A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer

Elizabeth R. Remily-Wood, Richard Z. Liu, Yun Xiang, Yi Chen, C. Eric Thomas, Neal Rajyaguru, Laura M. Kaufman, Joana E. Ochoa, Lori Hazlehurst, Javier Pinilla-Ibarz, Jeffrey Lancet, Guolin Zhang, Eric Haura, David Shibata, Timothy Yeatman, Keiran S.M. Smalley, William S. Dalton, Emina Huang, Ed Scott, Gregory C. Bloom & 2 others Steven A. Eschrich, John M. Koomen

Research output: Contribution to journalArticle

43 Citations (Scopus)

Abstract

Purpose: The Quantitative Assay Database (QuAD), facilitates widespread implementation of quantitative mass spectrometry in cancer biology and clinical research through sharing of methods and reagents for monitoring protein expression and modification. Experimental design: Liquid chromatography coupled to multiple reaction monitoring (LC-MRM) mass spectrometry assays are developed using SDS-PAGE fractionated lysates from cancer cell lines. Pathway maps created using GeneGO Metacore provide the biological relationships between proteins and illustrate concepts for multiplexed analysis; each protein can be selected to examine assay development at the protein and peptide levels. Results: The coupling of SDS-PAGE and multiple reaction monitoring mass spectrometry screening has been used to detect 876 peptides from 218 cancer-related proteins in model systems including colon, lung, melanoma, leukemias, and myeloma, which has led to the development of 95 quantitative assays including stable-isotope-labeled peptide standards. Methods are published online and peptide standards are made available to the research community. Protein expression measurements for heat shock proteins, including a comparison with ELISA and monitoring response to the HSP90 inhibitor, 17-(dimethylaminoethylamino)-17-demethoxygeldanamycin (17-DMAG), are used to illustrate the components of the QuAD and its potential utility. Conclusions and Clinical Relevance: This resource enables quantitative assessment of protein components of signaling pathways and biological processes and holds promise for systematic investigation of treatment responses in cancer.

Original languageEnglish (US)
Pages (from-to)383-396
Number of pages14
JournalProteomics - Clinical Applications
Volume5
Issue number7-8
DOIs
StatePublished - Aug 1 2011

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Mass spectrometry
Assays
Mass Spectrometry
Databases
Monitoring
Neoplasms
Proteins
Peptides
17-(dimethylaminoethylamino)-17-demethoxygeldanamycin
Therapeutics
Polyacrylamide Gel Electrophoresis
Biological Phenomena
Mass Screening
Liquid chromatography
Heat-Shock Proteins
Research
Liquid Chromatography
Isotopes
Design of experiments
Melanoma

All Science Journal Classification (ASJC) codes

  • Clinical Biochemistry

Cite this

Remily-Wood, E. R., Liu, R. Z., Xiang, Y., Chen, Y., Thomas, C. E., Rajyaguru, N., ... Koomen, J. M. (2011). A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. Proteomics - Clinical Applications, 5(7-8), 383-396. https://doi.org/10.1002/prca.201000115

A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. / Remily-Wood, Elizabeth R.; Liu, Richard Z.; Xiang, Yun; Chen, Yi; Thomas, C. Eric; Rajyaguru, Neal; Kaufman, Laura M.; Ochoa, Joana E.; Hazlehurst, Lori; Pinilla-Ibarz, Javier; Lancet, Jeffrey; Zhang, Guolin; Haura, Eric; Shibata, David; Yeatman, Timothy; Smalley, Keiran S.M.; Dalton, William S.; Huang, Emina; Scott, Ed; Bloom, Gregory C.; Eschrich, Steven A.; Koomen, John M.

In: Proteomics - Clinical Applications, Vol. 5, No. 7-8, 01.08.2011, p. 383-396.

Research output: Contribution to journalArticle

Remily-Wood, ER, Liu, RZ, Xiang, Y, Chen, Y, Thomas, CE, Rajyaguru, N, Kaufman, LM, Ochoa, JE, Hazlehurst, L, Pinilla-Ibarz, J, Lancet, J, Zhang, G, Haura, E, Shibata, D, Yeatman, T, Smalley, KSM, Dalton, WS, Huang, E, Scott, E, Bloom, GC, Eschrich, SA & Koomen, JM 2011, 'A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer', Proteomics - Clinical Applications, vol. 5, no. 7-8, pp. 383-396. https://doi.org/10.1002/prca.201000115
Remily-Wood, Elizabeth R. ; Liu, Richard Z. ; Xiang, Yun ; Chen, Yi ; Thomas, C. Eric ; Rajyaguru, Neal ; Kaufman, Laura M. ; Ochoa, Joana E. ; Hazlehurst, Lori ; Pinilla-Ibarz, Javier ; Lancet, Jeffrey ; Zhang, Guolin ; Haura, Eric ; Shibata, David ; Yeatman, Timothy ; Smalley, Keiran S.M. ; Dalton, William S. ; Huang, Emina ; Scott, Ed ; Bloom, Gregory C. ; Eschrich, Steven A. ; Koomen, John M. / A database of reaction monitoring mass spectrometry assays for elucidating therapeutic response in cancer. In: Proteomics - Clinical Applications. 2011 ; Vol. 5, No. 7-8. pp. 383-396.
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