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Peptide sequencing using a patchwork approach and surface-induced dissociation in sector-TOF and dual quadrupole mass spectrometers

  • Focus: Ion Activation
  • Published:
Journal of the American Society for Mass Spectrometry

Abstract

Surface-induced ion activation in combination with a database search strategy based on the Patchwork concept is applied to the determination of peptide sequences. Surface-induced dissociation (SID) is performed in a tandem quadrupole mass spectrometer and in a hybrid sector/time-of-flight mass spectrometer in order to evaluate the importance of accurate mass analysis of the SID fragment ions for peptide identification. The modified Patchwork approach is based on piecing together the peptide blocks in a bidirectional way, simultaneously using low-mass fragments originating from the C-terminus and N-terminus of the molecule, and relying on the measurement of the peptide’s molecular weight with moderate mass accuracy. The results from this analysis are used as search filters in MASCOT’s (http://www.matrixscience.com) Sequence Query search engine, with the simultaneous addition of the full MS/MS peak list. SID is performed with collision targets coated with pure and mixed composition self-assembled monolayers produced by fluorocarbon and hydrocarbon alkanethiolate solutions of varying chemical composition. The resulting MS/MS spectra produced on pure and mixed hydrocarbon SAMs are submitted to the modified version of Patchwork sequencing. It is found that hydrocarbon surfaces improve the relative abundance of larger fragments. Under the moderate mass accuracy conditions (±0.3 u) offered by our linear-TOF-SID instrument, it is found that increasing the abundance of larger fragments dramatically improves the sequencing scores.

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References

  1. Yates, J. R. Mass Spectrometry and the Age of the Proteome. J. Mass Spectrom. 1998, 33, 1–19.

    Article  CAS  Google Scholar 

  2. Yates, J. R. Database Searching Using Mass Spectrometry Data. Electrophoresis 1998, 19, 893–900.

    Article  CAS  Google Scholar 

  3. Simpson, R. J.; Connelly, L. M.; Eddes, J. S.; Pereira, J. J.; Moritz, R. L.; Reid, G. E. Proteomic Analysis of the Human Colon Carcinoma Cell Line (LIM 1215): Development of a Membrane Protein Database. Electrophoresis 2000, 21, 1707–1732.

    Article  CAS  Google Scholar 

  4. Washburn, M. P.; Wolters, D.; Yates, J. R. Large-Scale Analysis of the Yeast Proteome by Multidimensional Protein Identification Technology. Nat. Biotech. 2001, 19, 242–247.

    Article  CAS  Google Scholar 

  5. Peng, J. M.; Elias, J. E.; Thoreen, C. C. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC-MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. J. Prot. Res. 2003, 2, 43–50.

    Article  CAS  Google Scholar 

  6. Gevaert, K.; Van Damme, J.; Goethals, M. Chromatographic Isolation of Methionine-Containing Peptides for Gel-Free Proteome Analysis—Identification of More than 800 Escherichia Coli Proteins. Mol. Cell. Prot. 2002, 1, 896–903.

    Article  CAS  Google Scholar 

  7. Domon, B.; Alving, K.; He, T. Enabling Parallel Protein Analysis through Mass Spectrometry. Curr. Opin. Mol. Ther. 2002, 4, 577–586.

    CAS  Google Scholar 

  8. Gras, R.; Muller, M. Computational Aspects of Protein Identification by Mass Spectrometry. Curr. Opin. Mol. Ther. 2001, 3, 526–532.

    CAS  Google Scholar 

  9. Tabb, D. L.; Smith, L. L.; Breci, L. A. Statistical Characterization of Ion Trap Mass Spectra from Doubly Charged Tryptic Peptides. Anal. Chem. 2003, 75, 1155–1163.

    Article  CAS  Google Scholar 

  10. Dongre, A. R.; Jones, J. L.; Somogyi, A.; Wysocki, V. H. Influence of Peptide Composition, Gas-Phase Basicity, and Chemical Modification on Fragmentation Efficiency: Evidence for the Mobile Proton Model. J. Am. Chem. Soc. 1996, 118, 8365–8374.

    Article  CAS  Google Scholar 

  11. Laskin, J.; Denisov, E.; Futrell, J. A Comparative Study of Collision-Induced and Surface-Induced Dissociation. 1. Fragmentation of Protonated Dialanine. J. Am. Chem. Soc. 2000, 122, 9703–9714.

    Article  CAS  Google Scholar 

  12. Laskin, J.; Denisov, E.; Futrell, J. Comparative Study of Collision-Induced and Surface-Induced Dissociation. 2: Fragmentation of Small Alanine-Containing Peptides in FT-ICR MS. J. Phys. Chem. B 2001, 105, 1895–1900.

    Article  CAS  Google Scholar 

  13. Senko, M. W.; Speir, J. P.; McLafferty, F. W. Collisional Activation of Large Multiply Charged Ions Using Fourier Transform Mass Spectrometry. Anal. Chem. 1994, 66, 2801–2808.

    Article  CAS  Google Scholar 

  14. Feng, R.; Konishi, Y. Analysis of Antibodies and Other Large Glycoproteins in the Mass Range of 150,000–200,000 Da by Electrospray Ionization Mass Spectrometry. Anal. Chem. 1992, 64, 2090–2095.

    Article  CAS  Google Scholar 

  15. Dongre, A. R.; Somogyi, A.; Wysocki, V. H. Surface-Induced Dissociation: An Effective Tool to Probe Structure, Energetics, and Fragmentation Mechanisms of Protonated Peptides. J. Mass Spectrom. 1996, 31, 339–350.

    Article  CAS  Google Scholar 

  16. DeKrey, M. J.; Kenttamaa, H. I.; Wysocki, V. H.; Cooks, R. G. Energy Deposition in [Fe(CO)5]+·Upon Collision with a Metal Surface. Org. Mass Spectrom 1986, 21, 193–195.

    Article  CAS  Google Scholar 

  17. Clauser, K. R.; Baker, P.; Burlingame, A. L. Role of Accurate Mass Measurement (+/− 10 ppm) in Protein Identification Strategies Employing MS or MS MS and Database Searching. Anal. Chem. 1999, 71, 2871–2882.

    Article  CAS  Google Scholar 

  18. Perkins, D. N.; Pappin, D. J. C.; Creasy, D. M.; Cottrell, J. S. Probability-Based Protein Identification by Searching Sequence Databases Using Mass Spectrometry Data. Electrophoresis 1999, 20, 3551–3567.

    Article  CAS  Google Scholar 

  19. Schlosser, A.; Lehmann, W. D. Patchwork Peptide Sequencing: Extraction of Sequence Information from Accurate Mass Data of Peptide Tandem Mass Spectra Recorded at High Resolution. Proteomics 2002, 2, 524–533.

    Article  CAS  Google Scholar 

  20. Smith, D. L.; Wysocki, V. H.; Colorado, R.; Shmakova, O. E.; Graupe, M.; Lee, T. R. Low-Energy Ion-Surface Collisions Characterize Alkyl and Fluoroalkyl-Terminated Self-Assembled Monolayers on Gold. Langmuir 2002, 18, 3895–3902.

    Article  CAS  Google Scholar 

  21. Nikolaev, E. N.; Somogyi, A.; Smith, D. L.; Gu, C.; Wysocki, V. H.; Martin, C. D.; Samuelson, G. L. Implementation of Low-Energy Surface-Induced Dissociation (eV SID) and High-Energy Collision-Induced Dissociation (keV CID) in a Linear Sector-TOF Hybrid Tandem Mass Spectrometer. Int. J. Mass Spectrom. 2001, 212, 535–551.

    Article  CAS  Google Scholar 

  22. Kimmel, J. R.; Engelke, F.; Zare, R. N. Novel Method for the Production of Finely Spaced Bradbury-Nielson Gates. Rev. Sci. Instrum. 2001, 72, 4354–4357.

    Article  CAS  Google Scholar 

  23. Grill, V.; Shen, J.; Evans, C.; Cooks, R. G. Collisions of Ions with Surfaces at Chemically Relevant Energies: Instrumentation and Phenomena. Rev. Sci. Instrum. 2001, 72, 3149–3179.

    Article  CAS  Google Scholar 

  24. McLuckley, S. A.; Wells, M. Mass Analysis at the Advent of the 21st Century. Chem. Rev. 2001, 101, 571–606.

    Article  Google Scholar 

  25. Cotter, R. J. The New Time-of-Flight Mass Spectrometry. Anal. Chem. 1999, 71, 445A-451A.

    CAS  Google Scholar 

  26. Beck, R. D.; St. John, P.; Homer, M. L.; Whetten, R. L. Impact-Induced Cleaving and Melting of Alkali-Halide Nanocrystals. Science 1991, 253, 879–883.

    Article  CAS  Google Scholar 

  27. de Maaijer-Gielbert, J.; Beijersbergen, J. H. M.; Kistemaker, P. G.; Weeding, T. L. Surface-Induced Dissociation of Benzene on a PFPE Liquid Insulator in a Time-of-Flight Mass Spectrometer. Int. J. Mass Spectrom. Ion Processes 1996, 153, 119–128.

    Article  CAS  Google Scholar 

  28. Haney, L. L.; Riederer, D. E. Delayed Extraction for Improved Resolution of Ion/Surface Collision Products by Time-of-Flight Mass Spectrometry. Anal. Chim. Acta 1999, 397, 225–233.

    Article  CAS  Google Scholar 

  29. Kimura, T.; Sugai, T.; Shinohara, H. Surface-Induced Fragmentation of Higher Fullerenes and Endohedral Metallofullerenes. J. Chem. Phys. 1999, 110, 9681–9687.

    Article  CAS  Google Scholar 

  30. Williams, E. R.; Fang, L.; Zare, R. N. Surface Induced Dissociation for Tandem Time-of-Flight Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes 1993, 123, 233–241.

    Article  CAS  Google Scholar 

  31. Fernandez, F. M., Smith, D. L., Somogyi, A., Yang, X., Wysocki, V. H. Comparison of Surface Energy Transfer by Low-energy Collisions on Mixed Self-Assembled Monolayers in a Sector/TOF Mass Spectrometer and in a Dual Quadrupole Mass Spectrometer, submitted.

  32. Laskin, J.; Futrell, J. H. Energy Transfer in Collisions of Peptide Ions with Surfaces. J. Chem. Phys. 2003, 119, 3413–3420.

    Article  CAS  Google Scholar 

  33. Meroueh, O.; Hase, W. L. Effect of Surface Stiffness on the Efficiency of Surface-Induced Dissociation. Phys. Chem., Chem. Phys. 2001, 3, 2306–2314.

    Article  CAS  Google Scholar 

  34. Schultz, D. G.; Wainhaus, S. B.; Hanley, L. L.; de Sainte Claire, P.; Hase, W. L. Classical Dynamics Simulations of SiMe +3 Ion-Surface Scattering. J. Chem. Phys. 1997, 106, 10337–10348.

    Article  CAS  Google Scholar 

  35. Meroueh, O.; Hase, W. L. Dynamics of Energy Transfer in Peptide-Surface Collisions. J. Am. Chem. Soc. 2001, 124, 1524–1531.

    Article  Google Scholar 

  36. Alves, C.; Porter, M. D. Atomic Force Microscopic Characterization of a Fluorinated Alkanethiolate Monolayer at Gold and Correlations to Electrochemical and Infrared Reflection Spectroscopic Structural Descriptions. Langmuir 1993, 9, 3507–3512.

    Article  CAS  Google Scholar 

  37. Schönherr, H.; Vancso, G. J. Lattice Imaging of Self-Assembled Monolayers of Partially Fluorinated Disulfides and Thiols on Sputtered Gold by Atomic Force Microscopy. Langmuir 1997, 13, 3769–3774.

    Article  Google Scholar 

  38. Cohen, S. R.; Naaman, R.; Sagiv, J. Translational Energy Transfer from Molecules and Atoms to Adsorbed Organic Monolayers of Long-Chain Amphiphiles. Phys. Rev. Lett. 1987, 58, 1208–1211.

    Article  CAS  Google Scholar 

  39. Tsao, M. W.; Hoffmann, C. L.; Rabolt, J. F.; Johnson, H. E.; Castner, D. G.; Erdelen, C.; Ringsdorf, H. Studies of Molecular Orientation and Order in Self-Assembled Semifluorinated N-Alkanethiols: Single and Dual Component Mixtures. Langmuir 1997, 13, 4317–4322.

    Article  CAS  Google Scholar 

  40. Stone, E.; Gillig, K. J.; Ruotolo, B.; Fuhrer, K.; Gonin, M.; Schultz, A.; Russell, D. H. Surface-Induced Dissociation on a MALDI-Ion Mobility-Orthogonal Time-of-Flight Mass Spectrometer: Sequencing Peptides from an “In-Solution” Protein Digest. Anal. Chem. 2001, 73, 2233–2238.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, University of Arizona, 1306 E. University Blvd., 85721-0041, Tucson, AZ, USA

    Facundo M. Fernández, Lori L. Smith, Krishnamoorthy Kuppannan, Xi Yang & Vicki H. Wysocki

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  1. Facundo M. Fernández
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  2. Lori L. Smith
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  3. Krishnamoorthy Kuppannan
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  4. Xi Yang
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  5. Vicki H. Wysocki
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Correspondence to Vicki H. Wysocki.

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Published online October 23, 2003

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Fernández, F.M., Smith, L.L., Kuppannan, K. et al. Peptide sequencing using a patchwork approach and surface-induced dissociation in sector-TOF and dual quadrupole mass spectrometers. J Am Soc Mass Spectrom 14, 1387–1401 (2003). https://doi.org/10.1016/j.jasms.2003.09.003

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  • DOI: https://doi.org/10.1016/j.jasms.2003.09.003

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