Targeted proteomics strategy applied to biomarker evaluation

Proteomics - Clinical Applications

Volumn 7, Issue 11-12, 2013, Pages 739-747

  Kim, Yeoun Jin ^a   Gallien, Sebastien ^a   van Oostrum, Jan ^a   Domon, Bruno ^a  

^a LUXEMBOURG INSTITUTE OF HEALTH   (Luxembourg)

Author keywords

Parallel reaction monitoring; Targeted proteomics

Indexed keywords

BIOLOGICAL MARKER;

ACCURACY; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; CLINICAL EVALUATION; HIGH THROUGHPUT SCREENING; HUMAN; LIMIT OF DETECTION; LIQUID CHROMATOGRAPHY; PARALLEL REACTION MONITORING; PREDICTION; PRIORITY JOURNAL; PROCESS DESIGN; PROTEIN EXPRESSION; PROTEIN TARGETING; PROTEOMICS; SENSITIVITY AND SPECIFICITY; TANDEM MASS SPECTROMETRY; ANIMAL; MASS SPECTROMETRY; PROCEDURES;

ANIMALS; BIOLOGICAL MARKERS; HUMANS; MASS SPECTROMETRY; PROTEOMICS;

EID: 84890036668     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201300070     Document Type: Article

References (40)

1. Kohler, K., Seitz, H., Validation processes of protein biomarkers in serum: a cross platform comparison. Sensors 2012, 12, 12710-12728.
2. Huttenhain, R., Malmstrom, J., Picotti, P., Aebersold, R., Perspectives of targeted mass spectrometry for protein biomarker verification. Curr. Opin. Chem. Biol. 2009, 13, 518-525.
3. Desiderio, D. M., Kai, M., Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biologic tissue. Biomed. Mass Spectromet. 1983, 10, 471-479.
4. Gallien, S., Duriez, E., Domon, B., Selected reaction monitoring applied to proteomics. J. Mass Spectromet. 2011, 46, 298-312.
5. Domon, B., Considerations on selected reaction monitoring experiments: implications for the selectivity and accuracy of measurements. Proteomics. Clin. Appl. 2012, 6, 609-614.
6. Gallien, S., Duriez, E., Crone, C., Kellmann, M. et al., Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol. Cell. Proteomics 2012, 11, 1709-1723.
7. Mallick, P., Schirle, M., Chen, S. S., Flory, M. R. et al., Computational prediction of proteotypic peptides for quantitative proteomics. Nature Biotechnol. 2007, 25, 125-131.
8. Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3, 1234-1242.
9. Deutsch, E. W., Lam, H., Aebersold, R., PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 2008, 9, 429-434.
10. Jones, P., Cote, R. G., Cho, S. Y., Klie, S. et al., PRIDE: new developments and new datasets. Nucleic Acids Res. 2008, 36, D878-883.
11. Picotti, P., Lam, H., Campbell, D., Deutsch, E. W. et al., A database of mass spectrometric assays for the yeast proteome. Nat. Methods 2008, 5, 913-914.
12. Abbatiello, S. E., Mani, D. R., Keshishian, H., Carr, S. A., Automated detection of inaccurate and imprecise transitions in peptide quantification by multiple reaction monitoring mass spectrometry. Clin. Chem. 2010, 56, 291-305.
13. Bao, Y., Waldemarson, S., Zhang, G., Wahlander, A. et al., Detection and correction of interference in SRM analysis. Methods 2013, 61, 299-303.
14. Domanski, D., Percy, A. J., Yang, J., Chambers, A. G. et al., MRM-based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma. Proteomics 2012, 12, 1222-1243.
15. Percy, A. J., Chambers, A. G., Yang, J., Hardie, D. B., Borchers, C. H., Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility. Biochim. Biophys. Acta 2013. [Epub ahead of print]
16. Clough, T., Thaminy, S., Ragg, S., Aebersold, R., Vitek, O., Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs. BMC Bioinformat. 2012, 13(Suppl 16), S6.
17. Wei, C., Li, J., Bumgarner, R. E., Sample size for detecting differentially expressed genes in microarray experiments. BMC Genom. 2004, 5, 87.
18. Sakpal, T. V., Sample size estimation in clinical trial. Perspect. Clin. Res. 2010, 1, 67-69.
19. Gallien, S., Peterman, S., Kiyonami, R., Souady, J. et al., Highly multiplexed targeted proteomics using precise control of peptide retention time. Proteomics 2012, 12, 1122-1133.
20. Picotti, P., Aebersold, R., Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9, 555-566.
21. Percy, A. J., Chambers, A. G., Yang, J., Borchers, C. H., Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma. Proteomics 2013, 13, 2202-2215.
22. Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K. et al., High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 2007, 6, 1809-1817.
23. Karakiewicz, P. I., Aprikian, A. G., Prostate cancer: 5. Diagnostic tools for early detection. Can. Med. Assoc. J. 1998, 159, 1139-1146.
24. Anderson, L., Hunter, C. L., Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 2006, 5, 573-588.
25. Klaassen, T., Szwandt, S., Kapron, J. T., Roemer, A., Validated quantitation method for a peptide in rat serum using liquid chromatography/high-field asymmetric waveform ion mobility spectrometry. Rapid Commun. Mass spectrometr. 2009, 23, 2301-2306.
26. Kolakowski, B. M., Mester, Z., Review of applications of high-field asymmetric waveform ion mobility spectrometry (FAIMS) and differential mobility spectrometry (DMS). Analyst 2007, 132, 842-864.
27. Ting, L., Rad, R., Gygi, S. P., Haas, W., MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat. Methods 2011, 8, 937-940.
28. Gallart-Ayala, H., Moyano, E., Galceran, M. T., Liquid chromatography/tandem mass spectrometry (highly selective selected reaction monitoring) for the analysis of isopropylthioxanthone in packaged food. J. Chromatograph A 2008, 1208, 182-188.
29. Michalski, A., Damoc, E., Hauschild, J. P., Lange, O. et al., Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 2011, 10, M111 011015.
30. Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., Coon, J. J., Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics. Mol. Cell. Proteomics 2012, 11, 1475-1488.
31. Gallien, S., Duriez, E., Demeure, K., Domon, B., Selectivity of LC-MS/MS analysis: implication for proteomics experiments. J. Proteomics 2013, 81, 148-158.
32. Gillet, L. C., Navarro, P., Tate, S., Rost, H. et al., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 2012, 11, O111 016717.
33. Venable, J. D., Dong, M. Q., Wohlschlegel, J., Dillin, A., Yates, J. R., Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 2004, 1, 39-45.
34. Liu, Y., Huttenhain, R., Surinova, S., Gillet, L. C. et al., Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 2013, 13, 1247-1256.
35. Krokhin, O. V., Craig, R., Spicer, V., Ens, W. et al., An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol. Cell. Proteomics 2004, 3, 908-919.
36. Percy, A. J., Chambers, A. G., Yang, J., Domanski, D., Borchers, C. H., Comparison of standard- and nano-flow liquid chromatography platforms for MRM-based quantitation of putative plasma biomarker proteins. Anal. Bioanal. Chem. 2012, 404, 1089-1101.
37. Meierhofer, D., Weidner, C., Hartmann, L., Mayr, J. A. et al., Protein sets define disease states and predict in vivo effects of drug treatment. Mol. Cell. Proteomics 2013, 12, 1965-1979.
38. Kim, Y. J., Zaidi-Ainouch, Z., Gallien, S., Domon, B., Mass spectrometry-based detection and quantification of plasma glycoproteins using selective reaction monitoring. Nat. Protocols 2012, 7, 859-871.
39. Gillette, M. A., Carr, S. A., Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry. Nat. Methods 2013, 10, 28-34.
40. Lopez, M. F., Rezai, T., Sarracino, D. A., Prakash, A. et al., Selected reaction monitoring-mass spectrometric immunoassay responsive to parathyroid hormone and related variants. Clin. Chem. 2010, 56, 281-290.