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Journal of Biomedicine and Biotechnology
Volume 2010 (2010), Article ID 840518, 6 pages
http://dx.doi.org/10.1155/2010/840518
Review Article

Mass Spectrometry-Based Label-Free Quantitative Proteomics

1Center on Proteolytic Pathways, Burnham Institute for Medical Research, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
2Department of Dermatology, University of California, San Diego, CA 92093, USA

Received 1 July 2009; Accepted 1 September 2009

Academic Editor: Pieter C. Dorrestein

Copyright © 2010 Wenhong Zhu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. B. F. Cravatt, G. M. Simon, and J. R. Yates III, “The biological impact of mass-spectrometry-based proteomics,” Nature, vol. 450, no. 7172, pp. 991–1000, 2007. View at Publisher · View at Google Scholar · View at Scopus
  2. R. Aebersold and M. Mann, “Mass spectrometry-based proteomics,” Nature, vol. 422, no. 6928, pp. 198–207, 2003. View at Publisher · View at Google Scholar · View at Scopus
  3. H. J. Issaq and T. D. Veenstra, “Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives,” BioTechniques, vol. 44, no. 5, pp. 697–700, 2008. View at Publisher · View at Google Scholar · View at Scopus
  4. T. Kondo, “Tissue proteomics for cancer biomarker development: laser microdissection and 2D-DIGE,” Journal of Biochemistry and Molecular Biology, vol. 41, no. 9, pp. 626–634, 2008. View at Google Scholar · View at Scopus
  5. A. Motoyama and J. R. Yates III, “Multidimensional LC separations in shotgun proteomics,” Analytical Chemistry, vol. 80, no. 19, pp. 7187–7193, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. B. Domon and R. Aebersold, “Mass spectrometry and protein analysis,” Science, vol. 312, no. 5771, pp. 212–217, 2006. View at Publisher · View at Google Scholar · View at Scopus
  7. E. I. Chen and J. R. Yates III, “Cancer proteomics by quantitative shotgun proteomics,” Molecular Oncology, vol. 1, no. 2, pp. 144–159, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. T. D. Veenstra, “Global and targeted quantitative proteomics for biomarker discovery,” Journal of Chromatography B, vol. 847, no. 1, pp. 3–11, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. V. J. Patel, K. Thalassinos, S. E. Slade et al., “A comparison of labeling and label-free mass spectrometry-based proteomics approaches,” Journal of Proteome Research, vol. 8, no. 7, pp. 3752–3759, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. A. H. P. America and J. H. G. Cordewener, “Comparative LC-MS: a landscape of peaks and valleys,” Proteomics, vol. 8, no. 4, pp. 731–749, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. W. M. Old, K. Meyer-Arendt, L. Aveline-Wolf et al., “Comparison of label-free methods for quantifying human proteins by shotgun proteomics,” Molecular and Cellular Proteomics, vol. 4, no. 10, pp. 1487–1502, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. R. D. Voyksner and H. Lee, “Investigating the use of an octupole ion guide for ion storage and high-pass mass filtering to improve the quantitative performance of electrospray ion trap mass spectrometry,” Rapid Communications in Mass Spectrometry, vol. 13, no. 14, pp. 1427–1437, 1999. View at Publisher · View at Google Scholar · View at Scopus
  13. D. Chelius and P. V. Bondarenko, “Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry,” Journal of Proteome Research, vol. 1, no. 4, pp. 317–323, 2002. View at Publisher · View at Google Scholar · View at Scopus
  14. P. V. Bondarenko, D. Chelius, and T. A. Shaler, “Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry,” Analytical Chemistry, vol. 74, no. 18, pp. 4741–4749, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. M. C. Wiener, J. R. Sachs, E. G. Deyanova, and N. A. Yates, “Differential mass spectrometry: a label-free LC-MS method for finding significant differences in complex peptide and protein mixtures,” Analytical Chemistry, vol. 76, no. 20, pp. 6085–6096, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. W. Wang, H. Zhou, H. Lin et al., “Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards,” Analytical Chemistry, vol. 75, no. 18, pp. 4818–4826, 2003. View at Publisher · View at Google Scholar · View at Scopus
  17. R. E. Higgs, M. D. Knierman, V. Gelfanova, J. P. Butler, and J. E. Hale, “Comprehensive label-free method for the relative quantification of proteins from biological samples,” Journal of Proteome Research, vol. 4, no. 4, pp. 1442–1450, 2005. View at Publisher · View at Google Scholar · View at Scopus
  18. J. Lengqvist, J. Andrade, Y. Yang, G. Alvelius, R. Lewensohn, and J. Lehtiö, “Robustness and accuracy of high speed LC-MS separations for global peptide quantitation and biomarker discovery,” Journal of Chromatography B, vol. 877, no. 13, pp. 1306–1316, 2009. View at Publisher · View at Google Scholar · View at Scopus
  19. N. Fatima, D. Chelius, B. T. Luke et al., “Label-free global serum proteomic profiling reveals novel celecoxib-modulated proteins in familial adenomatous polyposis patients,” Cancer Genomics and Proteomics, vol. 6, no. 1, pp. 41–49, 2009. View at Google Scholar · View at Scopus
  20. S. K. Huang, M. M. Darfler, M. B. Nicholl et al., “LC/MS-based quantitative proteomic analysis of paraffin-embedded archival melanomas reveals potential proteomic biomarkers associated with metastasis,” PLoS ONE, vol. 4, no. 2, article e4430, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Levin, E. Schwarz, L. Wang, F. M. Leweke, and S. Bahn, “Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples,” Journal of Separation Science, vol. 30, no. 14, pp. 2198–2203, 2007. View at Publisher · View at Google Scholar · View at Scopus
  22. J. P. C. Vissers, J. I. Langridge, and J. M. F. G. Aerts, “Analysis and quantification of diagnostic serum markers and protein signaturs for Gaucher disease,” Molecular and Cellular Proteomics, vol. 6, no. 5, pp. 755–766, 2007. View at Publisher · View at Google Scholar · View at Scopus
  23. J. T.-J. Huang, T. McKenna, C. Hughes, F. M. Leweke, E. Schwarz, and S. Bahn, “CSF biomarker discovery using label-free nano-LC-MS based proteomic profiling: technical aspects,” Journal of Separation Science, vol. 30, no. 2, pp. 214–225, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. M. P. Washburn, D. Wolters, and J. R. Yates III, “Large-scale analysis of the yeast proteome by multidimensional protein identification technology,” Nature Biotechnology, vol. 19, no. 3, pp. 242–247, 2001. View at Publisher · View at Google Scholar · View at Scopus
  25. H. Liu, R. G. Sadygov, and J. R. Yates III, “A model for random sampling and estimation of relative protein abundance in shotgun proteomics,” Analytical Chemistry, vol. 76, no. 14, pp. 4193–4201, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. B. Zybailov, M. K. Coleman, L. Florens, and M. P. Washburn, “Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling,” Analytical Chemistry, vol. 77, no. 19, pp. 6218–6224, 2005. View at Publisher · View at Google Scholar · View at Scopus
  27. M.-Q. Dong, J. D. Venable, N. Au et al., “Quantitative mass spectrometry identifies insulin signaling targets in C. elegans,” Science, vol. 317, no. 5838, pp. 660–663, 2007. View at Publisher · View at Google Scholar · View at Scopus
  28. B. Zybailov, A. L. Mosley, M. E. Sardiu, M. K. Coleman, L. Florens, and M. P. Washburn, “Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae,” Journal of Proteome Research, vol. 5, no. 9, pp. 2339–2347, 2006. View at Publisher · View at Google Scholar · View at Scopus
  29. L. Florens, M. J. Carozza, S. K. Swanson et al., “Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors,” Methods, vol. 40, no. 4, pp. 303–311, 2006. View at Publisher · View at Google Scholar · View at Scopus
  30. A. C. Paoletti, T. J. Parmely, C. Tomomori-Sato et al., “Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 50, pp. 18928–18933, 2006. View at Publisher · View at Google Scholar · View at Scopus
  31. B. Zhang, N. C. VerBerkmoes, M. A. Langston, E. Uberbacher, R. L. Hettich, and N. F. Samatova, “Detecting differential and correlated protein expression in label-free shotgun proteomics,” Journal of Proteome Research, vol. 5, no. 11, pp. 2909–2918, 2006. View at Publisher · View at Google Scholar · View at Scopus
  32. J. X. Pang, N. Ginanni, A. R. Dongre, S. A. Hefta, and G. J. Opiteck, “Biomarker discovery in urine by proteomics,” Journal of Proteome Research, vol. 1, no. 2, pp. 161–169, 2002. View at Publisher · View at Google Scholar · View at Scopus
  33. P. V. Rao, A. P. Reddy, X. Lu et al., “Proteomic identification of salivary biomarkers of type-2 diabetes,” Journal of Proteome Research, vol. 8, no. 1, pp. 239–245, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. J. Pan, H.-Q. Chen, Y.-H. Sun, J.-H. Zhang, and X.-Y. Luo, “Comparative proteomic analysis of non-small-cell lung cancer and normal controls using serum label-free quantitative shotgun technology,” Lung, vol. 186, no. 4, pp. 255–261, 2008. View at Publisher · View at Google Scholar · View at Scopus
  35. J. M. Asara, H. R. Christofk, L. M. Freimark, and L. C. Cantley, “A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen,” Proteomics, vol. 8, no. 5, pp. 994–999, 2008. View at Publisher · View at Google Scholar · View at Scopus
  36. N. T. Seyfried, L. C. Huysentruyt, J. A. Atwood III, Q. Xia, T. N. Seyfried, and R. Orlando, “Up-regulation of NG2 proteoglycan and interferon-induced transmembrane proteins 1 and 3 in mouse astrocytoma: a membrane proteomics approach,” Cancer Letters, vol. 263, no. 2, pp. 243–252, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. J. Rappsilber, U. Ryder, A. I. Lamond, and M. Mann, “Large-scale proteomic analysis of the human spliceosome,” Genome Research, vol. 12, no. 8, pp. 1231–1245, 2002. View at Publisher · View at Google Scholar · View at Scopus
  38. Y. Ishihama, Y. Oda, T. Tabata et al., “Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein,” Molecular and Cellular Proteomics, vol. 4, no. 9, pp. 1265–1272, 2005. View at Publisher · View at Google Scholar · View at Scopus
  39. P. Lu, C. Vogel, R. Wang, X. Yao, and E. M. Marcotte, “Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation,” Nature Biotechnology, vol. 25, no. 1, pp. 117–124, 2007. View at Publisher · View at Google Scholar · View at Scopus
  40. J. C. Braisted, S. Kuntumalla, C. Vogel et al., “The APEX quantitative proteomics tool: generating protein quantitation estimates from LC-MS/MS proteomics results,” BMC Bioinformatics, vol. 9, article 529, 2008. View at Publisher · View at Google Scholar · View at Scopus
  41. L. N. Mueller, M.-Y. Brusniak, D. R. Mani, and R. Aebersold, “An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data,” Journal of Proteome Research, vol. 7, no. 1, pp. 51–61, 2008. View at Publisher · View at Google Scholar · View at Scopus
  42. U. Rajcevic, S. P. Niclou, and C. R. Jimenez, “Proteomics strategies for target identification and biomarker discovery in cancer,” Frontiers in Bioscience, vol. 14, pp. 3292–3303, 2009. View at Google Scholar · View at Scopus
  43. H. Neubert, T. P. Bonnert, K. Rumpel, B. T. Hunt, E. S. Henle, and I. T. Lames, “Label-free detection of differential protein expression by LC/MALDI mass spectrometry,” Journal of Proteome Research, vol. 7, no. 6, pp. 2270–2279, 2008. View at Publisher · View at Google Scholar · View at Scopus