Abstract
A simple procedure is described that increases sensitivity and dynamic range for the analysis of a proteome batch digest by FT-ICR mass spectrometry. Ions at the low and high mass ranges are preferentially collected using two different sets of tuning conditions. By combing data collected using tuning conditions that favor low mass (m/z<2000) and high mass (m/z>2000) ions, 277 proteins are identified for a whole cell lysate of Methanococcus maripaludis in a single HPLC-MALDI FT-ICR mass spectrometry experiment, a 70% improvement compared with previous analyses using a wide mass range acquisition. This procedure improves the detection of low abundance ions and thereby increases the range of proteins that are observed. Because the observed mass range is effectively narrower for each spectrum, mass calibration is more accurate than for the standard method that provides a wide range of masses. The trap plate potential on the analyzer cell may be set to a higher value than used for wide mass range measurements, increasing the ion capacity of the analyzer cell and extending the dynamic range, while still maintaining mass accuracy.
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Gygi, S. P.; Aebersold, R. Mass Spectrometry and Proteomics. Curr. Opin. Chem. Biol. 2000, 4, 489–494.
Conrads, T. P.; Anderson, G. A.; Veenstra, T. D.; Pasa-Tolic, L.; Smith, R. D. Utility of Accurate Mass Tags for Proteome-Wide Protein Identification. Anal. Chem. 2000, 72, 3349–3354.
Smith, R. D.; Anderson, G. A.; Lipton, M. S.; Pasa-Tolic, L.; Shen, Y. F.; Conrads, T. P.; Veenstra, T. D.; Udseth, H. R. An Accurate Mass Tag Strategy for Quantitative and High-Throughput Proteome Measurements. Proteomics 2002, 2, 513–523.
Yates, J. R. Mass Spectrometry—from Genomics to Proteomics. Trends Genet. 2000, 16, 5–8.
McDonald, W. H.; Yates, J. R. Shotgun Proteomics and Biomarker Discovery. Disease Markers 2002, 18, 99–105
Washburn, M. P.; Ulaszek, R.; Deciu, C.; Schieltz, D. M.; Yates, J. R. Analysis of Quantitative Proteomic Data Generated via Multidimensional Protein Identification Technology. Anal. Chem. 2002, 74, 1650–1657.
Gao, H. Y.; Shen, Y. F.; Veenstra, T. D.; Harkewicz, R.; Anderson, G. A.; Bruce, J. E.; Pasa-Tolic, L.; Smith, R. D. Two-Dimensional Electrophoretic/Chromatographic Separations Combined with Electrospray Ionization FTICR Mass Spectrometry for High Throughput Proteome Analysis. J. Microcolumn Sep. 2000, 12, 383–390.
Conrads, T. P.; Alving, K.; Veenstra, T. D.; Belov, M. E.; Anderson, G. A.; Anderson, D. J.; Lipton, M. S.; Pasa-Tolic, 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 N-15-Metabolic Labeling. Anal. Chem. 2001, 73, 2132–2139.
Lipton, M. S.; Pasa-Tolic, L.; Anderson, G. A.; Anderson, D. J.; Auberry, D. L.; Battista, J. R.; Daly, M. J.; Fredrickson, J.; Hixson, K. K.; Kostandarithes, H.; Masselon, C.; Markillie, L. M.; Moore, R. J.; Romine, M. F.; Shen, Y. F.; Stritmatter, E.; Tolic, N.; Udseth, H. R.; Venkateswaran, A.; Wong, K. K.; Zhao, R.; Smith, R. D. Global Analysis of the Deinococcus radiodurans Proteome by Using Accurate Mass Tags. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049–11054.
Pasa-Tolic, L.; Harkewicz, R.; Anderson, G. A.; Tolic, N.; Shen, Y. F.; Zhao, R.; Thrall, B.; Masselon, C.; Smith, R. D. Increased Proteome Coverage for Quantitative Peptide Abundance Measurements Based upon High Performance Separations and DREAMS FTICR Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2002, 13, 954–963.
Petritis, K.; Kangas, L. J.; Ferguson, P. L.; Anderson, G. A.; Pasa-Tolic, L.; Lipton, M. S.; Auberry, K. J.; Strittmatter, E. F.; Shen, Y. F.; Zhao, R.; Smith, R. D. Use of Artificial Neural Networks for the Accurate Prediction of Peptide Liquid Chromatography Elution Times in Proteome Analyses. Anal. Chem. 2003, 75, 1039–1048.
Strittmatter, E. F.; Ferguson, P. L.; Tang, K. Q.; Smith, R. D. Proteome Analyses Using Accurate Mass and Elution Time Peptide Tags with Capillary LC Time-of-Flight Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2003, 14, 980–991.
Jacobs, J. M.; Mottaz, H. M.; Yu, L. R.; Anderson, D. J.; Moore, R. J.; Chen, W. N. U.; Auberry, K. J.; Strittmatter, E. F.; Monroe, M. E.; Thrall, B. D.; Camp, D. G.; Smith, R. D. Multidimensional Proteome Analysis of Human Mammary Epithelial Cells. J. Proteome Res. 2004, 3, 68–75.
Hogan, J. D.; Laude, D. A. Suspended Trapping Gas Chromatography/Fourier Transform Mass Spectrometry for Analysis of Complex Organic Mixtures. J. Am. Soc. Mass Spectrom. 1990, 1, 431–439.
Williams, E. R.; Henry, K. D.; McLafferty, F. W. Multiple Remeasurement of Ions in Fourier-Transform Mass-Spectrometry. J. Am. Chem. Soc. 1990, 112, 6157–6162.
Speir, J. P.; Gorman, G. S.; Pitsenberger, C. C.; Turner, C. A.; Wang, P. P.; Amster, I. J. Remeasurement of Ions Using Quadrupolar Excitation Fourier Transform Ion Cyclotron Resonance Spectrometry. Anal. Chem. 1993, 65, 1746–1752.
Pitsenberger, C. C.; Easterling, M. L.; Amster, I. J. Efficient Ion Remeasurement Using Broadband Quadrupolar Excitation FTICR Mass Spectrometry. Anal. Chem. 1996, 68, 3732–3739.
Guan, S. H.; Wahl, M. C.; Wood, T. D.; Marshall, A. G. Enhanced Mass Resolving Power, Sensitivity, and Selectivity in Laser Desorption Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry by Ion Axialization and Cooling. Anal. Chem. 1993, 65, 1753–1757.
Solouki, T.; Marto, J. A.; White, F. M.; Guan, S. H.; Marshall, A. G. Attomole Biomolecule Mass Analysis by Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance. Anal. Chem. 1995, 67, 4139–4144.
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.
Belov, M. E.; Nikolaev, E. N.; Anderson, G. A.; Auberry, K. J.; Harkewicz, R.; Smith, R. D. Electrospray Ionization-Fourier Transform Ion Cyclotron Mass Spectrometry Using Ion Preselection and External Accumulation for Ultrahigh Sensitivity. J. Am. Soc. Mass Spectrom. 2001, 12, 38–48.
Belov, M. E.; Anderson, G. A.; Angell, N. H.; Shen, Y. F.; Tolic, 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.; Pasa-Tolic, 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, 144–154.
Belov, M. E.; Anderson, G. A.; Wingerd, M. A.; Udseth, H. R.; Tang, K. Q.; Prior, D. C.; Swanson, K. R.; Buschbach, M. A.; Strittmatter, E. F.; Moore, R. J.; Smith, R. D. An Automated High Performance Capillary Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for High-Throughput Proteomics. J. Am. Soc. Mass Spectrom. 2004, 15, 212–232.
Mize, T. H.; Amster, I. J. Broad-Band Ion Accumulation with an Internal Source MALDI-FTICR-MS. Anal. Chem. 2000, 72, 5886–5891.
O’;Connor, P. B.; Costello, C. E. Application of Multishot Acquisition in Fourier Transform Mass Spectrometry. Anal. Chem. 2000, 72, 5125–5130.
Kutz, K. K.; Schmidt, J. J.; Li, L. J. In Situ Tissue Analysis of Neuropeptides by MALDI FTMS In-Cell Accumulation. Anal. Chem. 2004, 76, 5630–5640.
Patrie, S. M.; Charlebois, J. P.; Whipple, D.; Kelleher, N. L.; Hendrickson, C. L.; Quinn, J. P.; Marshall, A. G.; Mukhopadhyay, B. Construction of a Hybrid Quadrupole/Fourier Transform Ion Cyclotron Resonance Mass Spectrometer for Versatile MS/MS above 10 kDa. J. Am. Soc. Mass Spectrom. 2004, 15, 1099–1108.
Zientek, K. D.; Eyler, J. R. Improved Sensitivity for Low Abundance Ions in Glow Discharge Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Following Ion Preselection in an External Octopole Ion Guide. J. Anal. At. Spectrom. 2004, 19, 1513–1516.
Caravatti, P. Method and Apparatus for The Accumulation of Ions in a Trap of an Ion Cyclotron Resonance Spectrometer, by Transferring the Kinetic Energy of the Motion Parallel to the Magnetic Field into Directions Perpendicular to the Magnetic Field; U.S. Patent. 4, 924089, 1990.
Smith, P. K.; Krohn, R. I.; Hermanson, G. T.; Mallia, A. K.; Gartner, F. H.; Provenzano, M. D.; Fujimoto, E. K.; Goeke, N. M.; Olson, B. J.; Klenk, D. C. Measurement of Protein Using Bicinchoninic Acid. Anal. Biochem. 1985, 150, 76–85.
Wilcox, B. E.; Hendrickson, C. L.; Marshall, A. G. Improved Ion Extraction from a Linear Octopole Ion Trap: SIMION Analysis and Experimental Demonstration. J. Am. Soc. Mass Spectrom. 2002, 13, 1304–1312.
Wood, T. D.; Schweikhard, L.; Marshall, A. G. Mass-to-Charge Ratio Upper Limits for Matrix-Assisted Laser Desorption Fourier-Transform Ion-Cyclotron Resonance Mass-Spectrometry. Anal. Chem. 1992, 64, 1461–1469.
May, M. A.; Grosshans, P. B.; Marshall, A. G. Theoretical Mass and Energy Upper Limits for Thermal Ions in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes 1992, 120, 193–205.
Arkin, C. R.; Laude, D. A. Collision Induced Ion Ejection in an FTICR Trapped-Ion Cell. J. Am. Soc. Mass Spectrom. 2005, 16, 422–430.
Jeffries, J. B.; Barlow, S. E.; Dunn, G. H. Theory of Space-Charge Shift of Ion-Cyclotron Resonance Frequencies. Int. J. Mass Spectrom. Ion Processes 1983, 54, 169–187.
Francl, T. J.; Sherman, M. G.; Hunter, R. L.; Locke, M. J.; Bowers, W. D.; McIver, R. T. Experimental Determination of the Effects of Space Charge on Ion Cyclotron Resonance Frequencies. Int. J. Mass Spectrom. Ion Processes 1983, 54, 189–199.
Easterling, M. L.; Mize, T. H.; Amster, I. J. Routine Part-Per-Million Mass Accuracy for High-Mass Ions: Space-Charge Effects in MALDI FT-ICR. Anal. Chem. 1999, 71, 624–632.
Inoue, Y. N.; Inoue, M. Peak Confluence Phenomenon in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Mass Spectrom. Soc. Jpn. 1994, 42, 1–9.
Marshall, A. G.; Hendrickson, C. L. Fourier Transform Ion Cyclotron Resonance Detection: Principles and Experimental Configurations. Int. J. Mass Spectrom. 2002, 215, 59–75.
Washburn, M. P.; Ulaszek, R. R.; Yates, J. R. Reproducibility of Quantitative Proteomic Analyses of Complex Biological Mixtures by Multidimensional Protein Identification Technology. Anal. Chem. 2003, 75, 5054–5061.
Gaucher, S. P.; Taylor, S. W.; Fahy, E.; Zhang, B.; Warnock, D. E.; Ghosh, S. S.; Gibson, B. W. Expanded Coverage of the Human Heart Mitochondrial Proteome Using Multidimensional Liquid Chromatography Coupled with Tandem Mass Spectrometry. J. Proteome Res. 2004, 3, 495–505.
Breci, L.; Hattrup, E.; Keeler, M.; Letarte, J.; Johnson, R.; Haynes, P. A. Comprehensive Proteomics in Yeast Using Chromatographic Fractionation, Gas Phase Fractionation, Protein Gel Electrophoresis, and Isoelectric Focusing. Proteomics 2005, 5, 2018–2028.
Wang, Y.; Shi, S. D. H.; Hendrickson, C. L.; Marshall, A. G. Mass-Selective Ion Accumulation and Fragmentation in a Linear Octopole Ion Trap External to a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer. Int. J. Mass Spectrom. 2000, 198, 113–120.
Paul, W.; Steinwedel, H. Ein Neues Massenspektrometer Ohne Magnetfeld. Z. Naturforsch., A: Phys. Sci. 1953, 8, 448–450.
Campbell, J. M.; Collings, B. A.; Douglas, D. J. A New Linear Ion Trap Time-of-Flight System with Tandem Mass Spectrometry Capabilities. Rapid Commun. Mass Spectrom. 1998, 12, 1463–1474.
Marshall, A. G.; Wang, T. C. L.; Ricca, T. L. Tailored Excitation for Fourier Transform Ion-Cyclotron Resonance Mass Spectrometry. J. Am. Chem. Soc. 1985, 107, 7893–7897.
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Published online January 18, 2006
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Wong, R.L., Amster, I.J. Combining low and high mass ion accumulation for enhancing shotgun proteome analysis by accurate mass measurement. The official journal of The American Society for Mass Spectrometry 17, 205–212 (2006). https://doi.org/10.1016/j.jasms.2005.10.016
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DOI: https://doi.org/10.1016/j.jasms.2005.10.016