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Theme: Pharmacogenomic, Proteomic & Metabolomic Applications - Special Report

The current status of clinical proteomics and the use of MRM and MRM3 for biomarker validation

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Pages 333-342 | Published online: 09 Jan 2014

References

  • Gold P, Freedman SO. Demonstration of tumor-specific antigens in human colonic carcinomata by immunological tolerance and absorption techniques. J. Exp. Med.121, 439–462 (1965).
  • McIntire KR, Vogel CL, Princler GL, Patel IR. Serum alpha-fetoprotein as a biochemical marker for hepatocellular carcinoma. Cancer Res.32(9), 1941–1946 (1972).
  • Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin. Chem.56(2), 177–185 (2010).
  • Hellstrom I, Raycraft J, Hayden-Ledbetter M et al. The HE4 (WFDC2) protein is a biomarker for ovarian carcinoma. Cancer Res.63(13), 3695–3700 (2003).
  • Zhang Z, Bast RC Jr, Yu Y et al. Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer. Cancer Res.64(16), 5882–5890 (2004).
  • Fung ET. A recipe for proteomics diagnostic test development: the OVA1 test, from biomarker discovery to FDA clearance. Clin. Chem.56(2), 327–329 (2010).
  • Boja E, Rivers R, Kinsinger C et al. Restructuring proteomics through verification. Biomark. Med.4(6), 799–803 (2010).
  • Whiteaker JR, Lin C, Kennedy J et al. A targeted proteomics-based pipeline for verification of biomarkers in plasma. Nat. Biotechnol.29(7), 625–634 (2011).
  • Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol.24(8), 971–983 (2006).
  • Regnier FE, Skates SJ, Mesri M et al. Protein-based multiplex assays: mock presubmissions to the US Food and Drug Administration. Clin. Chem.56(2), 165–171 (2010).
  • Makawita S, Diamandis EP. The bottleneck in the cancer biomarker pipeline and protein quantification through mass spectrometry-based approaches: current strategies for candidate verification. Clin. Chem.56(2), 212–222 (2010).
  • Prakash C, Shaffer CL, Nedderman A. Analytical strategies for identifying drug metabolites. Mass Spectrom. Rev.26(3), 340–369 (2007).
  • Xu RN, Fan L, Rieser MJ, El-Shourbagy TA. Recent advances in high-throughput quantitative bioanalysis by LC–MS/MS. J. Pharm. Biomed. Anal.44(2), 342–355 (2007).
  • Thevis M, Thomas A, Schanzer W. Current role of LC–MS(/MS) in doping control. Anal. Bioanal. Chem.401(2), 405–420 (2011).
  • Petrovic M, Farre M, de Alda ML et al. Recent trends in the liquid chromatography–mass spectrometry analysis of organic contaminants in environmental samples. J. Chromatogr. A1217(25), 4004–4017 (2010).
  • Peters FT. Recent advances of liquid chromatography–(tandem) mass spectrometry in clinical and forensic toxicology. Clin. Biochem.44(1), 54–65 (2011).
  • Zhong D, Chen X, Gu J, Li X, Guo J. Applications of liquid chromatography–tandem mass spectrometry in drug and biomedical analyses. Clin. Chim. Acta313(1–2), 147–150 (2001).
  • Carrascal M, Schneider K, Calaf RE et al. Quantitative electrospray LC–MS and LC–MS/MS in biomedicine. J. Pharm. Biomed. Anal.17(6–7), 1129–1138 (1998).
  • Fu Q, Schoenhoff FS, Savage WJ, Zhang P, Van Eyk JE. Multiplex assays for biomarker research and clinical application: translational science coming of age. Proteomics Clin. Appl.4(3), 271–284 (2010).
  • Meng Z, Veenstra TD. Targeted mass spectrometry approaches for protein biomarker verification. J. Proteomics74(12), 2650–2659 (2011).
  • Dupuis A, Hennekinne JA, Garin J, Brun V. Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks. Proteomics8(22), 4633–4636 (2008).
  • Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods2(8), 587–589 (2005).
  • Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl Acad. Sci. USA100(12), 6940–6945 (2003).
  • Brownridge P, Holman SW, Gaskell SJ et al. Global absolute quantification of a proteome: challenges in the deployment of a QconCAT strategy. Proteomics11(15), 2957–2970 (2011).
  • Southworth PM, Hyde JE, Sims PF. A mass spectrometric strategy for absolute quantification of Plasmodium falciparum proteins of low abundance. Malar. J.10, 315 (2011).
  • Mayya V, Rezual K, Wu L, Fong MB, Han DK. Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol. Cell. Proteomics5(6), 1146–1157 (2006).
  • Wang Q, Chaerkady R, Wu J et al. Mutant proteins as cancer-specific biomarkers. Proc. Natl Acad. Sci. USA108(6), 2444–2449 (2011).
  • Anderson L, Hunter CL. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics5(4), 573–588 (2006).
  • Lim SL, Ichinose H, Shinoda T, Ueda H. Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay. Anal. Chem.79(16), 6193–6200 (2007).
  • Lin S, Shaler TA, Becker CH. Quantification of intermediate-abundance proteins in serum by multiple reaction monitoring mass spectrometry in a single-quadrupole ion trap. Anal. Chem.78(16), 5762–5767 (2006).
  • Kuzyk MA, Smith D, Yang J et al. Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma. Mol. Cell. Proteomics8(8), 1860–1877 (2009).
  • Kiyonami R, Schoen A, Prakash A et al. Increased selectivity, analytical precision, and throughput in targeted proteomics. Mol. Cell. Proteomics10(2), M110 (2011).
  • Agger SA, Marney LC, Hoofnagle AN. Simultaneous quantification of apolipoprotein A-I and apolipoprotein B by liquid-chromatography–multiple-reaction-monitoring mass spectrometry. Clin. Chem.56(12), 1804–1813 (2010).
  • Keshishian H, Addona T, Burgess M, Kuhn E, Carr SA. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics6(12), 2212–2229 (2007).
  • Fortin T, Salvador A, Charrier JP et al. Clinical quantitation of prostate-specific antigen biomarker in the low nanogram/milliliter range by conventional bore liquid chromatography–tandem mass spectrometry (multiple reaction monitoring) coupling and correlation with ELISA tests. Mol. Cell. Proteomics8(5), 1006–1015 (2009).
  • Kulasingam V, Smith CR, Batruch I et al. “Product ion monitoring” assay for prostate-specific antigen in serum using a linear ion-trap. J. Proteome Res.7(2), 640–647 (2008).
  • Kuhn E, Addona T, Keshishian H et al. Developing multiplexed assays for troponin I and interleukin-33 in plasma by peptide immunoaffinity enrichment and targeted mass spectrometry. Clin. Chem.55(6), 1108–1117 (2009).
  • Hoofnagle AN, Becker JO, Wener MH, Heinecke JW. Quantification of thyroglobulin, a low-abundance serum protein, by immunoaffinity peptide enrichment and tandem mass spectrometry. Clin. Chem.54(11), 1796–1804 (2008).
  • Anderson NL, Anderson NG, Haines LR et al. Mass spectrometric quantitation of peptides and proteins using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Proteome. Res.3(2), 235–244 (2004).
  • Whiteaker JR, Zhao L, Anderson L, Paulovich AG. An automated and multiplexed method for high throughput peptide immunoaffinity enrichment and multiple reaction monitoring mass spectrometry-based quantification of protein biomarkers. Mol. Cell. Proteomics9(1), 184–196 (2010).
  • Kuhn E, Whiteaker JR, Mani DR et al. Inter-laboratory evaluation of automated, multiplexed peptide immunoaffinity enrichment coupled to multiple reaction monitoring mass spectrometry for quantifying proteins in plasma. Mol. Cell. Proteomics doi:10.1074/mcp.M111.013854 (2011) (Epub ahead of print).
  • Anderson NL, Anderson NG, Pearson TW et al. A human proteome detection and quantitation project. Mol. Cell. Proteomics8(5), 883–886 (2009).
  • Fortin T, Salvador A, Charrier JP et al. Multiple reaction monitoring cubed for protein quantification at the low nanogram/milliliter level in nondepleted human serum. Anal. Chem.81(22), 9343–9352 (2009).
  • Mollah S, Chisholm J, Mollova N, Leung K, Bramwell-German C. Probing mass spectrometric strategies for high sensitivity quantitation of clinically relevant peptides. (519). Presented at: 59th ASMS Conference on Mass Spectrometry and Allied Topics. Denver, CO, USA, 5–9 June 2011.
  • Kusebauch U, Hunter CL, Aebersold R, Moritz RL. Improving selectivity using MRM3 quantitation for the definitive detection of human protein kinases. (169). Presented at: 58th ASMS Conference on Mass Spectrometry and Allied Topics. Salt Lake City, UT, USA, 23–27 May 2010.
  • Ceglarek U, Wielsch N, Dojahn J et al. Comparing multiple strategies for targeted protein quantitation in human serum. (184). Presented at: 58th ASMS Conference on Mass Spectrometry and Allied Topics. Salt Lake City, UT, USA, 23–27 May 2010.
  • Geyer R, Besa A, Lenz CE. LC-MRM3 and LC-MS3: alternative strategies for highly selective quantitation and for sensitive additional structural elucidation. (641). Presented at: 58th ASMS Conference on Mass Spectrometry and Allied Topics. Salt Lake City, UT, USA, 23–27 May 2010.
  • Fortin T, Salvador A, Charrier JP, Choquet-Kastylevsky G, Lemoine J. Peptide choice for MRM3 quatification in clinical evaluation of biomarkers. (232). Presented at: 58th ASMS Conference on Mass Spectrometry and Allied Topics. Salt Lake City, UT, USA, 23–27 May 2010.
  • Fortin T, Charrier JP, Lemoine A et al. Biomarker validation for colorectal cancer screening using SRM and MRM3 and correlation with ELISA test. (HUPO11–3458). Presented at: HUPO 10th Annual World Congress. Geneva, Switzerland, 4–7 September 2011.
  • Pucci V, Bonelli F, Monteagudo E, Laufer R. Enhanced mass resolution method development, validation and assay application to support preclinical studies of a new drug candidate. Rapid Commun. Mass Spectrom.20(8), 1240–1246 (2006).
  • Jemal M, Ouyang Z, Zhao W, Zhu M, Wu WW. A strategy for metabolite identification using triple-quadrupole mass spectrometry with enhanced resolution and accurate mass capability. Rapid Commun. Mass Spectrom.17(24), 2732–2740 (2003).
  • Klaassen T, Szwandt S, Kapron JT, Roemer A. Validated quantitation method for a peptide in rat serum using liquid chromatography/high-field asymmetric waveform ion mobility spectrometry. Rapid Commun. Mass Spectrom.23(15), 2301–2306 (2009).
  • Xia YQ, Wu ST, Jemal M. LC–FAIMS-MS/MS for quantification of a peptide in plasma and evaluation of FAIMS global selectivity from plasma components. Anal. Chem.80(18), 7137–7143 (2008).
  • Addona TA, Abbatiello SE, Schilling B et al. Multi-site assessment of the precision and reproducibility of multiple reaction monitoring-based measurements of proteins in plasma. Nat. Biotechnol.27(7), 633–641 (2009).
  • Prakash A, Rezai T, Krastins B et al. Platform for establishing interlaboratory reproducibility of selected reaction monitoring-based mass spectrometry peptide assays. J. Proteome Res.9(12), 6678–6688 (2010).
  • Yocum AK, Khan AP, Zhao R, Chinnaiyan AM. Development of selected reaction monitoring-MS methodology to measure peptide biomarkers in prostate cancer. Proteomics10(19), 3506–3514 (2010).
  • Garcia-Bailo B, Brenner DR, Nielsen D et al. Dietary patterns and ethnicity are associated with distinct plasma proteomic groups. Am. J. Clin. Nutr.95(2), 352–361 (2012).
  • Proc JL, Kuzyk MA, Hardie DB et al. A quantitative study of the effects of chaotropic agents, surfactants, and solvents on the digestion efficiency of human plasma proteins by trypsin. J. Proteome Res.9(10), 5422–5437 (2010).
  • Reiter l, Rinner O, Picotti P et al. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods8(5), 430–435 (2012).
  • Stahl-Zeng J, Lange V, Ossola R et al. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics6(10), 1809–1817 (2007).
  • Rodriguez H, Tezak Z, Mesri M et al. Analytical validation of protein-based multiplex assays: a workshop report by the NCI-FDA interagency oncology task force on molecular diagnostics. Clin. Chem.56(2), 237–243 (2010).
  • Boja ES, Jortani SA, Ritchie J et al. The journey to regulation of protein-based multiplex quantitative assays. Clin. Chem.57(4), 560–567 (2011).
  • van Belkum BA, Welker M, Erhard M, Chatellier S. Biomedical mass spectrometry in today’s and tomorrow’s clinical microbiology laboratory. J. Clin. Microbiol. doi: 10.1128/JCM.00420-12 (2012) (Epub ahead of print).
  • Anderson DS, Kirchner M, Kellogg M et al. Design and validation of a high-throughput matrix-assisted laser desorption ionization time-of-flight mass spectrometry method for quantification of hepcidin in human plasma. Anal. Chem.83(21), 8357–8362 (2011).
  • Reid JD, Holmes DT, Mason DR, Shah B, Borchers CH. Towards the development of an immuno MALDI (iMALDI) mass spectrometry assay for the diagnosis of hypertension. J. Am. Soc. Mass Spectrom.21(10), 1680–1686 (2010).

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