Restructuring Proteomics Through Verification

Overview

Journal Biomark Med

Specialties Biochemistry
General Medicine

Date 2010 Dec 8

PMID 21133699

Citations 7

Authors

Emily Boja

Robert Rivers

Christopher Kinsinger

Mehdi Mesri

Tara Hiltke

Amir Rahbar

Henry Rodriguez

Affiliations

Soon will be listed here.

Abstract

Proteomics technologies have revolutionized cell biology and biochemistry by providing powerful new tools to characterize complex proteomes, multiprotein complexes and post-translational modifications. Although proteomics technologies could address important problems in clinical and translational cancer research, attempts to use proteomics approaches to discover cancer biomarkers in biofluids and tissues have been largely unsuccessful and have given rise to considerable skepticism. The National Cancer Institute has taken a leading role in facilitating the translation of proteomics from research to clinical application, through its Clinical Proteomic Technologies for Cancer. This article highlights the building of a more reliable and efficient protein biomarker development pipeline that incorporates three steps: discovery, verification and qualification. In addition, we discuss the merits of multiple reaction monitoring mass spectrometry, a multiplex targeted proteomics platform, which has emerged as a potentially promising, high-throughput protein biomarker measurements technology for preclinical 'verification'.

Citing Articles

Mass spectrometry-assisted gel-based proteomics in cancer biomarker discovery: approaches and application.

Huang R, Chen Z, He L, He N, Xi Z, Li Z Theranostics. 2017; 7(14):3559-3572.

PMID: 28912895 PMC: 5596443. DOI: 10.7150/thno.20797.

The Role of Proteomics in Biomarker Development for Improved Patient Diagnosis and Clinical Decision Making in Prostate Cancer.

Tonry C, Leacy E, Raso C, Finn S, Armstrong J, Pennington S Diagnostics (Basel). 2016; 6(3).

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Measurement of glycosylated alpha-fetoprotein improves diagnostic power over the native form in hepatocellular carcinoma.

Kim H, Kim K, Jin J, Park J, Yu S, Yoon J PLoS One. 2014; 9(10):e110366.

PMID: 25310463 PMC: 4195728. DOI: 10.1371/journal.pone.0110366.

Proteogenomic convergence for understanding cancer pathways and networks.

Boja E, Rodriguez H Clin Proteomics. 2014; 11(1):22.

PMID: 24994965 PMC: 4067069. DOI: 10.1186/1559-0275-11-22.

Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens.

Prieto D, Johann Jr D, Wei B, Ye X, Chan K, Nissley D Biomark Med. 2014; 8(2):269-86.

PMID: 24521024 PMC: 4201940. DOI: 10.2217/bmm.13.101.

References

Levin Y, Schwarz E, Wang L, Leweke F, Bahn S . Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples. J Sep Sci. 2007; 30(14):2198-203. DOI: 10.1002/jssc.200700189. View

Lee J, Soper S, Murray K . Microfluidic chips for mass spectrometry-based proteomics. J Mass Spectrom. 2009; 44(5):579-93. DOI: 10.1002/jms.1585. View

Regnier F, Skates S, Mesri M, Rodriguez H, Tezak Z, Kondratovich M . Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin Chem. 2009; 56(2):165-71. DOI: 10.1373/clinchem.2009.140087. View

Anderson L . Candidate-based proteomics in the search for biomarkers of cardiovascular disease. J Physiol. 2004; 563(Pt 1):23-60. PMC: 1665562. DOI: 10.1113/jphysiol.2004.080473. View

Addona T, Abbatiello S, Schilling B, Skates S, Mani D, Bunk D . Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat Biotechnol. 2009; 27(7):633-41. PMC: 2855883. DOI: 10.1038/nbt.1546. View

Rodriguez H, Tezak Z, Mesri M, Carr S, Liebler D, Fisher S . Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin Chem. 2009; 56(2):237-43. DOI: 10.1373/clinchem.2009.136416. View

Workman P . Strategies for treating cancers caused by multiple genome abnormalities: from concepts to cures?. Curr Opin Investig Drugs. 2004; 4(12):1410-5. View

Anderson N, Anderson N, Haines L, Hardie D, Olafson R, Pearson T . Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J Proteome Res. 2004; 3(2):235-44. DOI: 10.1021/pr034086h. View

Etzioni R, Urban N, Ramsey S, McIntosh M, Schwartz S, Reid B . The case for early detection. Nat Rev Cancer. 2003; 3(4):243-52. DOI: 10.1038/nrc1041. View

10.

Hoofnagle A, Becker J, Wener M, Heinecke J . Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin Chem. 2008; 54(11):1796-804. PMC: 2739673. DOI: 10.1373/clinchem.2008.109652. View

11.

Kuhn E, Addona T, Keshishian H, Burgess M, Mani D, Lee R . Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin Chem. 2009; 55(6):1108-17. PMC: 2865473. DOI: 10.1373/clinchem.2009.123935. View

12.

Nibbe R, Chance M . Approaches to biomarkers in human colorectal cancer: looking back, to go forward. Biomark Med. 2010; 3(4):385-396. PMC: 2749258. DOI: 10.2217/BMM.09.33. View

13.

Ramachandran N, Raphael J, Hainsworth E, Demirkan G, Fuentes M, Rolfs A . Next-generation high-density self-assembling functional protein arrays. Nat Methods. 2008; 5(6):535-8. PMC: 3070491. DOI: 10.1038/nmeth.1210. View

14.

Garcia-Foncillas J, Bandres E, Zarate R, Remirez N . Proteomic analysis in cancer research: potential application in clinical use. Clin Transl Oncol. 2006; 8(4):250-61. DOI: 10.1007/BF02664935. View

15.

Wang H, Wong C, Chin A, Kennedy J, Zhang Q, Hanash S . Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS. J Proteome Res. 2009; 8(12):5412-22. PMC: 4684172. DOI: 10.1021/pr900158n. View

16.

Anderson L, Hunter C . Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol Cell Proteomics. 2005; 5(4):573-88. DOI: 10.1074/mcp.M500331-MCP200. View

17.

Polanski M, Anderson N . A list of candidate cancer biomarkers for targeted proteomics. Biomark Insights. 2009; 1:1-48. PMC: 2716785. View

18.

Jolly Graham A, Potti A . Translating genomics into clinical practice: applications in lung cancer. Curr Oncol Rep. 2009; 11(4):263-8. DOI: 10.1007/s11912-009-0037-z. View

19.

Makawita S, Diamandis E . The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin Chem. 2009; 56(2):212-22. DOI: 10.1373/clinchem.2009.127019. View

20.

Rifai N, Gillette M, Carr S . Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat Biotechnol. 2006; 24(8):971-83. DOI: 10.1038/nbt1235. View