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Mass Spectrometry Based Proteomics in Cancer Research

  • Mohamad A. Abbani
  • Parag Mallick
  • Maryann S. Vogelsang
Chapter
Part of the Applied Bioinformatics and Biostatistics in Cancer Research book series (ABB)

Abstract

Proteomics has become an important component of biological and ­clinical research. Numerous proteomics methods have been developed to identify and quantify the proteins present in biological and clinical samples (Gerber et al., Proc Natl Acad Sci U S A 100:6940–6945, 2003; Ong et al., Methods 29:124–130, 2003). Differences among cell types or treatment groups have been used to identify cellular functions and pathways affected by disease or perturbations (Wright et al., Genome Biol 5:R4, 2003; Durr et al., Nat Biotechnol 22:985–992, 2004), new components and changes in the composition of protein complexes and ­organelles (Andersen et al., Nature 426:570–574, 2003; Blagoev et al., Nat Biotechnol 21:315–318, 2003; Ranish et al., Nat Genet 36:707–713, 2004), and putative disease biomarkers (Marko-Varga et al., J Proteome Res 4:1200–1212, 2005). Despite widespread success, the application of these approaches to discovery of relevant protein markers from clinical samples has been hampered by sample complexity and variability. To begin to broach this challenge, complex experimental protocols for enrichment, separation, and quantification have been developed for selective or comprehensive proteome analysis. In this chapter, we describe techniques for enrichment, separation, quantification, fundamentals of mass spectrometry, and the computational analysis of data generated by these processes within the context of using these approaches for asking and answering biologically and clinically important questions.

Keywords

Electron Capture Dissociation Electron Transfer Dissociation Immobilize Metal Affinity Chromatography Stable Isotope Label Spectral Counting 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Alvarez-Manilla G, Atwood Guo Y, Warren NL, Orlando R, Pierce M (2006) Tools for glycoproteomic analysis:  size exclusion chromatography facilitates identification of tryptic glycopeptides with N-linked glycosylation sites. J Proteome Res 5:701–708.PubMedCrossRefGoogle Scholar
  2. Andersen JS, Wilkinson CJ, Mayor T, Mortensen P, Nigg EA, Mann M (2003) Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426:570–574.PubMedCrossRefGoogle Scholar
  3. Anderson NL, Anderson NG (2002) The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 1:845–867.PubMedCrossRefGoogle Scholar
  4. Bakhtiar R, Guan Z (2005) Electron capture dissociation mass spectrometry in characterization of post-translational modifications. Biochem Biophys Res Commun 334:1–8.PubMedCrossRefGoogle Scholar
  5. Beynon RJ, Doherty MK, Pratt JM, Gaskell SJ (2005) Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods 2:587–589.PubMedCrossRefGoogle Scholar
  6. Blagoev B, Kratchmarova I, Ong SE, Nielsen M, Foster LJ, Mann M (2003) A proteomics strategy to elucidate functional protein–protein interactions applied to EGF signaling. Nat Biotechnol 21:315–318.PubMedCrossRefGoogle Scholar
  7. Blagoev B, Ong S-E, Kratchmarova I, Mann M (2004) Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics. Nat Biotechnol 22:1139–1145.PubMedCrossRefGoogle Scholar
  8. Bondarenko PV, Chelius D, Shaler TA (2002) Identification and relative quantitation of protein mixtures by enzymatic digestion followed by capillary reversed-phase liquid chromatography−tandem mass spectrometry. Anal Chem 74:4741–4749.PubMedCrossRefGoogle Scholar
  9. Brill LM, Motamedchaboki K, Wu S, Wolf DA (2009) Comprehensive proteomic analysis of Schizosaccharomyces pombe by two-dimensional HPLC-tandem mass spectrometry. Methods 48:311–319.PubMedCrossRefGoogle Scholar
  10. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R (2007) A high-quality catalog of the Drosophila melanogaster proteome. Nat Biotechnol 25:576–583.PubMedCrossRefGoogle Scholar
  11. Bunkenborg J, Pilch BJ, Podtelejnikov AV, Wisniewski JR (2004) Screening for N-glycosylated proteins by liquid chromatography mass spectrometry. Proteomics 4:454–465.PubMedCrossRefGoogle Scholar
  12. Burke TW, Mant CT, Black JA, Hodges RS (1989) Strong cation-exchange high-performance liquid chromatography of peptides. Effect of non-specific hydrophobic interactions and linearization of peptide retention behaviour. J Chromatogr 476:377–389.PubMedCrossRefGoogle Scholar
  13. Bylund D, Danielsson R, Malmquist G, Markides KE (2002) Chromatographic alignment by warping and dynamic programming as a pre-processing tool for PARAFAC modelling of liquid chromatography–mass spectrometry data. J Chromatogr A 961:237–244.PubMedCrossRefGoogle Scholar
  14. Che F-y, Fricker LD (2002) Quantitation of neuropeptides in Cpefat/Cpefat mice using differential isotopic tags and mass spectrometry. Anal Chem 74:3190–3198.PubMedCrossRefGoogle Scholar
  15. Chelius D, Bondarenko PV (2002) Quantitative profiling of proteins in complex mixtures using liquid chromatography and mass spectrometry. J Proteome Res 1:317–323.PubMedCrossRefGoogle Scholar
  16. Chelius D, Zhang T, Wang G, Shen R-F (2003) Global protein identification and quantification technology using two-dimensional liquid chromatography nanospray mass spectrometry. Anal Chem 75:6658–6665.PubMedCrossRefGoogle Scholar
  17. Colinge J, Masselot A, Giron M, Dessingy T, Magnin J (2003) OLAV: towards high-throughput tandem mass spectrometry data identification. Proteomics 3:1454–1463.PubMedCrossRefGoogle Scholar
  18. Comisarow MB, Marshall AG (1974) Fourier transform ion cyclotron resonance spectroscopy. Chem Phys Lett 25:282–283.CrossRefGoogle Scholar
  19. Cooper HJ, Hudgins RR, Hakansson K, Marshall AG (2002) Characterization of amino acid side chain losses in electron capture dissociation. J Am Soc Mass Spectrom 13:241–249.PubMedCrossRefGoogle Scholar
  20. Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20:1466–1467.PubMedCrossRefGoogle Scholar
  21. Craig R, Cortens JP, Beavis RC (2005) The use of proteotypic peptide libraries for protein identification. Rapid Commun Mass Spectrom 19:1844–1850.PubMedCrossRefGoogle Scholar
  22. Craig R, Cortens JC, Fenyo D, Beavis RC (2006) Using annotated peptide mass spectrum libraries for protein identification. J Proteome Res 5:1843–1849.PubMedCrossRefGoogle Scholar
  23. Cummings RD, Kornfeld S (1982) Fractionation of asparagine-linked oligosaccharides by serial lectin-Agarose affinity chromatography. A rapid, sensitive, and specific technique. J Biol Chem 257:11235–11240.PubMedGoogle Scholar
  24. Domon B, Aebersold R (2006) Mass spectrometry and protein analysis. Science 312:212–217.PubMedCrossRefGoogle Scholar
  25. Durr E, Yu J, Krasinska KM, Carver LA, Yates JR, Testa JE, Oh P, Schnitzer JE (2004) Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture. Nat Biotechnol 22:985–992.PubMedCrossRefGoogle Scholar
  26. Elias JE, Gygi SP (2007) Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 4:207–214.PubMedCrossRefGoogle Scholar
  27. Eng JK, McCormack AL, Yates JR (1994) An approach to correlate tandem mass spectral data of peptides with amino-acid-sequence in a protein database. J Am Soc Mass Spectrom 5:976–989.CrossRefGoogle Scholar
  28. Faca V, Pitteri SJ, Newcomb L, Glukhova V, Phanstiel D, Krasnoselsky A, Zhang Q, Struthers J, Wang H, Eng J, Fitzgibbon M, McIntosh M, Hanash S (2007) Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res 6:3558–3565.PubMedCrossRefGoogle Scholar
  29. Fan X, She YM, Bagshaw RD, Callahan JW, Schachter H, Mahuran DJ (2004) A method for proteomic identification of membrane-bound proteins containing Asn-linked oligosaccharides. Anal Biochem 332:178–186.PubMedCrossRefGoogle Scholar
  30. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, Shabanowitz J, Hunt DF, White FM (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20:301–305.PubMedCrossRefGoogle Scholar
  31. Frank A, Pevzner P (2005) PepNovo: de novo peptide sequencing via probabilistic network modeling. Anal Chem 77:964–973.PubMedCrossRefGoogle Scholar
  32. Frewen BE, Merrihew GE, Wu CC, Noble WS, MacCoss MJ (2006) Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal Chem 78:5678–5684.PubMedCrossRefGoogle Scholar
  33. Gao J, Opiteck GJ, Friedrichs MS, Dongre AR, Hefta SA (2003) Changes in the protein expression of yeast as a function of carbon source. J Proteome Res 2:643–649.PubMedCrossRefGoogle Scholar
  34. Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH (2004) Open mass spectrometry search algorithm. J Proteome Res 3:958–964.PubMedCrossRefGoogle Scholar
  35. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci U S A 100:6940–6945.PubMedCrossRefGoogle Scholar
  36. Gilchrist A, Au CE, Hiding J, Bell AW, Fernandez-Rodriguez J, Lesimple S, Nagaya H, Roy L, Gosline SJ, Hallett M, Paiement J, Kearney RE, Nilsson T, Bergeron JJ (2006) Quantitative proteomics analysis of the secretory pathway. Cell 127:1265–1281.PubMedCrossRefGoogle Scholar
  37. Glocker MO, Borchers C, Fiedler W, Suckau D, Przybylski M (1994) Molecular characterization of surface topology in protein tertiary structures by amino-acylation and mass spectrometric peptide mapping. Bioconjug Chem 5:583–590.PubMedCrossRefGoogle Scholar
  38. Goodlett DR, Keller A, Watts JD, Newitt R, Yi EC, Purvine S, Eng JK, von Haller P, Aebersold R, Kolker E (2001) Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun Mass Spectrom 15:1214–1221.CrossRefGoogle Scholar
  39. Goshe MB, Conrads TP, Panisko EA, Angell NH, Veenstra TD, Smith RD (2001) Phosphoprotein isotope-coded affinity tag approach for isolating and quantitating phosphopeptides in proteome-wide analyses. Anal Chem 73:2578–2586.PubMedCrossRefGoogle Scholar
  40. Goshe MB, Veenstra TD, Panisko EA, Conrads TP, Angell NH, Smith RD (2002) Phosphoprotein isotope-coded affinity tags:  application to the enrichment and identification of low-abundance phosphoproteins. Anal Chem 74:607–616.PubMedCrossRefGoogle Scholar
  41. Gruhler A, Schulze WX, Matthiesen R, Mann M, Jensen ON (2005) Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry. Mol Cell Proteomics 4:1697–1709.PubMedCrossRefGoogle Scholar
  42. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17:994–999.PubMedCrossRefGoogle Scholar
  43. Hansen KC, Schmitt-Ulms G, Chalkley RJ, Hirsch J, Baldwin MA, Burlingame AL (2003) Mass spectrometric analysis of protein mixtures at low levels using cleavable C-13-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics 2:299–314.PubMedGoogle Scholar
  44. Hardman M, Makarov AA (2003) Interfacing the orbitrap mass analyzer to an electrospray ion source. Anal Chem 75:1699–1705.PubMedCrossRefGoogle Scholar
  45. Higgs RE, Knierman MD, Gelfanova V, Butler JP, Hale JE (2005) Comprehensive label-free method for the relative quantification of proteins from biological samples. J Proteome Res 4:1442–1450.PubMedCrossRefGoogle Scholar
  46. Hirabayashi J (2004) Lectin-based structural glycomics: glycoproteomics and glycan profiling. Glycoconj J 21:35–40.PubMedCrossRefGoogle Scholar
  47. Hsu J-L, Huang S-Y, Chow N-H, Chen S-H (2003) Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 75:6843–6852.PubMedCrossRefGoogle Scholar
  48. Hsu J-L, Huang S-Y, Chen S-H (2006) Dimethyl multiplexed labeling combined with microcolumn separation and MS analysis for time course study in proteomics. Electrophoresis 27:3652–3660.PubMedCrossRefGoogle Scholar
  49. Hu Q, Noll RJ, Li H, Makarov A, Hardman M, Graham Cooks R (2005) The Orbitrap: a new mass spectrometer. J Mass Spectrom 40:430–443.PubMedCrossRefGoogle Scholar
  50. Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M (2005) 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 4:1265–1272.PubMedCrossRefGoogle Scholar
  51. Jaitly N, Monroe ME, Petyuk VA, Clauss TRW, Adkins JN, Smith RD (2006) Robust algorithm for alignment of liquid chromatography mass spectrometry analyses in an accurate mass and time tag data analysis pipeline. Anal Chem 78:7397–7409.PubMedCrossRefGoogle Scholar
  52. James P, Quadroni M, Carafoli E, Gonnet G (1993) Protein identification by mass profile fingerprinting. Biochem Biophys Res Commun 195:58–64.PubMedCrossRefGoogle Scholar
  53. Jensen ON, Podtelejnikov AV, Mann M (1997) Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal Chem 69:4741–4750.PubMedCrossRefGoogle Scholar
  54. Ji J, Chakraborty A, Geng M, Zhang X, Amini A, Bina M, Regnier F (2000) Strategy for qualitative and quantitative analysis in proteomics based on signature peptides. J Chromatogr B Biomed Sci Appl 745:197–210.PubMedCrossRefGoogle Scholar
  55. Ji C, Guo N, Li L (2005) Differential dimethyl labeling of N-termini of peptides after guanidination for proteome analysis. J Proteome Res 4:2099–2108.PubMedCrossRefGoogle Scholar
  56. Johnson KL, Muddiman DC (2004) A method for calculating 16o/18o peptide ion ratios for the relative quantification of proteomes. J Am Soc Mass Spectrom 15:437–445.PubMedCrossRefGoogle Scholar
  57. Karas M, Hillenkamp F (1988) Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal Chem 60:2299–2301.PubMedCrossRefGoogle Scholar
  58. Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74:5383–5392.PubMedCrossRefGoogle Scholar
  59. Khalsa-Moyers G, McDonald WH (2006) Developments in mass spectrometry for the analysis of complex protein mixtures. Brief Funct Genomic Proteomic 5:98–111.PubMedCrossRefGoogle Scholar
  60. Kirkpatrick DS, Gerber SA, Gygi SP (2005) The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35:265–273.PubMedCrossRefGoogle Scholar
  61. Kito K, Ota K, Fujita T, Ito T (2007) A synthetic protein approach toward accurate mass spectrometric quantification of component stoichiometry of multiprotein complexes. J Proteome Res 6:792–800.PubMedCrossRefGoogle Scholar
  62. Krijgsveld J, Ketting RF, Mahmoudi T, Johansen J, Artal-Sanz M, Verrijzer CP, Plasterk RHA, Heck AJR (2003) Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics. Nat Biotechnol 21:927–931.PubMedCrossRefGoogle Scholar
  63. Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R (2007) Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7:655–667.PubMedCrossRefGoogle Scholar
  64. Li J, Steen H, Gygi SP (2003) Protein profiling with cleavable isotope-coded affinity tag (cICAT) reagents: the yeast salinity stress response. Mol Cell Proteomics 2:1198–1204.PubMedCrossRefGoogle Scholar
  65. Li X-j, Yi EC, Kemp CJ, Zhang H, Aebersold R (2005) A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography–mass spectrometry. Mol Cell Proteomics 4:1328–1340.PubMedCrossRefGoogle Scholar
  66. Liu H, Sadygov RG, Yates JR (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76:4193–4201.PubMedCrossRefGoogle Scholar
  67. Lee YH, Han H, Chang SB, Lee SW (2004) Isotope-coded N-terminal sulfonation of peptides allows quantitative proteomic analysis with increased de novo peptide sequencing capability. Rapid Commun Mass Spectrom 18:3019–3027.PubMedCrossRefGoogle Scholar
  68. Louris JN, Cooks RG, Syka JEP, Kelley PE, Stafford GC, Todd JFJ (1987) Instrumentation, applications, and energy deposition in quadrupole ion-trap tandem mass spectrometry. Anal Chem 59:1677–1685.CrossRefGoogle Scholar
  69. Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25:117–124.PubMedCrossRefGoogle Scholar
  70. Ma B, Zhang K, Hendrie C, Liang C, Li M, Doherty-Kirby A, Lajoie G (2003) PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry. Rapid Commun Mass Spectrom 17:2337–2342.PubMedCrossRefGoogle Scholar
  71. Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high-performance technique of mass analysis. Anal Chem 72:1156–1162.PubMedCrossRefGoogle Scholar
  72. Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T, Kuster B, Aebersold R (2007) Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol 25:125–131.PubMedCrossRefGoogle Scholar
  73. Mann M, Hojrup P, Roepstorff P (1993) Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 22:338–345.PubMedCrossRefGoogle Scholar
  74. March RE (1997) An introduction to quadrupole ion trap mass spectrometry. J Mass Spectrom 32:351–369.CrossRefGoogle Scholar
  75. Marko-Varga G, Lindberg H, Lofdahl CG, Jonsson P, Hansson L, Dahlback M, Lindquist E, Johansson L, Foster M, Fehniger TE (2005) Discovery of biomarker candidates within disease by protein profiling: principles and concepts. J Proteome Res 4:1200–1212.PubMedCrossRefGoogle Scholar
  76. Mason DE, Liebler DC (2003) Quantitative analysis of modified proteins by LC−MS/MS of peptides labeled with phenyl isocyanate. J Proteome Res 2:265–272.PubMedCrossRefGoogle Scholar
  77. McLafferty FW, Horn DM, Breuker K, Ge Y, Lewis MA, Cerda B, Zubarev RA, Carpenter BK (2001) Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance. J Am Soc Mass Spectrom 12:245–249.PubMedCrossRefGoogle Scholar
  78. Nesvizhskii AI, Vitek O, Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4:787–797.PubMedCrossRefGoogle Scholar
  79. Oda Y, Owa T, Sato T, Boucher B, Daniels S, Yamanaka H, Shinohara Y, Yokoi A, Kuromitsu J, Nagasu T (2003) Quantitative chemical proteomics for identifying candidate drug targets. Anal Chem 75:2159–2165.PubMedCrossRefGoogle Scholar
  80. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4:1487–1502.PubMedCrossRefGoogle Scholar
  81. Olsen JV, Andersen JR, Nielsen PA, Nielsen ML, Figeys D, Mann M, Wisniewski JR (2004) HysTag – a novel proteomic quantification tool applied to differential display analysis of membrane proteins from distinct areas of mouse brain. Mol Cell Proteomics 3:82–92.PubMedGoogle Scholar
  82. Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127:635–648.PubMedCrossRefGoogle Scholar
  83. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1:376–386.PubMedCrossRefGoogle Scholar
  84. Ong SE, Foster LJ, Mann M (2003) Mass spectrometric-based approaches in quantitative proteomics. Methods 29:124–130.PubMedCrossRefGoogle Scholar
  85. Ono M, Shitashige M, Honda K, Isobe T, Kuwabara H, Matsuzuki H, Hirohashi S, Yamada T (2006) Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics 5:1338–1347.PubMedCrossRefGoogle Scholar
  86. Pappin DJ, Hojrup P, Bleasby AJ (1993) Rapid identification of proteins by peptide-mass fingerprinting. Curr Biol 3:327–332.PubMedCrossRefGoogle Scholar
  87. Parish R (1989) Comparison of linear regression methods when both variables contain error: relation to clinical studies. Ann Pharmacother 23:891–898.Google Scholar
  88. Park K-S, Mohapatra DP, Misonou H, Trimmer JS (2006) Graded regulation of the Kv2.1 potassium channel by variable phosphorylation. Science 313:976–979.PubMedCrossRefGoogle Scholar
  89. Perkins DN, Pappin DJ, Creasy DM, Cottrell JS (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:3551–3567.PubMedCrossRefGoogle Scholar
  90. Porath J (1992) Immobilized metal ion affinity chromatography. Protein Expr Purif 3:263–281.PubMedCrossRefGoogle Scholar
  91. Qian W-J, Goshe MB, Camp DG, Yu L-R, Tang K, Smith RD (2003) Phosphoprotein isotope-coded solid-phase tag approach for enrichment and quantitative analysis of phosphopeptides from complex mixtures. Anal Chem 75:5441–5450.PubMedCrossRefGoogle Scholar
  92. Ramos-Fernandez A, Lopez-Ferrer D, Vazquez J (2007) Improved method for differential expression proteomics using trypsin-catalyzed 18O labeling with a correction for labeling efficiency. Mol Cell Proteomics 6:1274–1286.PubMedCrossRefGoogle Scholar
  93. Ranish JA, Hahn S, Lu Y, Yi EC, Li XJ, Eng J, Aebersold R (2004) Identification of TFB5, a new component of general transcription and DNA repair factor IIH. Nat Genet 36:707–713.PubMedCrossRefGoogle Scholar
  94. Rao KCS, Carruth RT, Miyagi M (2005) Proteolytic 18O labeling by peptidyl-Lys metalloendopeptidase for comparative proteomics. J Proteome Res 4:507–514.PubMedCrossRefGoogle Scholar
  95. Reynolds JA, Tanford C (1970) The gross conformation of protein-sodium dodecyl sulfate complexes. J Biol Chem 245:5161–5165.PubMedGoogle Scholar
  96. Reynolds KJ, Yao X, Fenselau C (2002) Proteolytic 18O labeling for comparative proteomics:  evaluation of endoprotease Glu-C as the catalytic agent. J Proteome Res 1:27–33.PubMedCrossRefGoogle Scholar
  97. Ross PL, Huang YN, Marchese JN, 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 DJ (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3:1154–1169.PubMedCrossRefGoogle Scholar
  98. Saito A, Nagasaki M, Oyama M, Kozuka-Hata H, Semba K, Sugano S, Yamamoto T, Miyano S (2007) AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. BMC Bioinform 8:15.CrossRefGoogle Scholar
  99. Salomon AR, Ficarro SB, Brill LM, Brinker A, Phung QT, Ericson C, Sauer K, Brock A, Horn DM, Schultz PG, Peters EC (2003) Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry. Proc Natl Acad Sci U S A 100:443–448.PubMedCrossRefGoogle Scholar
  100. Schmidt A, Kellermann J, Lottspeich F (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics 5:4–15.PubMedCrossRefGoogle Scholar
  101. Schnölzer M, Jedrzejewski P, Lehmann WD (1996) Protease-catalyzed incorporation of 18O into peptide fragments and its application for protein sequencing by electrospray and matrix-assisted laser desorption/ionization mass spectrometry. Electrophoresis 17:945–953.CrossRefGoogle Scholar
  102. Schuchardt S, Sickmann A (2007) Protein identification using mass spectrometry: a method overview. EXS 97:141–170.PubMedGoogle Scholar
  103. Senko MW, Hendrickson CL, Emmett MR, Shi SD, Marshall AG (1997) External accumulation of ions for enhanced electrospray ionization fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 8:970–976.CrossRefGoogle Scholar
  104. Shukla AK, Futrell JH (2000) Tandem mass spectrometry: dissociation of ions by collisional activation. J Mass Spectrom 35:1069–1090.PubMedCrossRefGoogle Scholar
  105. Sleno L, Volmer DA (2004) Ion activation methods for tandem mass spectrometry. J Mass Spectrom 39:1091–1112.PubMedCrossRefGoogle Scholar
  106. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440–9445.PubMedCrossRefGoogle Scholar
  107. Strittmatter EF, Ferguson PL, Tang K, Smith RD (2003) Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry. J Am Soc Mass Spectrom 14:980–991.PubMedCrossRefGoogle Scholar
  108. Strittmatter EF, Kangas LJ, Petritis K, Mottaz HM, Anderson GA, Shen Y, Jacobs JM, Camp DG 2nd, Smith RD (2004) Application of peptide LC retention time information in a discriminant function for peptide identification by tandem mass spectrometry. J Proteome Res 3:760–769.PubMedCrossRefGoogle Scholar
  109. Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J, Hunt DF (2004a) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc Natl Acad Sci U S A 101:9528–9533.PubMedCrossRefGoogle Scholar
  110. Syka JEP, Marto JA, Bai DL, Horning S, Senko MW, Schwartz JC, Ueberheide B, Garcia B, Busby S, Muratore T, Shabanowitz J, Hunt DF (2004b) Novel linear quadrupole ion trap/FT mass spectrometer: performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J Proteome Res 3:621–626.PubMedCrossRefGoogle Scholar
  111. Tang H, Arnold RJ, Alves P, Xun Z, Clemmer DE, Novotny MV, Reilly JP, Radivojac P (2006) A computational approach toward label-free protein quantification using predicted peptide detectability. Bioinformatics 22:e481–e488.PubMedCrossRefGoogle Scholar
  112. Tao WA, Wollscheid B, O’Brien R, Eng JK, Li X-j, Bodenmiller B, Watts JD, Hood L, Aebersold R (2005) Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nat Methods 2:591–598.PubMedCrossRefGoogle Scholar
  113. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Hamon C (2003) Tandem mass tags:  a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75:1895–1904.PubMedCrossRefGoogle Scholar
  114. Wada Y, Tajiri M, Yoshida S (2004) Hydrophilic affinity isolation and MALDI multiple-stage tandem mass spectrometry of glycopeptides for glycoproteomics. Anal Chem 76:6560–6565.PubMedCrossRefGoogle Scholar
  115. Wang W, Zhou H, Lin H, Roy S, Shaler TA, Hill LR, Norton S, Kumar P, Anderle M, Becker CH (2003) Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem 75:4818–4826.PubMedCrossRefGoogle Scholar
  116. Wang P, Tang H, Fitzgibbon MP, Mcintosh M, Coram M, Zhang H, Yi E, Aebersold R (2007) A statistical method for chromatographic alignment of LC-MS data. Biostatistics 8:357–367.PubMedCrossRefGoogle Scholar
  117. Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM (2007) Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks. Proc Natl Acad Sci U S A 104:5860–5865.PubMedCrossRefGoogle Scholar
  118. Wright ME, Eng J, Sherman J, Hockenbery DM, Nelson PS, Galitski T, Aebersold R (2003) Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells. Genome Biol 5:R4.PubMedCrossRefGoogle Scholar
  119. Wu CC, MacCoss MJ, Howell KE, Matthews DE, Yates JR (2004) Metabolic labeling of mammalian organisms with stable isotopes for quantitative proteomic analysis. Anal Chem 76:4951–4959.PubMedCrossRefGoogle Scholar
  120. Yang Z, Hancock WS (2004) Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multi-lectin affinity column. J Chromatogr A 1053:79–88.PubMedGoogle Scholar
  121. Yao X, Freas A, Ramirez J, Demirev PA, Fenselau C (2001) Proteolytic 18O labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73:2836–2842.PubMedCrossRefGoogle Scholar
  122. Yates JR 3rd, Morgan SF, Gatlin CL, Griffin PR, Eng JK (1998) Method to compare collision-induced dissociation spectra of peptides: potential for library searching and subtractive analysis. Anal Chem 70:3557–3565.PubMedCrossRefGoogle Scholar
  123. Zhang R, Regnier FE (2002) Minimizing resolution of isotopically coded peptides in comparative proteomics. J Proteome Res 1:139–147.PubMedCrossRefGoogle Scholar
  124. Zhang R, Sioma CS, Wang S, Regnier FE (2001) Fractionation of isotopically labeled peptides in quantitative proteomics. Anal Chem 73:5142–5149.PubMedCrossRefGoogle Scholar
  125. Zhang X, Jin QK, Carr SA, Annan RS (2002) N-terminal peptide labeling strategy for incorporation of isotopic tags: a method for the determination of site-specific absolute phosphorylation stoichiometry. Rapid Commun Mass Spectrom 16:2325–2332.PubMedCrossRefGoogle Scholar
  126. Zhang H, Li X-j, Martin DB, Aebersold R (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 21:660–666.PubMedCrossRefGoogle Scholar
  127. Zhang H, Yi EC, Li XJ, Mallick P, Kelly-Spratt KS, Masselon CD, Camp DG 2nd, Smith RD, Kemp CJ, Aebersold R (2005a) High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry. Mol Cell Proteomics 4:144–155.PubMedGoogle Scholar
  128. Zhang J, Schubothe K, Li B, Russell S, Lebrilla CB (2005b) Infrared multiphoton dissociation of O-linked mucin-type oligosaccharides. Anal Chem 77:208–214.PubMedCrossRefGoogle Scholar
  129. Zubarev RA (2004) Electron-capture dissociation tandem mass spectrometry. Curr Opin Biotechnol 15:12–16.PubMedCrossRefGoogle Scholar
  130. Zubarev RA, Kelleher NL, McLafferty FW (1998) Electron capture dissociation of multiply charged protein cations. A non-ergodic process. J Am Chem Soc 120:3265–3266.CrossRefGoogle Scholar
  131. Zubarev RA, Horn DM, Fridriksson EK, Kelleher NL, Kruger NA, Lewis MA, Carpenter BK, McLafferty FW (2000) Electron capture dissociation for structural characterization of multiply charged protein cations. Anal Chem 72:563–573.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Mohamad A. Abbani
  • Parag Mallick
    • 1
    • 2
  • Maryann S. Vogelsang
  1. 1.Center for Applied Molecular MedicineUniversity of Southern CaliforniaLos AngelesUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of CaliforniaLos AngelesUSA

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