Mass spectrometry-based approaches toward absolute quantitative proteomics

Current Genomics

Volumn 9, Issue 4, 2008, Pages 263-274

  Kito, Keiji ^a   Ito, Takashi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Absolute quantification; Label free; Mass spectrometry; Quantitative proteomics; Stable isotope labeling

Indexed keywords

PROTEOME; STABLE ISOTOPE;

ACCURACY; CHEMICAL LABELING; FEASIBILITY STUDY; HUMAN; ISOTOPE LABELING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PEPTIDE ANALYSIS; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; QUANTITATIVE ANALYSIS; RELIABILITY; REVIEW; SENSITIVITY AND SPECIFICITY; SIGNAL NOISE RATIO; STOICHIOMETRY;

EID: 45749100868     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920208784533647     Document Type: Review

References (109)

1. Pandey, A., Mann, M. Proteomics to study genes and genomes. Nature 2000, 405: 837-846.
2. Aebersold, R., Goodlett, D.R. Mass spectrometry in proteomics. Chem. Rev. 2001, 101: 269-295.
3. Aebersold, R., Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422: 198-207.
4. Smith, J.C., Lambert, J.P., Elisma, F., Figeys, D. Proteomics in 2005/ 2006: developments, applications and challenges. Anal. Chem. 2007, 79: 4325-4343.
5. Cravatt, B.F., Simon, G.M., Yates, J.R., III. The biological impact of mass-spectrometry-based proteomics. Nature 2007, 450: 991-1000.
6. Washburn, M.P., Wolters, D., Yates, J.R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 2001, 19: 242-247.
7. Peng, J., Elias, J.E., Thoreen, C.C., Licklider, L.J., Gygi, S.P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. J. Proteome Res. 2003, 2: 43-50.
8. Liu, H., Sadygov, R.G., Yates, J.R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76: 4193-4201.
9. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B. Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389: 1017-1031.
10. Mueller, L.N., Brusniak, M.Y., Mani, D.R., Aebersold, R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7: 51-61.
11. Ong, S.E., Foster, L.J., Mann, M. Mass spectrometric-based approaches in quantitative proteomics. Methods 2003, 29: 124-130.
12. Sechi, S., Oda, Y. Quantitative proteomics using mass spectrometry. Curr. Opin. Chem. Biol. 2003, 7: 70-77.
13. Goshe, M.B., Smith, R.D. Stable isotope-coded proteomic mass spectrometry. Curr. Opin. Biotechnol. 2003, 14: 101-109.
14. Tao, W.A., Aebersold, R. Advances in quantitative proteomics via stable isotope tagging and mass spectrometry. Curr. Opin. Biotechnol. 2003, 14: 110-118.
15. Ong, S.E., Mann, M. Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. 2005, 1: 252-262.
16. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., Aebersold, R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17: 994-999
17. Han, D.K., Eng, J., Zhou, H., Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 2001, 19: 946-951.
18. Regnier, F.E., Julka, S. Primary antine coding as a path to comparative proteomics. Proteomics 2006, 6: 3968-3979.
19. 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal. Chem. 2001, 73: 2836-2842.
20. 18O labeling: a tool for proteomics. Rapid Commun. Mass Spectrom. 2001, 15: 2456-2465.
21. Thompson, A., Schäfer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., Johnstone, R., Mohammed, A.K., Hamon, C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75: 1895-1904.
22. Ross, P.L., Huang, Y.N., Marchese, J.N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., Pappin, D.J. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3: 1154-1169
23. Oda, Y., Huang, K., Cross, F.R., Cowburn, D., Chait, B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc. Natl. Acad. Sci. USA 1999, 96: 6591-6596.
24. Ong, S.E., Blagoev, B., Kratchmarova, I., Kristensen, D.B., Steen, H., Pandey, A., Mann, M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics. 2002, 1: 376-386.
25. Berger, S.J., Lee, S.W., Anderson, G.A., Pasa-Tolic, L., Tolic, N., Shen, Y., Zhao, R., Smith, R.D. High-throughput global peptide proteomic analysis by combining stable isotope amino acid labeling and data-dependent multiplexed-MS/MS. Anal. Chem. 2002, 74: 4994-5000.
26. Zhu, H., Pan, S., Gu,-S., Bradbury, E.M., Chen, X. Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 2002, 16: 2115-2123.
27. Krijgsveld, J.; Ketting, R.F., Mahmoudi, T., Johansen, J., Artal-Sanz M., Verrijzer, C.P., Plasterk, R-H., Heck, A.J. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat. Biotechnol. 2003, 21: 927-931.
28. Wu, C.C., MacCoss, M.J., Howell, K.E., Matthews, D.E., Yates, J.R., III. Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal. Chem. 2004, 76: 4951-4959.
29. Ishihama, Y., Sato, T., Tabata, T., Miyamoto, N., Sagane, K., Nagasu, T., Oda, Y. Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat. Biotechnol. 2005, 23: 617-621.
30. Washburn, M.P., Ulaszek, R., Deciu, C., Schieltz, D.M., Yates, J.R., III. Analysis of quantitative proteomic data generated via multidimensional protein identification technology. Anal. Chem. 2002, 74: 1650-1657.
31. Washburn, M.P., Koller, A., Oshiro, G., Ulaszek, R.R., Plouffe, D., Deciu, C., Winzeler, E., Yates, J.R., III. Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 2003, 100: 3107-3112.
32. Kolkman, A., Olsthoom, M.M., Heeremans, C.E., Heck, A.J., Slijper, M. Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Mol Cell Proteomics 2005, 4: 1 -11.
33. Kolkman, A., Daran-Lapujade, P., Fullaondo, A., Olsthoom, M.M., Pronk, J.T., Slijper, M., Heck, A.J. Proteome analysis of yeast response to various nutrient limitations. Mol Syst. Biol. 2006, 2: 2006.0026.
34. Ranish, J.A., Yi, E.C., Leslie, D.M., Purvine, S.O., Goodlett, D.R., Eng, J., Aebersold, R. The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 2003, 33: 349-355.
35. Foster, L.J., de Hong, C.L., Mann M. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. USA 2003, 100: 5813-5818.
36. Blagoev, B., Kratchmarova, I., Ong, S.E., Nielsen, M., Foster, L.J., Mann, M. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat. Biotechnol. 2003, 21: 315-318.
37. Foster, L.J., Rudich, A., Talior, I., Patel, N., Huang, X., Furtado, L.M., Bilan, P.J., Mann, M., Klip, A. Insulin-dependent interactions of proteins with GLUT4 revealed through stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2006, 5: 64-75.
38. Pflieger, D., Jüger, M.A., Müller, M., Rinner, O., Lee, H., Gehrig, P.M., Gstaiger, M., Aebersold, R. Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Mol. Cell Proteomics 2008, 7: 326-346.
39. Gingras, A.C., Gstaiger, M., Raught, B., Aebersold, R. Analysis of protein complexes using mass spectrometry. Nat. Rev. Mol. Cell Biol. 2007, 8: 645-654.
40. Yang, W., Steen, H., Freeman, M.R. Proteomic approaches to the analysis of multiprotein signaling complexes. Proteomics 2008, 8: 832-851.
41. Blagoev, B., Ong, S.E., Kratchmarova, I., Mann, M. Temporal analysis of phospholyrosine-dependent signaling networks by quantitative proteomics. Nat. Biotechnol. 2004, 22: 1139-1145.
42. Gruhler, A., Olsen, J.V., Mohammed, S., Mortensen, P., Faergeman, N.J., Mann, M., Jensen, O.N. Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway. Mol. Cell Proteomics 2005, 4: 310-327.
43. Zhang, Y., Wolf-Yadlin, A., Ross, P.L., Pappin, D.J., Rush, J., Lauffenburger, D.A., White, F.M. Time-resolved mass spectrometry of tyrosine phosphorylation sites in the epidermal growth factor receptor signaling network reveals dynamic modules. Mol. Cell Proteomics 2005, 4: 1240-1250.
44. Olsen, J.V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., Mann, M. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 2006, 127: 635-648.
45. Li, X., Gerber, S.A., Rudner, A.D., Beausoleil, S.A., Haas, W., Villén, J., Elias, J.E., Gygi, S.P. Large-scale- phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae, J. Proteome Res. 2007, 6: 1190-1197.
46. 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 Spectrom. 1983, 10: 471-479.
47. Kusmierz, J.J., Sumrada, R., Desiderio, D.M. Fast atom bombardment mass spectrometric, quantitative- analysis of methionine-enkephalin in human pituitary tissues. Anal. Chem. 1990, 62: 2395-2400.
48. Barr, J.R., Maggio, V.L., Patterson, D.G., Jr, Cooper, G.R., Henderson, L.O., Turner, W.E., Smith, S.J., Hannon, W.H., Needham, L.L., Sampson, E.I. Isotope dilution-mass spectrometric quantification of specific proteins: model application with apolipo-protein A-I. Clin. Chem. 1996, 42: 1676-1682.
49. Barnidge, D.R., Dratz, E.A., Martin, T., Bonilla, L.E., Moran, L.B., Lindall, A. Absolute quantification of the G protein-coupled receptor rhodopsin by LC/MS/MS using proteolysis product peptides and synthetic peptide standards. Anal. Chem. 2003, 75: 445-451.
50. Gerber, S.A., Rush, J., Stemman, O., Kirschner, M.W., Gygi, S.P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. USA 2003, 100: 6940-6945.
51. 135C-labeled. peptide standards. Proteomics 2004, 4: 1175-1186.
52. Zhang, F., Bartels, M.J., Stott, W.T. Quantitation of human glutathione S-transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature pcptides. Rapid Commun. Mass Spectrom. 2004, 18: 491-498.
53. Hochleitner, E.O., Kastner, B., Fröhlich, T., Schmidt, A., Lührmann, R., Arnold, G., Lottspeich, F. Protein stoichiometry of a multiprotein complex, the human spliceosomal Ul small nuclear ribonucleoprotein: absolute quantification using isotope-coded tags and mass spectrometry. J. Biol. Chem. 2005, 280: 2536-2542.
54. Pan, S., Zhang, H., Rush, J., Eng, J., Zhang, N., Patterson, D., Comb, M.J., Aebersold, R. High throughput proteome screening for biomarker detection. Mol. Cell Proteomics 2005, 4: 182-190.
55. Cheng, D., Hoogenraad, C.C., Rush, J., Ramm, E., Schlager, M.A., Duong, D.M., Xu, P., Wijayawardana, S.R., Hanfelt, J., Nakagawa, T., Sheng, M., Peng, J. Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol Cell Proteomics 2006, 5: 1158-1170.
56. Stemmann, O., Zou, H., Gerber, S.A., Gygi, S.P., Kirschner, M.W. Dual inhibition of sister chromatid separation at metaphase. Cell 2001, 107: 715-726.
57. Mayya, V., Rezual, K., Wu, L., Fong, M.B., Han, D.K. Absolute quantification of multisite phosphorylation by selective reaction monitoring mass spectrometry: determination of inhibitory phosphorylation status of cyclin-dependent kinases. Mol. Cell Proteomics 2006, 5: 1146-1157.
58. Kirkpatrick, D.S., Gerber, S.A., Gygi, S.P. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 2005, 35: 265-273.
59. Kirkpatrick, D.S., Hathaway, N.A., Hanna, J., Elsasser, S., Rush, J., Finley, D., King, R.W., Gygi, S.P. Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology. Nat. Cell Biol. 2006, 8: 700-710.
60. Appels, N.M., Rosing, H., Stephens, T.C., Hughes, A., Schellens, J.H., Beijnen, J.H. Absolute quantification of farnesylated Ras levels in complex samples using liquid chromatography fractionation combined with tryptic digestion and electrospray tandem mass spectrometry. Anal. Biochem. 2006, 352: 33-40.
61. Havlis, J., Shevchenko, A. Absolute quantification of proteins in solutions and in polyacrylamide gels by mass spectrometry. Anal. Chem. 2004, 76: 3029-3036.
62. Kippen, A.D., Cerini, F., Vadas, L., Stocklin, R., Vu, L., Offord, R.E., Rose, K. Development of an isotope dilution assay for precise determination of insulin, C-peptide, and proinsulin levels in non-diabetic and type II diabetic individuals with comparison to immunoassay. J. Biol. Chem. 1997, 272: 12513-12522.
63. Peng, J., Kim, M.J., Cheng, D., Duong, D.M., Gyji, S.P., Sheng, M. Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry. J. Mol. Chem. 2004, 279: 21003-21011
64. Janecki, D.J., Bemis, K.G., Tegeler, T.J., Sangbani, P.C., Zhai, L., Hurley, T.D., Boston, W.F., Wang, M. A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme. Anal. Biochem. 2007, 369: 18-26.
65. Brun, V., Dupuis, A., Adrait, A., Marcellin, M., Thomas, D., Court, M., Vandenesch, F., Garin, J. Isotope-labeled protein standards: toward absolute quantitative proteomics. Mol. Cell Proteomics 2007, 6: 2139-2149.
66. Beynon, R.J., Doherty, M.K., Pratt, J.M., Gaskell, S.J. Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods 2005, 2: 587-589.
67. Kito, K., Ota, K., Fujita, T., Ito, T. A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes. J. Proteome Res. 2007, 6: 792-800.
68. Rivers, J., Simpson, D.M., Robertson, D.H., Gaskell, S.J., Beynon, R.J. Absolute multiplexed quantitative analysis of protein expression during muscle development using QconCAT. Mol. Cell Proteomics 2007, 6: 1416-1427.
69. Anderson, L., Hunter, C.L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell Proteomics 2006, 5: 573-588.
70. Yen, C.Y., Russell, S., Mendoza, A.M., Meyer-Arendt, K., Sun, S., Cios, K.J., Alm, N.G., Resing, K.A. Improving sensitivity in shotgun proteomics using a peptide-centric database with reduced complexity: protease cleavage and SCX elution rules from data mining of MS/MS spectra. Anal. Chem. 2006, 78: 1071-1084.
71. Siepen, J.A., Keevil, E.J., Knight D., Hubbard, S.J. Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics. J. Proteome Res. 2007, 6: 399-408.
72. Nanavati, D., Gucek, M., Milne, J.L., Subramaniam, S., Markey, S.P. Stoichiometry and absolute quantification of proteins with mass spectrometry using fluorescent and isotope-labelod concatenated peptide standards. Mol. Cell Proteomics 2008, 7: 442-447.
73. Mirzaei, H., McBee, J., Watts, J., Aebersold, R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol. Cell Proteomics 2007, 7: 813-823.
74. Old, W.M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K.G., Mendoza, A., Sevinsky, J.R., Resing, K.A., Alan, N.G. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 2005, 4: 1487-1502.
75. Wang, G., Wu, W.W., Zeng, W., Chou, C.L., Shen, R.F. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J. Proteome Res. 2006, 5: 1214-1223.
76. Andersen, J.S., Wilkinson, C.J., Mayor, T., Mortensen, P., Nigg, E.A., Mann, M. Proteomic characterization of the human centro-some by protein correlation profiling. Nature 2003, 426: 570-574.
77. Rinner, O., Mueller, L.N., Hubilek, M., Müller, M., Gstaiger, M., Aebersold, R. An integrated mass spectrometric and computational framework for the analysis of protein interaction networks. Nat. Biotechnol. 2007, 25: 345-352.
78. Kim, Y.J., Zhan, P., Field, B., Ruben, S.M., He, T. Reproducibility assessment of relative quantitation strategies for LC-MS based proteomics. Anal. Chem. 2007, 79: 5651-5658.
79. Bondarenko, P.V., Chelius, D., Shaler, T.A. Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography-tandem mass spectrometry. Anal. Chem. 2002, 74: 4741-4749.
80. Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T.A., Hill, L.R., Norton, S., Kumar, P., Anderle, M., Becker, C.H. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 2003, 75: 4818-4826.
81. Tabata, T., Sato, T., Kuromitsu, J., Oda, Y. Pseudo internal standard approach for label-free quantitative proteomics. Anal. Chem. 2007, 79: 8440-8445.
82. Jaitly, N., Monroe, M.E., Petyuk, V.A., Clauss, T.R., Adkins, J.N., Smith, R.D. Robust algorithm for alignment of liquid chromatography-mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal. Chem. 2006, 78: 7397-7409.
83. Pang, J.X., Ginanni, N., Dongre, A.R., Hefta, S.A., Opitek, G.J. Biomarker discovery in urine by proteomics. J. Proteome Res. 2002, 1: 161-169.
84. Gao, J., Opiteck, G.J., Friedrichs, M.S., Dongre, A.R., Hefta, S.A. Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2003, 2: 643-649.
85. Zybailov, B., Coleman, M.K., Florens, L., Washburn, M.P. Correlation of relative abundance ratios derived from peptide ion chromatograms and spectrum counting for quantitative proteomic analysis using stable isotope labeling. Anal. Chem. 2005, 77: 6218-6224.
86. Asara, J.M., Christofk, H.R., Freimark, L.M., Cantley, L.C. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 2000, 8: 994-999.
87. E: a virtue of parallel MS acquisition. Mol. Cell Proteomics 2006, 5: 144-156.
88. Blondeau, F., Ritter, B., Allaire, P.D., Wasiak, S., Girard, M., Hussain, N.K., Angers, A., Legendre-Guillemin, V., Roy, L., Boismenu, D., Kearney, R.E., Bell, A.W., Bergeron, J.J., McPherson, P.S. Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc. Natl. Acad. Sci. USA 2004, 101: 3833-3838.
89. Powell, D.W., Weaver, C.M., Jennings, J.L., McAfee, K.J., He, Y., Weil, P.A., Link, A.J. Cluster analysis of mass spectrometry data reveals a novel component of SAGA. Mol. Cell Biol. 2004, 24: 7249-7259.
90. Zybailov, B., Mosley, A.L., Sardiu, M.E., Coleman, M.K., Florens, L., Washburn, M.P. Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 2006, 5: 2339-2347.
91. Paoletti, A.C., Parmely, T.J., Tomomori-Sato, C., Sato, S., Zhu, D., Conaway, R.C., Conaway, J.W., Florens, L., Washburn, M.P. Quantitative, proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc. Natl. Acad. Sci. USA 2006, 103: 18928-18933.
92. Rappsilber, J., Ryder, U., Lamond, A.I., Mann, M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002, 12: 1231-1245.
93. Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., Mann, M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell Proteomics 2005, 4: 1265-1272.
94. Tang, H., Arnold, R.J., Alves, P., Xun, Z., Clemmer, D.E., Novotny, M.V., Reily, J.P., Radivojac, P. A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 2006, 22: e481-488.
95. Lu, P., Vogel, C., Wang, R., Yao, X., Marcotte, E.M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat. Biotechnol. 2007, 25: 117-124.
96. Nesvizhskii, A.I., Keller, A., Kolker, E., Acbersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75: 4646-4658.
97. Mallick, P., Schirle, M., Chen, S.S., Flory, M.R., Lee, H., Martin, D., Ranish, J., Raught, B., Schmitt, R., Werner, T., Kuster, B., Aebersold, R. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 2007, 25: 125-131.
98. Kuster, B., Schirle, M., Mallick, P., Aebersold, R. Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 2005, 6(7): 577-583.
99. Craig, R., Cortens, J.P., Beavis, R.C. The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom. 2005, 19: 1844-1850.
100. Sanders, W.S., Bridges, S.M., McCarthy, F.M., Nanduri, B., Burgess, S.C. Prediction of peptides observable by mass spectrometry applied at the experimental set level. BMC Bioinformatics 2007, 8: S23.
101. Wei, J., Sun, J., Yu, W., Jones, A., Oeller, P., Keller, M., Woodnutt, G., Short, J.M. Global proteome discovery using an online three-dimensional LC-MS/MS. J. Proteome Res. 2005, 4: 801-808.
102. de Godoy, L.M., Olsen, J.V., de Souza, G.A., Li, G., Mortensen, P., Mann, M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol. 2006, 7: R50.
103. Ghaemmaghami, S., Huh, W.K., Bower, K., Howson, R.W., Belle, A., Dephoure, N., O'Shea, E.K., Weissman, J.S. Global analysis of protein expression in yeast. Nature 2003, 425: 737-741.
104. Brunner, E., Ahrens, C.H. Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E.W., Pause, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P.G., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgsveld, J., Kregenow, F., Heck, A.J., Hafen, E., Schlapbach, R., Acbersold, R. A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol. 2007, 25: 576-583.
105. Elias, J.E., Haas, W., Faherty, B.K., Gygi, S.P. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2: 667-675.
106. Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X, Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P., Punna, T., Peregrin-Alvarez, J.M., Shales, M., Zhang, X., Davey, M., Robinson, M.D., Paccanaro, A., Bray, J.E., Sheung, A., Beattie, B., Richards, D.P., Canadien, V., Lalev, A., Mena, F., Wong, P., Starostine, A., Canete, M.M., Vlasblom, J., Wu, S., Orsi, C., Collins, S.R., Chandran, S., Haw, R., Rilstone, I.J., Gandi, K., Thompson, N.J., Musso, G., St Onge, P., Ghanny, S., Lam, M.H., Butland, G., Altaf-Ul, A.M., Kanaya, S., Shilatifard, A., O'Shea, E., Weissman, J.S., Ingles, C.J., Hughes, T.R., Parkinson, J., Gerstein, M., Wodak, S.J., Emili, A., Greenblatt, J.F. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 2006, 440: 637-643.
107. Keshishian, H., Addona, T., Burgess, K, Kuhn, E., Carr, S.A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell Proteomics 2007, 6: 2212-2229.
108. Scigelova, M., Makarov, A. Orbitrap mass analyzer - overview and applications in proteomics. Proteomics 2006, 6: S16-21.
109. Hanke, S., Besir, H., Oesterhelt, D., Mann, M. Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level. J. Proteome Res. 2008, 7: 1118-1130.