Proteomics pp 189-205 | Cite as

Liquid Chromatography–Mass Spectrometry-Based Quantitative Proteomics

  • Michael W. Linscheid
  • Robert Ahrends
  • Stefan Pieper
  • Andreas Kühn
Protocol
First Online:
Part of the Methods in Molecular Biology™ book series (MIMB, volume 564)

Summary

During the last decades, molecular sciences revolutionized biomedical research and gave rise to the biotechnology industry. During the next decades, the application of the quantitative sciences – informatics, physics, chemistry, and engineering – to biomedical research brings about the next revolution that will improve human healthcare and certainly create new technologies, since there is no doubt that small changes can have great effects. It is not a question of “yes” or “no,” but of “how much,” to make best use of the medical options we will have.

In this context, the development of accurate analytical methods must be considered a cornerstone, since the understanding of biological processes will be impossible without information about the minute changes induced in cells by interactions of cell constituents with all sorts of endogenous and exogenous influences and disturbances.

The first quantitative techniques, which were developed, allowed monitoring relative changes only, but they clearly showed the significance of the information obtained. The recent advent of techniques claiming to quantify proteins and peptides not only relative to each other, but also in an absolute fashion, promised another quantum leap, since knowing the absolute amount will allow comparing even unrelated species and the definition of parameters will permit to model biological systems much more accurate than before. To bring these promises to life, several approaches are under development at this point in time and this review is focused on those developments.

Key words

Isotope dilution concept Stable-isotope labeling Label-free quantitation LC–/MS 
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References

  1. 1.
    Sanz-Medel, A., et al, Elemental mass spectrometry for quantitative proteomics. Anal Bioanal Chem, 2008. 390(1): 3–16.PubMedCrossRefGoogle Scholar
  2. 2.
    Mueller, L.N., et al, An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res, 2008. 7(1): 51–61.PubMedCrossRefGoogle Scholar
  3. 3.
    Veenstra, T.D., Global and targeted quantitative proteomics for biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci, 2007. 847(1): 3–11.PubMedCrossRefGoogle Scholar
  4. 4.
    Nakamura, T. and Y. Oda, Mass spectrometry-based quantitative proteomics. Biotechnol Genet Eng Rev, 2007. 24: 147–63.PubMedGoogle Scholar
  5. 5.
    Miyagi, M. and K.C. Rao, Proteolytic 18O-labeling strategies for quantitative proteomics. Mass Spectrom Rev, 2007. 26(1): 121–36.PubMedCrossRefGoogle Scholar
  6. 6.
    Karp, N.A. and K.S. Lilley, Design and analysis issues in quantitative proteomics studies. Proteomics, 2007. 7 Suppl 1: 42–50.PubMedCrossRefGoogle Scholar
  7. 7.
    Chen, X., et al, Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev Proteomics, 2007. 4(1): 25–37.PubMedCrossRefGoogle Scholar
  8. 8.
    Mann, M., Functional and quantitative proteomics using SILAC. Nat Rev Mol Cell Biol, 2006. 7(12): 952–8.PubMedCrossRefGoogle Scholar
  9. 9.
    Lilley, K.S. and P. Dupree, Methods of quantitative proteomics and their application to plant organelle characterization. J Exp Bot, 2006. 57(7): 1493–9.PubMedCrossRefGoogle Scholar
  10. 10.
    Ivakhno, S. and A. Kornelyuk, Quantitative proteomics and its applications for systems biology. Biochemistry (Mosc), 2006. 71(10): 1060–72.CrossRefGoogle Scholar
  11. 11.
    Linscheid, M.W., Quantitative proteomics. Anal Bioanal Chem, 2005. 381(1): 64–6.PubMedCrossRefGoogle Scholar
  12. 12.
    Zhang, H., W. Yan, and R. Aebersold, Chemical probes and tandem mass spectrometry: a strategy for the quantitative analysis of proteomes and subproteomes. Curr Opin Chem Biol, 2004. 8(1): 66–75.PubMedCrossRefGoogle Scholar
  13. 13.
    Bantscheff, M., et al.Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem, 2007. 389(4): 1017–31.PubMedCrossRefGoogle Scholar
  14. 14.
    Baldwin, M.A., Protein identification by mass spectrometry: issues to be considered. Mol Cell Proteomics, 2004. 3(1): 1–9.PubMedGoogle Scholar
  15. 15.
    Stein, R.C. and M.J. Zvelebil, The application of 2D gel-based proteomics methods to the study of breast cancer. J Mammary Gland Biol Neoplasia, 2002. 7(4): 385–93.PubMedCrossRefGoogle Scholar
  16. 16.
    Washburn, M.P., R.R. Ulaszek, and J.R. Yates, 3rd, Reproducibility of quantitative proteomic analyses of complex biological mixtures by multidimensional protein identification technology. Anal Chem, 2003. 75(19): 5054–61.PubMedCrossRefGoogle Scholar
  17. 17.
    Hofmann, S., et al, Rapid and sensitive identification of major histocompatibility complex class I-associated tumor peptides by Nano-LC MALDI MS/MS. Mol Cell Proteomics, 2005. 4(12): 1888–97.PubMedCrossRefGoogle Scholar
  18. 18.
    Gygi, S.P., et al, Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 1999. 17(10): 994–9. java/Propub/biotech/nbt1099_994.fulltext java/Propub/biotech/nbt1099_994.abstract.PubMedCrossRefGoogle Scholar
  19. 19.
    Hansen, K.C., et al, Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol Cell Proteomics, 2003. 2(5): 299–314.PubMedGoogle Scholar
  20. 20.
    Turecek, F., Mass spectrometry in coupling with affinity capture-release and isotope- coded affinity tags for quantitative protein analysis. J Mass Spectrom, 2002. 37(1): 1–14.PubMedCrossRefGoogle Scholar
  21. 21.
    Patterson, S.D. and R.H. Aebersold, Proteomics: the first decade and beyond. Nat Genet, 2003. 33 Suppl: 311–23.PubMedCrossRefGoogle Scholar
  22. 22.
    Klose, J., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik, 1975. 26: 231–43.PubMedGoogle Scholar
  23. 23.
    O’Farrell, P., High resolution two-dimensional electrophoresis of proteins. J Biol Chem 1975. 250: 4007–4021.PubMedGoogle Scholar
  24. 24.
    Miller, I., J. Crawford, and E. Gianazza, Protein stains for proteomic applications: which, when, why? Proteomics, 2006. 6(20): 5385–408.PubMedCrossRefGoogle Scholar
  25. 25.
    Patton, W.F., A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis, 2000. 21(6): 1123–44.PubMedCrossRefGoogle Scholar
  26. 26.
    Wozny, W., et al., Differential radioactive quantification of protein abundance ratios between benign and malignant prostate tissues: cancer association of annexin A3. Proteomics, 2007. 7(2): 313–22.PubMedCrossRefGoogle Scholar
  27. 27.
    Schrattenholz, A. and K. Groebe, What does it need to be a biomarker? Relationships between resolution, differential quantification and statistical validation of protein surrogate biomarkers. Electrophoresis, 2007. 28(12): 1970–79.PubMedCrossRefGoogle Scholar
  28. 28.
    Gygi, S.P., et al, Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol, 1999. 17(10): 994–9.PubMedCrossRefGoogle Scholar
  29. 29.
    Ahrends, R., et al, A metal-coded affinity tag approach to quantitative proteomics. Mol Cell Proteomics, 2007. l6: 1907–16.Google Scholar
  30. 30.
    Washburn, M.P., D. Wolters, and J.R. Yates, 3rd, Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol, 2001. 19(3): 242–7.PubMedCrossRefGoogle Scholar
  31. 31.
    Sheng, S., D. Chen, and J.E. Van Eyk, Multidimensional liquid chromatography separation of intact proteins by chromatographic focusing and reversed phase of the human serum proteome: optimization and protein database. Mol Cell Proteomics, 2006. 5(1): 26–34.PubMedGoogle Scholar
  32. 32.
    Mallik, R. and D.S. Hage, Affinity monolith chromatography. J Sep Sci, 2006. 29(12): 1686–704.PubMedCrossRefGoogle Scholar
  33. 33.
    Azarkan, M., et al, Affinity chromatography: a useful tool in proteomics studies. J Chromatogr B Analyt Technol Biomed Life Sci, 2007. 849(1-2): 81–90.PubMedCrossRefGoogle Scholar
  34. 34.
    Johnson, R.D. and R.J. Lewis, Quantitation of atenolol, metoprolol, and propranolol in postmortem human fluid and tissue specimens via LC/APCI-MS. Forensic Sci Int, 2006. 156(2-3): 106–17.PubMedCrossRefGoogle Scholar
  35. 35.
    Tang, K., J.S. Page, and R.D. Smith, Charge competition and the linear dynamic range of detection in electrospray ionization mass spectrometry. J Am Soc Mass Spectrom, 2004. 15(10): 1416–23.PubMedCrossRefGoogle Scholar
  36. 36.
    Knochenmuss, R., et al, Secondary ion-molecule reactions in matrix-assisted laser desorption/ionization. J Mass Spectrom, 2000. 35(11): 1237–45.PubMedCrossRefGoogle Scholar
  37. 37.
    Bauer, A. and B. Kuster, Affinity purification-mass spectrometry. Powerful tools for the characterization of protein complexes. Eur J Biochem, 2003. 270(4): 570–8.PubMedCrossRefGoogle Scholar
  38. 38.
    Lichty, J.J., et al, Comparison of affinity tags for protein purification. Protein Expr Purif, 2005. 41(1): 98–105.PubMedCrossRefGoogle Scholar
  39. 39.
    Whetstone, P.A., et al, Element-coded affinity tags for peptides and proteins. Bioconjug Chem, 2004. 15(1): 3–6.PubMedCrossRefGoogle Scholar
  40. 40.
    Ahrends, R., et al, Identifying an interaction site between MutH and the C-terminal domain of MutL by crosslinking, affinity purification, chemical coding and mass spectrometry. Nucleic Acids Res, 2006. 34(10): 3169–80.PubMedCrossRefGoogle Scholar
  41. 41.
    Girault, S., et al, Coupling of MALDI-TOF mass analysis separation of biotinylated peptides streptavidin beads. Anal Chem, 1996. 68(13): 2122–6.PubMedCrossRefGoogle Scholar
  42. 42.
    Prange, A., Pröfrock, D., Chemical labels and natural element tags for the quantitative analysis of bio-molecules. J. Anal. At. Spectrom., 2008. 23(4): 432–59.CrossRefGoogle Scholar
  43. 43.
    Julka, S. and F., Regnier, Quantification in proteomics through stable isotope coding: a review. J Proteome Res, 2004. 3(3): 350–63.PubMedCrossRefGoogle Scholar
  44. 44.
    Hoehenwarter, W., et al, The necessity of functional proteomics: protein species and molecular function elucidation exemplified by in vivo alpha A crystallin N-terminal truncation. Amino Acids, 2006. 31(3): 317–23.PubMedCrossRefGoogle Scholar
  45. 45.
    Sachon, E., et al, Phosphopeptide quantitation using amine-reactive isobaric tagging reagents and tandem mass spectrometry: application to proteins isolated by gel electrophoresis. Rapid Commun Mass Spectrom, 2006. 20(7): 1127–34.PubMedCrossRefGoogle Scholar
  46. 46.
    Yang, Y., et al, A comparison of nLC-ESI-MS/MS and nLC-MALDI-MS/MS for GeLC-based protein identification and iTRAQ-based shotgun quantitative proteomics. J Biomol Tech, 2007. 18(4): 226–37.PubMedGoogle Scholar
  47. 47.
    Wiese, S., et al, Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics, 2007. 7(3): 340–50.PubMedCrossRefGoogle Scholar
  48. 48.
    Sui, J., et al, iTRAQ-coupled 2D LC-MS/MS analysis on protein profile in vascular smooth muscle cells incubated with S- and R-enantiomers of propranolol: possible role of metabolic enzymes involved in cellular anabolism and antioxidant activity. J Proteome Res, 2007. 6(5): 1643–51.PubMedCrossRefGoogle Scholar
  49. 49.
    Skalnikova, H., et al, Relative quantitation of proteins fractionated by the ProteomeLab PF 2D system using isobaric tags for relative and absolute quantitation (iTRAQ). Anal Bioanal Chem, 2007. 389(5): 1639–45.PubMedCrossRefGoogle Scholar
  50. 50.
    Li, Z., et al, Shotgun identification of the structural proteome of shrimp white spot syndrome virus and iTRAQ differentiation of envelope and nucleocapsid subproteomes. Mol Cell Proteomics, 2007. 6(9): 1609–20.PubMedCrossRefGoogle Scholar
  51. 51.
    Griffin, T.J., et al, iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer. J Proteome Res, 2007. 6(11): 4200–9.PubMedCrossRefGoogle Scholar
  52. 52.
    Dean, R.A. and C.M. Overall, Proteomics discovery of metalloproteinase substrates in the cellular context by iTRAQ labeling reveals a diverse MMP-2 substrate degradome. Mol Cell Proteomics, 2007. 6(4): 611–23.PubMedCrossRefGoogle Scholar
  53. 53.
    Bantscheff, M., et al, Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol, 2007. 25(9): 1035–44.PubMedCrossRefGoogle Scholar
  54. 54.
    Chong, P.K., et al, Isobaric tags for relative and absolute quantitation (iTRAQ) reproducibility: Implication of multiple injections. J Proteome Res, 2006. 5(5): 1232–40.PubMedCrossRefGoogle Scholar
  55. 55.
    Pierce, A., et al., Eight-channel iTRAQ enables comparison of the activity of 6 leukaemogenic tyrosine kinases. Mol Cell Proteomics, 2008. 7(5): 853–63.Google Scholar
  56. 56.
    White, F.M., On the iTRAQ of kinase inhibitors. Nat Biotechnol, 2007. 25(9): 994–6.PubMedCrossRefGoogle Scholar
  57. 57.
    Ong, S.E. and M. Mann, Stable isotope labeling by amino acids in cell culture for quantitative proteomics. Methods Mol Biol, 2007. 359: 37–52.PubMedCrossRefGoogle Scholar
  58. 58.
    Ong, S.E., I. Kratchmarova, and M. Mann, Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J Proteome Res, 2003. 2(2): 173–81.PubMedCrossRefGoogle Scholar
  59. 59.
    Foster, L.J., C.L. De Hoog, and M. Mann, Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc Natl Acad Sci USA, 2003. 100(10): 5813–8.PubMedCrossRefGoogle Scholar
  60. 60.
    Beynon, R.J., et al, Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat Methods, 2005. 2(8): 587–9.PubMedCrossRefGoogle Scholar
  61. 61.
    Old, W.M., et al, Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics, 2005. 4(10): 1487–502.PubMedCrossRefGoogle Scholar
  62. 62.
    Bondarenko, P.V., 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. Anal Chem, 2002. 74(18): 4741–9.PubMedCrossRefGoogle Scholar
  63. 63.
    Ono, M., et al, Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol Cell Proteomics, 2006. 5(7): 1338–47.PubMedCrossRefGoogle Scholar
  64. 64.
    Wang, W., et al, Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal Chem, 2003. 75(18): 4818–26.PubMedCrossRefGoogle Scholar
  65. 65.
    Meng, F., et al, Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry. J Am Soc Mass Spectrom, 2007. 18(2): 226–33.PubMedCrossRefGoogle Scholar
  66. 66.
    Wolters, D.A., M.P. Washburn, and J.R. Yates, 3rd, An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem, 2001. 73(23): 5683–90.PubMedCrossRefGoogle Scholar
  67. 67.
    Blagoev, B., et al, A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling. Nat Biotechnol, 2003. 21(3): 315–8.PubMedCrossRefGoogle Scholar
  68. 68.
    Heller, M., et al, Trypsin catalyzed 16O-to-18O exchange for comparative proteomics: tandem mass spectrometry comparison using MALDI-TOF, ESI-QTOF, and ESI-ion trap mass spectrometers. J Am Soc Mass Spectrom, 2003. 14(7): 704–18.PubMedCrossRefGoogle Scholar
  69. 69.
    Page, J.S., C.D. Masselon, and R.D. Smith, FTICR mass spectrometry for qualitative and quantitative bioanalyses. Curr Opin Biotechnol, 2004. 15(1): 3–11.PubMedCrossRefGoogle Scholar
  70. 70.
    Bonenfant, D., et al, Quantitation of changes in protein phosphorylation: a simple method based on stable isotope labeling and mass spectrometry. Proc Natl Acad Sci U S A, 2003. 100(3): 880–5.PubMedCrossRefGoogle Scholar
  71. 71.
    Edler, M., N. Jakubowski, and M. Linscheid, Quantitative determination of melphalan DNA adducts using HPLC - inductively coupled mass spectrometry. J Mass Spectrom, 2006. 41(4): 507–16.PubMedCrossRefGoogle Scholar
  72. 72.
    Edler, M., N. Jakubowski, and M. Linscheid, Styrene oxide DNA adducts: quantitative determination using 31P monitoring. Anal Bioanal Chem, 2005. 381(1): 205–11.PubMedCrossRefGoogle Scholar
  73. 73.
    Siethoff, C., et al, Quantitative determination of DNA adducts using liquid chromatography/electrospray ionization mass spectrometry and liquid chromatography/high-resolution inductively coupled plasma mass spectrometry. J Mass Spectrom, 1999. 34(4): 421–6.PubMedCrossRefGoogle Scholar
  74. 74.
    Houk, R.S., Mass-spectrometry of inductively coupled plasmas. Anal Chem, 1986. 58(1): A97–105.CrossRefGoogle Scholar
  75. 75.
    Wind, M., et al, Analysis of protein phosphorylation by capillary liquid chromatography coupled to element mass spectrometry with P-31 detection and to electrospray mass spectrometry. Anal Chem, 2001. 73(1): 29–35.PubMedCrossRefGoogle Scholar
  76. 76.
    Wind, M., et al, Sulfur as the key element for quantitative protein analysis by capillary liquid chromatography coupled to element mass spectrometry. Angew Chem Int Ed Engl, 2003. 42(29): 3425–7.PubMedCrossRefGoogle Scholar
  77. 77.
    Thermo, Finnigan, and Bremen, Finnigan ELEMENT XR: Extended Dynamic Range High Resolution ICP-MS. Technical Note, 2005(TN30064_E 01/05C): 4.Google Scholar
  78. 78.
    Baranov, V.I., et al, A sensitive and quantitative element-tagged immunoassay with ICPMS detection. Anal Chem, 2002. 74(7): 1629–36.PubMedCrossRefGoogle Scholar
  79. 79.
    Tanner, S., et al, Multiplex bio-assay with inductively coupled plasma mass spectrometry: Towards a massively multivariate single-cell technology. Spectrochim Acta Part B 2007. 62: 188–95.CrossRefGoogle Scholar
  80. 80.
    Baranov, V.I., S.D. Tanner, and D.R. Bandura, Method and apparatus for flow cytometry linked with elemental analysis (WO/2005/093784). 2005: US (CA).Google Scholar
  81. 81.
    Lee, S., et al, Method to site-specifically identify and quantitate carbonyl end products of protein oxidation using oxidation-dependent element coded affinity tags (O-ECAT) and nanoliquid chromatography Fourier transform mass spectrometry. J Proteome Res, 2006. 5(3): 539–47.PubMedCrossRefGoogle Scholar
  82. 82.
    Liu, H.L., et al, Method for quantitative proteomics research by using metal element chelated tags coupled with mass spectrometry. Anal Chem, 2006. 78(18): 6614–21.PubMedCrossRefGoogle Scholar
  83. 83.
    Byegard, J., G. Skarnemark, and M. Skahlberg, The stability of some metal EDTA, DTPA and DOTA complexes: Application as tracers in groundwater studies. J Radioanal Nuclear Chem, 1999. 241(2): 281–290.CrossRefGoogle Scholar
  84. 84.
    Moreau, J., et al, Complexing mechanism of the lanthanide cations Eu3 + , Gd3 + , and Tb3 + with 1,4,7,10-tetrakis(carboxymethyl)-1,4,7,10-tetraazacyclododecane (dota)-characterization of three successive complexing phases: study of the thermodynamic and structural properties of the complexes by potentiometry, luminescence spectroscopy, and EXAFS. Chemistry, 2004. 10(20): 5218–32.PubMedCrossRefGoogle Scholar
  85. 85.
    Bunzli, J.C., Benefiting from the unique properties of lanthanide ions. Acc Chem Res, 2006. 39(1): 53–61.PubMedCrossRefGoogle Scholar
  86. 86.
    Bohlke, J.K., et al, Isotopic compositions of the elements. J Phys Chem Ref Data, 2005. 34: 57–67.CrossRefGoogle Scholar
  87. 87.
    Carr, S.A., et al, The need for guidelines in publication of peptide and protein identification data: working group on publication guidelines for peptide and protein identification data. Mol Cell Proteomics, 2004. 3(6): 531–3.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Michael W. Linscheid
    • 1
  • Robert Ahrends
    • 1
  • Stefan Pieper
    • 1
  • Andreas Kühn
    • 1
  1. 1.Department of ChemistryHumboldt-Universität zu BerlinBerlinGermany

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