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.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Marshall, A. G. Milestones in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Technique Development. Int. J. Mass Spectrom. Ion Processes 2000, 200, 331–356.
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.
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.
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.
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.
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.
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.
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.
Zhang, R.; Sioma, C. S.; Wang, S.; Regnier, F. E. Fractionation of Isotopically Labeled Peptides in Quantitative Proteomics. Anal. Chem. 2001, 73, 5142–5149.
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.
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.
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.
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.
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.
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.
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.
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.
Valaskovic, G. A.; Kelleher, N. L.; Mclafferty, F. W. Attomole Protein Characterization by Capillary Electrophoresis Mass Spectrometry. Science 1996, 273, 1199–1202.
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.
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.
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.
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.
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.
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.
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.
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.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Paša-Tolić, L., Harkewicz, R., Anderson, G.A. et al. Increased proteome coverage for quantitative peptide abundance measurements based upon high performance separations and DREAMS FTICR mass spectrometry. J Am Soc Spectrom 13, 954–963 (2002). https://doi.org/10.1016/S1044-0305(02)00409-9
Received:
Accepted:
Issue Date:
DOI: https://doi.org/10.1016/S1044-0305(02)00409-9