | 15 | 15 | 15 |
| sum | 5 | 4.1 | 3.7 | 13.7 | 6.8 | 5 | 14.6 | 7.9 | 6.2 | 15 | 15 | 15 |