Computational Proteomics  (B071)
Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580
D-69120 Heidelberg, Germany.		 DKFZ Logo




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The Computational Proteomics Group was run by Béla Paizs, supported by a Heisenberg Fellowship of the Deutsche Forschungsgemeinschaft (DFG). He was developing new computer-based methods for the analysis of the proteome. His work combined the results from various techniques of mass spectrometry - such as MS/MS, action infrared multiphoton dissociation, ion mobility spectrometry and gas phase H/D-exchange - with theoretical processes.

In the various mass spectrometric analysis types, peptide fragments are produced, based on which the overall protein composition is being determined. This requires a deep understanding of the complex fragmentation networks occurring in mass spectrometers under various excitation conditions. The processes developed in the group have led to a detailed characterisation of peptide product ion structures and dissociation mechanisms and have demonstrated that the principle characteristics of peptide collision-induced dissociation spectra can be understood with basic physical and chemical laws. Raw experimental data are processed with the help of advanced modelling and provides structural, thermodynamic and kinetic data on peptide fragmentation chemistry. The work unifies diverse dissociation mechanisms into a comprehensive peptide fragmentation model and provides the background for novel analysis tools for peptide sequencing analyses. The improved protein identification made possible by this will have impact in both biological research and clinical application.
picture of Bela Paizs

In June 2011, Béla Paizs' achievements were honoured at a conference in Denver, USA, with the Bielman Medal, which is awarded by the American Society for Mass Spectrometry (ASMS).
  



In spring 2013, Béla Paizs left DKFZ and moved to
a professorship position at the School of Chemistry
at Bangor University in Wales, UK.

His current address details:
..
      Professor Béla Paizs
      The Rosalind Franklin Institute
      Harwell Campus
      Didcot, OX11 0QX
      UK
      https://www.rfi.ac.uk/people/dr-bela-paizs

  
  
 

Publications  2015
  1. Paizs, B. (2015). A divide-and-conquer approach to compute collision cross sections in the projection approximation method. Int. J. Mass. Spectrom. 378, 360-363.
  2. Hernandez, O., Paizs, B., & Maître, P. (2015). Rearrangement chemistry of an ions probed by IR spectroscopy. Int. J. Mass. Spectrom. 377, 172-178.

                2014
  3. Hernandez, O., Pulay, P., Maître, P. & Paizs, B. (2014). Zundel-type H-bonding in biomolecular ions. J. Am. Soc. Mass Spectrom., 2014, 25, 1511-1514.

                2013
  4. Durand, S., Rossa, M., Hernandez, O., Paizs, B. & Maitre, P. (2013). IR spectroscopy of b(4) fragment ions of protonated pentapeptides in the X-H (X = C, N, O) Region. J. Phys. Chem. 117, 2508-2516.

    5.             2012
  5. Somogyi, A., Harrison, A.G. & Paizs, B. (2012). Using gas-phase guest-host chemistry to probe the structures of b ions of peptides. J. Am. Soc. Mass Spectrom. 23, 2055-2058.
  6. Wassermann, T.N., Boyarkin, O.V., Paizs, B. & Rizzo, T.R. (2012). Conformation-specific spectroscopy of peptide fragment ions in a low-temperature ion trap. J. Am. Soc. Mass Spectr.  23, 1029-1045.
  7. Bythell, Benjamin J., Hernandez, O., Steinmetz, V., Paizs, B. & Maitre, P. (2012). Tyrosine side-chain catalyzed proton transfer in the YG a(2) ion revealed by theory and IR spectroscopy in the 'fingerprint' and X-H (X = C, N, O) stretching regions. Int. J. Mass Spectr. 316, 227-234.
  8. Bernier, M.C., Paizs, B. & Wysocki, V.H. (2012). Influence of a gamma amino acid on the structures and reactivity of peptide a(3) ions. Int. J. Mass Spectr. 316, 259-267.
  9. Paizs, B. & Mann, M. (2012). 23rd Sanibel Conference on Mass Spectrometry: From fragmentation mechanisms to sequencing: tandem mass spectrometry based peptide and protein identification. J. Am. Soc. Mass Spectr. 23, 575-576.
  10. Paizs, B., Bythell, B.J. & Maitre, P. (2012). Rearrangement Pathways of the a(4) Ion of Protonated YGGFL Characterized by IR Spectroscopy and Modeling. J. Am. Soc. Mass Spectr. 23, 664-675.
  11. Moss, C.L., Chamot-Rooke, J., Nicol, E., Brown, J., Campuzano, I., Richardson, K., Williams, J.P., Bush, M.F., Bythell, B., Paizs, B.. & Turecek, F. (2012). Assigning structures to gas-phase peptide cations and cation-radicals. An infrared multiphoton dissociation, ion mobility, electron transfer, and computational study of a histidine peptide ion. J. Phys. Chem. B 116, 3445-3456.

                2011
  12. Sinha, R.K., Erlekam, U., Bythell, B.J., Paizs, B. & Maitre, P.: Diagnosing the protonation site of b (2) peptide fragment ions using IRMPD in the X-H (X = O, N, and C) stretching region. J. Am. Soc. Mass Spectr. 22, 1645-165ß, 2011.
  13. Bleiholder, C., Suhai, S., Harrison, A.,G. & Paizs, B.: Towards understanding the tandem mass spectra of protonated oligopeptides. 2: the proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). J. Am. Soc. Mass Spectr. 22, 1032-1039, 2011.
  
 ..
  1. Bleiholder, C., Suhai, S., Harrison, A.,G. & Paizs, B.: Towards understanding the tandem mass spectra of protonated oligopeptides. 2: the proline effect in collision-induced dissociation of protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). J. Am. Soc. Mass Spectr. 22, 1032-1039, 2011.

                2010
  2. Bythell, B.J., Csonka, I.P., Suhai, S., Barofsky, D.F. & Paizs, B.: Gas-phase structure and fragmentation pathways of singly protonated peptides with N-terminal arginine. J. Phys. Chem. 114, 15092-15105, 2010.
  3. Bythell, B.J., Maitre, P., Paizs, B.: Cyclization and Rearrangement Reactions of a(n) Fragment Ions of Protonated Peptides. J. Am. Chem. Soc. 132, 14766-14779, 2010.
  4. Bythell, B.J., Knapp-Mohammady, M., Paizs, B., Harrison, A.G.: Effect of the His Residue on the Cyclization of b Ions. J. Am. Soc. Mass Spectr. 21, 1352-1363, 2010.
  5. Turecek, F., Chung, T.W., Moss, C.L., Wyer, J.A., Ehlerding, A., Holm, A.I.S., Zettergren, H., Nielsen, S.B., Hvelplund, P., Chamot-Rooke, J., Bythell, B., Paizs, B.: The Histidine Effect. Electron Transfer and Capture Cause Different Dissociations and Rearrangements of Histidine Peptide Cation-Radicals. J. Am. Chem. Soc. 132, 10728-10740, 2010.
  6. Bythell, B.J., Dain, R.P., Curtice, S.S., Oomens, J., Steill, J.D., Groenewold, G.S., Paizs, B., Van Stipdonk, M.J.: Structure of [M + H - H2O](+) from Protonated Tetraglycine Revealed by Tandem Mass Spectrometry and IRMPD Spectroscopy. J. Phys. Chem. 114, 5076-5082, 2010.
  7. Bleiholder,C., Paizs, B.: Competing gas-phase fragmentation pathways of asparagine-, glutamine-, and lysine-containing protonated dipeptides. Theor. Chem. Accounts 125, 387-396, 2010.

                2009
  8. Knapp-Mohammady, M, Young, AB, Paizs, B, Harrison, AG: Fragmentation of Doubly-Protonated Pro-His-Xaa Tripeptides: Formation of b(2)(2+) Ions. J. Am. Soc. Mass Spectr. 20: 2135-2143, 2009.
  9. Turecek, F, Panja, S, Wyer, JA, Ehlerding, A, Zettergren, H, Nielsen, SB, Hvelplund, P, Bythell, B, Paizs, B: Carboxyl-Catalyzed Prototropic Rearrangements in Histidine Peptide Radicals upon Electron Transfer: Effects of Peptide Sequence and Conformation. J. Am. Chem. Soc. 131: 16472-16487, 2009.
  10. Bythell, BJ, Suhai, S, Somogyi, A, Paizs, B: Proton-Driven Amide Bond-Cleavage Pathways of Gas-Phase Peptide Ions Lacking Mobile Protons. J. Am. Chem. Soc. 131: 14057-14065, 2009.
  11. Erlekam, U, Bythell, BJ, Scuderi, D, Van Stipdonk, M, Paizs, B, Maitre, P: Infrared Spectroscopy of Fragments of Protonated Peptides: Direct Evidence for Macrocyclic Structures of b(5) Ions. J. Am. Chem. Soc. 131: 11503-11508, 2009.
  12. Bythell, BJ, Erlekam, U, Paizs, B, Maitre, P: Infrared Spectroscopy of Fragments from Doubly Protonated Tryptic Peptides. Chemphyschem 10: 883-885, 2009.
  13. Bythell, BJ, Somogyi, A, Paizs, B: What is the Structure of b(2) Ions Generated from Doubly Protonated Tryptic Peptides? J. Am. Soc. Mass Spectr. 20: 618-624, 2009.









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