Download PDF

Increased proteome coverage for quantitative peptide abundance measurements based upon high performance separations and DREAMS FTICR mass spectrometry

  • Ljiljana Paša-Tolić
  • Richard Harkewicz
  • Gordon A. Anderson
  • Nikola Tolić
  • Yufeng Shen
  • Rui Zhao
  • Brian Thrall
  • Christophe Masselon
  • Richard D. Smith
Article
Received:
Accepted:

Abstract

A primary challenge in proteome measurements is to be able to detect, identify, and quantify the extremely complex mixtures of proteins. The relative abundances of interest span at least six orders of magnitude for mammalian proteomes, and this constitutes an intractable challenge for high throughput proteome studies. We have recently described a new approach, Dynamic Range Enhancement Applied to Mass Spectrometry (DREAMS), which is based upon the selective ejection of the most abundant species to expand the dynamic range of Fourier transform ion cyclotron resonanace (FTICR) measurements. The basis of our approach is on-the-fly data-dependent selective ejection of highly abundant species, followed by prolonged accumulation of remaining low-abundance species in a quadrupole external to the FTICR ion trap. Here we report the initial implementation of this approach with high efficiency capillary reverse phase LC separations and high magnetic field electrospray ionization FTICR mass spectrometry for obtaining enhanced coverage in quantitative measurements for mammalian proteomes. We describe the analysis of a sample derived from a tryptic digest of proteins from mouse B16 cells cultured in both natural isotopic abundance and 15N-labeled media. The FTICR mass spectrometric analysis allows the assignment of peptide pairs (corresponding to the two distinctive versions of each peptide), and thus provides the basis for quantiative measurements when one of the two proteomes in the mixture is perturbed or altered in some fashion. We show that implementation of the DREAMS approach allows assignment of approximately 80% more peptide pairs, thus providing quantitative information for approximately 18,000 peptide pairs in a single analysis.

Keywords

Natural Isotopic Abundance Capillary Liquid Chromatography Proteome Coverage Peptide Pair Multidimensional Protein Identification Technology 
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.
Download to read the full article text

References

  1. 1.
    Velculescu, V. E.; Zhang, L.; Zhou, W.; Vogelstein, J.; Basrai, M. A.; Bassett, D. E. J.; Hieter, P.; Vogelstein, B.; Kinzler, K. W. Characterization of the Yeast Transcriptome. Cell 1997, 88, 243–251.CrossRefGoogle Scholar
  2. 2.
    Zhang, L.; Zhou, W.; Vogelstein, B.; Velculescu, V. E.; Kern, S. E.; Hruban, R. H.; Hamilton, S. R.; Kinzler, K. W. Gene Expression Profiles in Normal and Cancer Cells. Science 1997, 276, 1268–1272.CrossRefGoogle Scholar
  3. 3.
    Schena, M.; Shalon, D.; Davis, R. W.; Brown, P. O. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray. Science 1995, 270, 467–70.CrossRefGoogle Scholar
  4. 4.
    Gygi, S. P.; Rochon, Y.; Franza, B. R.; Aebersold, R. Correlation Between Protein and mRNA Abundance in Yeast. Mol. Cell Biol. 1999, 19, 1720–1730.Google Scholar
  5. 5.
    Wilkins, M. R.; Sanchez, J.-C.; Gooley, A. A.; Appel, R. D.; Humphery-Smith, I.; Hochstrasser, D. F.; Williams, K. L. Progress with Proteome Projects: Why All of Proteins Expressed by a Genome Should Be Identified and How to Do it. Biotechnol. Gene Eng. Rev. 1995, 13, 19–50.Google Scholar
  6. 6.
    Wilkins, M. R.; Pasquali, C.; Appel, R. D.; Ou, K.; Golaz, O.; Sanchez, J. C.; Yan, J. X.; Gooley, A. A.; Hughes, G.; Humphery-Smith, I.; Williams, K. L.; Hochstrasser, D. F. From Proteins to Proteomes: Large Scale Protein Identification by Two-Dimensional Electrophoresis and Amino Acid Analysis. Bio/Technol. 1996, 14, 61–65.CrossRefGoogle Scholar
  7. 7.
    Wilkins, M. R.; Williams, K. L.; Appel, R. D.; Hochstrasser, D. F., Eds. Proteome Research: New Frontiers in Functional Genomics. Springer-Verlag: Berlin, Heidelberg, 1997.Google Scholar
  8. 8.
    Hillenkamp, F.; Karas, M.; Beavis, R. C.; Chait, B. T. Matrix-Assisted Laser Desorption Ionization Mass-Spectrometry of Biopolymers. Anal. Chem. 1991, 63, 1193–1202.CrossRefGoogle Scholar
  9. 9.
    Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M. Electrospray Ionization for Mass Spectrometry of Large Biomolecules. Science 1989, 246, 64–71.CrossRefGoogle Scholar
  10. 10.
    Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Evaluation of Two-Dimensional Gel Electrophoresis-Based Proteome Analysis Technology. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9390–9395.CrossRefGoogle Scholar
  11. 11.
    Westbrook, J. A.; Wait, R.; Welson, S. Y.; Dunn, M. J. Zooming-in on the Proteome: Very Narrow-Rrange Immobilized pH Gradients Reveal More Protein Species and Isoforms. Electrophoresis 2001, 22, 2865–2871.CrossRefGoogle Scholar
  12. 12.
    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.CrossRefGoogle Scholar
  13. 13.
    Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Paša-Tolić, L.; Smith, R. D. Utility of Accurate Mass Tags for Proteome-Wide Protein Identification. Anal. Chem. 2000, 72, 3349–3354.CrossRefGoogle Scholar
  14. 14.
    Smith, R. D.; Paša-Tolić, L.; Lipton, M. S.; Jensen, P. K.; Anderson, G. A.; Shen, Y.; Conrads, T. P.; Udseth, H. R.; Harkewicz, R.; Belov, M. E.; Masselon, C.; Veenstra, T. D. Rapid Quantitative Measurements of Proteomes by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Electrophoresis 2001, 22, 1652–1668.CrossRefGoogle Scholar
  15. 15.
    Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Masselon, C.; Paša-Tolić, L.; Shen, Y.; Udseth, H. R. The Use of Accurate Mass Tags for High-Throughput Microbial Proteomics. OMICS 2002, 6, 61–90.CrossRefGoogle Scholar
  16. 16.
    Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Paša-Tolić, L.; Shen Y., Conrads T. P.; Veenstra T. D.; Udseth H. R. An Accurate Mass Tag Strategy for Quantitative and High Throughput Proteome Measurements. Proteomics 2002, in press.Google Scholar
  17. 17.
    Marshall, A. G. Milestones in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Technique Development. Int. J. Mass Spectrom. Ion Processes 2000, 200, 331–356.Google Scholar
  18. 18.
    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.CrossRefGoogle Scholar
  19. 19.
    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. U.S.A. 1999, 96, 6591–6596.CrossRefGoogle Scholar
  20. 20.
    Paša-Tolić, L.; Jensen, P. K.; Anderson, G. A.; Lipton, M. S.; Peden, K. K.; Martinović, S.; Tolić, N.; Bruce, J. E.; Smith, R. D. High Throughput Proteome-Wide Precision Measurements of Protein Expression using Mass Spectrometry. J. Am. Chem Soc. 1999, 121, 7949–7950.CrossRefGoogle Scholar
  21. 21.
    Belov, M. E.; Anderson, G. A.; Angell, N. H.; Shen, Y.; Tolić, N.; Udseth, H. R.; Smith, R. D. Dynamic Range Expansion Applied to Mass Spectrometry Based on Data-Dependent Selective Ion Ejection in Capillary Liquid Chromatography Fourier Transform Ion Cyclotron Resonance for Enhanced Proteome Characterization. Anal. Chem. 2001, 73, 5052–5060.CrossRefGoogle Scholar
  22. 22.
    Harkewicz, R.; Belov, M. E.; Anderson, G. A.; Paša-Tolić, L.; Masselon, C. D.; Prior, D. C.; Udseth, H. R.; Smith, R. D. ESI-FTICR Mass Spectrometry Employing Data-Dependent External Ion Selection and Accumulation. J. Am. Soc. Mass Spectrom. 2002, 13, 144–54.CrossRefGoogle Scholar
  23. 23.
    Bruce, J. E.; Anderson, G. A.; Smith, R. D. “Colored” Noise Waveforms and Quadrupole Excitation for the Dynamic Range Expansion of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 1996, 68, 534–541.CrossRefGoogle Scholar
  24. 24.
    Conrads, T. P.; Alving, K.; Veenstra, T. D.; Belov, M. E.; Anderson, G. A.; Anderson, D. J.; Lipton, M. S.; Paša-Tolić, L.; Udseth, H. R.; Chrisler, W. B.; Thrall, B. D.; Smith, R. D. Quantitative Analysis of Bacterial and Mammalian Proteomes Using a Combination of Cysteine Affinity Tags and 15N-Metabolic Labeling. Anal. Chem. 2001, 73, 2132–2139.CrossRefGoogle Scholar
  25. 25.
    Zhang, R.; Sioma, C. S.; Wang, S.; Regnier, F. E. Fractionation of Isotopically Labeled Peptides in Quantitative Proteomics. Anal. Chem. 2001, 73, 5142–5149.CrossRefGoogle Scholar
  26. 26.
    Shen, Y.; Tolić, N.; Zhao, R.; Paša-Tolić, L.; Li, L.; Berger, S. J.; Harkewicz, R.; Anderson, G. A.; Belov, M. E.; Smith, R. D. High-Throughput Proteomics Using High Efficiency Multiple-Capillary Liquid Chromatography with On-Line High Performance ESI FTICR Mass Spectrometry. Anal. Chem. 2001, 73, 3011–3021.CrossRefGoogle Scholar
  27. 27.
    Shen, Y.; Zhao, R.; Belov, M. E.; Conrads, T. P.; Anderson, G. A.; Tang, K.; Paša-Tolić, L.; Veenstra, T. D.; Lipton, M. S.; Udseth, H. R.; Smith, R. D. Packed Capillary Reverse Phase Liquid Chromatography/Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Proteomics. Anal. Chem. 2001, 73, 1766–1775.CrossRefGoogle Scholar
  28. 28.
    Shaffer, S. A.; Prior, D. C.; Anderson, G. A.; Udseth, H. R.; Smith, R. D. An Ion Funnel Interface for Improved Ion Focusing and Sensitivity Using Electrospray Ionization Mass Spectrometry. Anal. Chem. 1998, 70, 4111–4119.CrossRefGoogle Scholar
  29. 29.
    Kim, T.; Tolmachev, V.; Harkewicz, R.; Prior, D. C.; Anderson, G. A.; Udseth, H. R.; Smith, R. D.; Bailey, T. H.; Rakov, S.; Futrell, J. H. Design and Implementation of a New Electrodynamic Ion Funnel. Anal. Chem. 2000, 72, 2247–2255.CrossRefGoogle Scholar
  30. 30.
    Belov, M. E.; Gorshkov, M. V.; Udseth, H. R.; Anderson, G. A.; Smith, R. D. Initial Implementation of an Electrodynamic Ion Funnel with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal. Chem. 2000, 72, 2271–2279.CrossRefGoogle Scholar
  31. 31.
    Belov, M. E.; Nikolaev, E. N.; Harkewicz, R.; Masselon, C.; Alving, K.; Smith, R. D. Ion Discrimination During Ion Accumulation in a Quadrupole Interface External to a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Int. J. Mass Spectrom. Ion Processes 2001, 208, 205–225.Google Scholar
  32. 32.
    Belov, M. E.; Gorshkov, M. V.; Alving, K.; Smith, R. D. Optimal Pressure Conditions for Unbiased External Ion Accumulation in a Two-Dimensional Radio-Frequency Quadrupole for Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Rapid Commun. Mass Spectrom. 2001, 15, 1988–1996.CrossRefGoogle Scholar
  33. 33.
    Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. J. Am. Soc. Mass Spectrom. 2000, 11, 320–332.CrossRefGoogle Scholar
  34. 34.
    Valaskovic, G. A.; Kelleher, N. L.; Mclafferty, F. W. Attomole Protein Characterization by Capillary Electrophoresis Mass Spectrometry. Science 1996, 273, 1199–1202.CrossRefGoogle Scholar
  35. 35.
    Belov, M. E.; Gorshkov, M. V.; Udseth, H. R.; Anderson, G. A.; Smith, R. D. Zeptomole-Sensitivity Electrospray Ionization-Fourier Transform Ion Cyclotron Resonance. Anal. Chem. 2000, 72, 2271–2279.CrossRefGoogle Scholar
  36. 36.
    Sannes-Lowery, K.; Griffey, R. H.; Kruppa, G. H.; Speir, J. P.; Hofstadler, S. A. Multipole Storage Assisted Dissociation, a Novel In-Source Dissociation Technique for Electrospray Ionization Generated Ions. Rapid Commun. Mass Spectrom. 1998, 12, 9.CrossRefGoogle Scholar
  37. 37.
    Tolmachev, A. V.; Udseth, H. R.; Smith, R. D. Radial Stratification of Ions as a Function of Mass to Charge Ratio in Collisional Cooling Radio Frequency Multipoles Used as Ion Guides or Ion Traps. Rapid Commun. Mass Spectrom. 2000, 14, 1907–1913.CrossRefGoogle Scholar
  38. 38.
    Guan, S. H.; Kim, H. S.; Marshall, A. G.; Wahl, M. C.; Wood, T. D.; Xiang, X. Z. Shrink-Wrapping an Ion Cloud for High-Performance Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Chem. Rev. 1994, 94, 2161–2182.CrossRefGoogle Scholar
  39. 39.
    Washburn, M. P.; Ulaszek, R.; Deciu, C.; Schieltz, D. M.; Yates, J. R. III. Analysis of Quantitative Proteomics Data Generated via Multidimensional Protein Identification Technology. Anal. Chem. 2002, in press.Google Scholar
  40. 40.
    Li, L.; Masselon, C.; Anderson, G. A.; Paša-Tolić, L.; Lee, S.-W.; Shen, Y.; Zhao, R.; Lipton, M. S.; Conrads, T. P.; Tolić, N.; Smith, R. D. High-Throughput Peptide Identification from Protein Digests Using Data-Dependent Multiplexed Tandem FTICR Mass Spectrometry Coupled with Capillary Liquid Chromatography. Anal. Chem. 2001, 73, 3312–3322.CrossRefGoogle Scholar
  41. 41.
    Masselon, C.; Anderson, G. A.; Harkewicz, R.; Bruce, J. E.; Paša-Tolić, L.; Smith, R. D. Accurate Mass Multiplexed Tandem Mass Spectrometry for High-Throughput Polypeptide Identification from Mixtures. Anal. Chem. 2000, 72, 1918–1924.CrossRefGoogle Scholar
  42. 42.
    Gorshkov, M. V.; Masselon, C.; Anderson, G. A.; Udseth, H. R.; Harkewicz, R.; Smith, R. D. A Dynamic Ion Cooling Technique for FTICR Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2001, 12, 1169–1173.CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2002

Authors and Affiliations

  • Ljiljana Paša-Tolić
    • 1
  • Richard Harkewicz
    • 1
  • Gordon A. Anderson
    • 1
  • Nikola Tolić
    • 1
  • Yufeng Shen
    • 1
  • Rui Zhao
    • 1
  • Brian Thrall
    • 1
  • Christophe Masselon
    • 1
  • Richard D. Smith
    • 1
  1. 1.Environmental and Molecular Sciences LaboratoryPacificNorthwest National LaboratoryRichlandUSA

Personalised recommendations