Publications

Publication list of R. A. Zubarev

April 9, 2012

PATENTS

  1. German, A. K.; Bulat, S. I.; Zubarev, R. A.; Bondarenko, P. V.; Knysh, A. N. Time-of-flight mass spectrometer, SU1773461, 1992-11-07.
  2. Zubarev R. A., Mass spectrometry methods using electron capture by ions, EC H01J49/10; H01J49/42B2; US2004155180 – 2004-08-12.
  3. Zubarev, R. A.; Kjeldsen, F.; Ivonin, I.; Silivra, O. A. Electron-ion fragmentation reactions in multipolar radiofrequency fields. GB2405526 – 2005-03-02.
  4. Zubarev, R. A.; Baykut, G.; Witt, M. Tandem mass spectrometry method. GB2414342 – 2005-11-23.
  5. Zubarev, R. A.; Savitski, M. M.; Nielsen, M. L. Tandem mass spectrometry with feedback control. H01J49/02; G01N30/72; H01J49/02; G01N30/00; H01J49/16A. GB2429835 – 2007-03-07.
  6. Zubarev, R. A.; Misharin A. Measuring cell for ion cyclotron resonance mass spectrometer. US2007278402 – 2007-12-06.
  7. Savitski, M. M.; Zubarev, R. A. Mass spectrometry (MS)/MS data processing method for identifying precursor ion species from fragments forwards sample data identifying mass of particular precursor sample ion species and mass of multiple fragment ion species to comparator , WO2009138179-A2, 2009.

PAPERS AND MONOGRAPHS

  1. Zubarev, R. A.; Lebedev, A. A.; Samotaev, N. A.; Soldatov, V. P. Programs of the Graphical Input of Electronic Networks for Matrix LSI Computer-Aided-Design, Izvestiya Vysshih Uchebnyh Zavedenii, Radioelektronika,1988, 31, 55-57.
  2. Zubarev, R. A. Some Second-order Errors in Average Mass Measurements of Complex Biological Molecules in Time-of-flight Particle Desorption Mass Spectrometry, Int. J. Mass Spectrom. Ion Processes 1991, 107, 17-27.
  3. Zubarev, R. A.; Bondarenko, P. V.; Knysh, A. N.; Rozynov, B. V. Electron Avalanche Desorption: A New Soft-Ionization Technique for Non-volatile and/or Thermally Labile Molecules, Rapid Commun. Mass Spectrom. 1991, 5, 32-34.
  4. Zubarev, R. A.; Bondarenko, P. V.; Knysh, A. N.; Rozynov, B. V. Comparison of Spectra Obtained Using 252Cf Plasma-desorption and Electron-avalanche-desorption Mass Spectrometry, Rapid Commun. Mass Spectrom. 1991, 5, 278-282.
  5. Belenki, B. G.; Bondarenko, P. V.; Gankina, E. S.; Zubarev, R. A.; Knysh, A. N.; Koltsova, O. Thin-Layer Chromatography and Mass Spectrometry with Ionization by 252Cf Fission Fragments in the Investigation of the Molecular Weight Distribution of Oligomers, J. Planar Chromatogr. 1991, 4, 230-234.
  6. Суходуб, Л. Ф.; Чиванов, В. Д.; Гребеник, Л. И.; Бондаренко, П. В.; Зубарев, Р. А.; Кныш, А. Н.  Наблюдение Продуктов Модификации Дезоксигуанозин-5,-фосфата Тиотэфом с Помощью Масс-спектрометрии с Ионизацией Осколками Деления Калифорния-252, Бииорганическая Химия, 1991, 17, 999-1001. Sukhodub, L. F.; Chivanov, V. D.; Grebenik, L. I.; Bondarenko, P. V.; Zubarev, R. A.; Knysh, A. N. Observation of Thiotepa doexyguanosine-5′-phosphate modification products by PDMS, Biorganicheskaya Khimiya, 1991, 17, 999-1001.
  7. Zubarev, R. A.; Bondarenko, P. V. An A Priori Relationship Between the Average and Monoisotopic Masses of Peptides and Oligonucleotides, Rapid Commun. Mass Spectrom. 1991, 5, 276-277.
  8. Zubarev, R. A.; Bondarenko, P. V.; Knysh, A. N.; Rozynov, B. V. On-target Deuteration Technique in Time-of-flight Cf-252 Plasma Desorption Mass Spectrometry, Org. Mass Spectrom. 1991, 26, 765-769.
  9. Bondarenko, P. V.; Zubarev, R. A.; Knysh, A. N.; Rozynov, B. V. Design and Optimization of a Micropump-based Electrospray Device for Preparation of Nitrocellulose Substrates for Plasma Desorption Time-of-flight Mass Spectrometry, Biolog. Mass Spectrom. 1992, 21, 323-330.
  10. 10. Elkin, Y. N.; Makhankov, V. V.; Uvarova, N. L.; Bondarenko, P. V.; Zubarev, R. A.; Knysh, A. N. Combination of HPLC and 252-Cf Plasma Desorption Mass Spectrometry for Identifying Composition of Ginseng Tinctures, 1993, 14, 97-100.
  11. 11. Bitensky I.; Brinkmalm, G.; Demirev, P.; Eriksson, J.; Håkansson, P.; Papaléo, R.; Sundqvist, B. U. R.; Zubarev, R. A. Plasma Desorption Mass Spectrometry in Studies of Formation and Sputtering of Fullerenes by MeV Atomic Ions, Int. J. Mass Spectrom. Ion Processes, 1994, 138, 159-172.
  12. 12. Zubarev, R. A.; Chivanov, V. D.; Håkansson, P.; Sundqvist, B. U. R. Peptide Sequencing by Partial Acid Hydrolysis and High Resolution Plasma Desorption Mass Spectrometry, Rapid Commun. Mass Spectrom. 1994, 8, 906-912.
  13. 13. Demirev, P. A.; Eriksson, J.; Papaléo, R.; Zubarev, R. A.; Brinkmalm, G.; Håkansson, P.; Sundqvist, B. U. R. Ion Desorption from Organic and Inorganic Targets Induced by 100 keV Gold Cluster Ions, Nucl. Instrum. Meth. Phys. Res. 1994, B 88, 138-142.
  14. 14. Demirev, P.; Brinkmalm, G.; Eriksson, J.; Håkansson, P.; Papaléo, R.; Zubarev, R. A.; Sundqvist, B. U. R. Formation and Sputtering of Fullerenes by MeV Atomic Ions, Carbon, 1994, 32, 809-814.
  15. 15. Zubarev, R. A.; Bitensky, I. S.; Demirev, P. A.; Sundqvist, B. U. R. Multiplicities of Secondary Ions Emitted in Macromolecular Ion Impact Events, Nucl. Instrum. Meth. Phys. Res. 1994, B 88, 143-148.
  16. 16. El’kin, Yu. N.; Komandrova, N. A.; Tomishich, S. V.; Bondarenko, P. V.; Zubarev, R. A.; Knysh, A. N. 252Cf-Plasma Desorption Mass Spectra of Bacterial Oligosaccharides, Russ. J. Bioorg. Chem. 1994, 20, 432-437.
  17. 17. Zubarev, R. A.; Demirev, P. A.; Håkansson, P.; Sundqvist, B. U. R. Approaches and Limits for Accurate Mass Characterization of Large Biomolecules, Anal. Chem. 1995, 67, 3793-3798.
  18. 18. Costa Vera, C.; Zubarev, R. A.; Ehring, H.; Håkansson, P.; Sundqvist, B. U. R. A Three-point Calibration Procedure for Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Utilizing Multiply Charged Ions and Their Mean Initial Velocities, Rapid Commun. Mass Spectrom. 1996, 10, 1429-1432.
  19. 19. Chivanov, V. D.; Zubarev, R. A.; Aksenov, S. A.; Bordunova, O. G.; Eremenko, V. I.; Kabanets, V. M.; Tatarinova, V. I.; Mishnev, A. K.; Kuraev, V. V.; Knysh, A. N.; Eremenko, I. A. An Improved Sample Preparation Technique for 252Cf Plasma Desorption Mass Spectrometry, Russ. J. Bioorg. Chem. 1996, 22, 585-588.
  20. 20. Zubarev, R. A.; Håkansson, P.; Sundqvist, B. U. R. Accurate Monoisotopic Mass Measurements of Peptides: Possibilities and Limitations of High Resolution Time-of-flight Particle Desorption Mass Spectrometry, Rapid Commun. Mass Spectrom. 1996, 10, 1386-1392.
  21. 21. Zubarev, R. A.; Abeywarna, U.; Håkansson, P.; Demirev, P.; Sundqvist, B. U. R. Kinetic Energies of Secondary Ions in MeV and keV Particle-induced Desorption, Rapid Commun. Mass Spectrom. 1996, 10, 1966-1974.
  22. 22. Zubarev, R. A.; Håkansson, P.; Sundqvist, B. Accuracy Requirements for peptide Characterization by Monoisotopic Molecular Mass Measurements, Anal. Chem. 1996, 68, 4060-4063.
  23. 23. Abeywarna, U. K.; Zubarev, R. A.; Håkansson, P.; Ariyaratne, T. R. Kinetic Energy Measurements of Ions Emitted from Alkali Halides and Their Mixtures in 252Cf Plasma Desorption Mass Spectrometry, Ceylon J. Sci.: Phys. Sci. 1997, 4, 1-8.
  24. 24. Zubarev, R. A.; Abeywarna, U. K.; Demirev, P. A.; Eriksson, J.; Papaléo, R.; Håkansson, P.; Sundqvist, B. U. R. Delayed, Gas-phase Ion Formation in Plasma Desorption Mass Spectrometry, Rapid Commun. Mass Spectrom. 1997, 11, 963-972.
  25. 25. Demirev, P. A.; Zubarev, R. A. Probing Combinatorial Library Diversity by Mass Spectrometry, Anal. Chem. 1997, 69, 2893-2900.
  26. 26. Zubarev, R. A.; Håkansson, P.; Sundqvist, B. U. R.; Talrose, V. L. Enhancement of the Molecular Ion Yield in Plasma Desorption Mass Spectrometry Using Explosive Matrices, Rapid Commun. Mass Spectrom. 1997, 11, 63-70.
  27. 27. Håkansson, K.; Zubarev, R. A.; Håkansson, P. Combination of Nozzle-skimmer Fragmentation and Partial Acid Hydrolysis in Electrospray Ionization Time-of-flight Mass Spectrometry of Synthetic Peptides, Rapid Commun. Mass Spectrom. 1998, 12, 705-711.
  28. 28. Zubarev, R. A.; Kelleher, N. L.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Protein Cations. A Non-ergodic Process, J. Am. Chem. Soc. 1998, 120, 3265-3266.
  29. 29. McLafferty, F. W.; Kelleher, N. L.; Begley, T. P.; Fridriksson, E. K.; Zubarev, R. A.; Horn, D. M. Two Dimensional Mass Spectrometry of Biomolecules at the Subfemtomole Level, Current Opinion Chem. Biol., 1998, 2, 571-578.
  30. 30. Zubarev, R. A.; Demirev, P. A. Isotope depletion of large biomolecules: Implications for molecular mass measurements, J. Am. Soc. Mass Spectrom. 1998, 9, 149-156.
  31. 31. Zubarev, R. A.; Fridriksson, E. K.; Horn, D. M.; Kelleher, N. L.; Kruger, N. A.; Lewis, M. A.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation Produces Many more Protein Backbone Cleavages than Collisional and IR Excitation, Proceedings of San Francisco Symposium, 1998.
  32. 32. Zubarev, R. A.; Kruger, N. A.; Fridriksson, E. K.; Lewis, M. A.; Horn, D. M.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation of Gaseous Multiply-Charged Proteins is Favored at Disulfide Bonds and Other Sites of High Hydrogen Atom Affinity, J. Am. Chem. Soc. 1999, 121, 2857-2862.
  33. 33. Kruger, N. A.; Zubarev, R. A.; Horn, D. M.; McLafferty, F. W. Electron Capture Dissociation of Multiply Charged Peptide Cations, Int. J. Mass Spectrom. Ion Processes, 1999, 185/186/187¸787-793.
  34. 34. Kruger, N. A.; Zubarev, R. A.; Carpenter, B. K.; Kelleher, N. L.; Horn, D. M.; McLafferty, F. W. Electron Capture Versus Energetic Dissociation of Protein Ions, Int. J. Mass Spectrom. Ion Processes, 1999, 182-183, 1-5.
  35. 35. McLafferty, F. W.; Fridriksson, E. K.; Horn, D. M.; Lewis, M. A.; Zubarev, R. A. Biomolecule Mass Spectrometry, Science, 1999, 284, 1289-1290.
  36. 36. Kelleher, N. L.; Zubarev R. A.; Bush, K.; Furie, B.; Furie, B. C.; Mclafferty, F. W.; Walsh, C. T. Localization of Labile Posttranslational Modifications by Electron Capture Dissociation: The Case of γ–Carboxyglutamic Acid, Anal. Chem. 1999, 71, 4250-4253.
  37. 37. Håkansson, K.; Zubarev, R. A.; Coorey, R. V.; Talrose, V. L.; Håkansson, P. Interaction Between Explosive and Analyte layers in Explosive Matrix-assisted Plasma Desorption Mass Spectrometry, Rapid Commun. Mass Spectrom. 1999, 13, 1169-1174.
  38. 38. Mirgorodskaya, E.; Roepstorff, P.; Zubarev, R. A. Localization of O-glycosylation Sites in Peptides by Electron Capture Dissociation in a Fourier Transform Mass Spectrometer, Anal. Chem. 1999, 71, 4431-4436.
  39. 39. Zubarev, R. A.; Fridriksson, E. K.; Horn, D. M.; Kelleher, N. L.; Kruger, N. A.; Carpenter, B. K.; McLafferty, F. W. Electron Capture Dissociation for Structural Characterization of Multiply Charged Protein Cations, Anal. Chem. 2000, 72, 563-573.
  40. 40. Budnik, B. A.; Zubarev, R. A. MH2+× ion production from protonated polypeptides by electron  impact: observation and determination of ionization energies and a cross-section, Chem. Phys. Lett. 2000, 316, 19-23.
  41. 41. Zubarev, R. A.; Budnik, B. A.; Nielsen, M. L. Tandem Ionization Mass Spectrometry of Biomolecules, Eur. J.  Mass Spectrom. 2000, 6, 235-240.
  42. 42. Budnik, B. A.; Jensen, K. B.; Jørgensen, T. J. D.; Haase, A.; Zubarev, R. A. Benefits of 2.94 μm Infra-red Matrix Assisted Laser Desorption Ionization for Analysis of Labile Molecules by Fourier Transform Mass Spectrometry, Rapid Commun. Mass Spectrom. 2000, 14, 578-584.
  43. 43. Bang, K. S.; Nielsen, M. B.; Zubarev, R. A.; Becher, J. Tetrathiafulvalene – phenanthroline macrocycles as redox sensors for metal ions, Chem. Commun. 2000, 215-216.
  44. 44. Håkansson, K.; Zubarev, R. A.; Håkansson, P.; Laiko, V.; Dodonov, A. F. Design and Performance of an Electrospray Ionization Time-of-flight Mass Spectrometer, Rev. Sci. Instrum. 2000, 71, 36-41.
  45. 45. Håkansson, K.; Coorey, R. V.; Zubarev, R. A.; Talrose, V, L.; Håkansson, P.; Low Mass Ions Observed in Plasma Desorption Mass Spectrometry of High Explosives, J. Mass Spectrom. 2000, 35, 337-346.
  46. 46.  Nielsen, M. L.; Budnik, B. A.; Haselmann, K. F.; Olsen, J. V.; Zubarev, R. A. Intramolecular Hydrogen Atom Transfer in Hydrogen-deficient Polypeptide Radical Cations, Chem. Phys. Lett. 2000, 330, 558-562.
  47. 47.  Zubarev, R. A. Electron Capture Dissociation of Large Biomolecules, in Dissociative Recombination, Theory, Experiments and Applications IV, Ed. Larsson, M.; Mitchell, J. B. A.; Schneider, I. F., World, Scientific, Singapore, 2000, pp. 214-217.
  48. 48.  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.
  49. 49.  Horn, D. M.; Zubarev, R. A.; McLafferty, F. W. Automated de novo Sequencing of Proteins by Tandem High-resolution Mass Spectrometry, Proc. Natl. Acad. Sci. USA, 2000, 97, 10313-10317.
  50. 50. Haselmann, K. F.; Budnik, B. A.; Zubarev, R. A. Electron capture dissociation of b2+ ions reveals the presence of the acylium ion structure, Rapid Commun. Mass Spectrom, 2000, 14, 2242-2246.
  51. 51. Stensballe, A.; Jensen, O. N.; Olsen, J. V.; Haselmann, K. F.; Zubarev, R. A. Electron capture dissociation of singly and multiply phosphorylated peptides, Rapid Commun. Mass Spectrom. 2000, 14, 1793-1800.
  52. 52. Damgaard, D.; Nielsen, M. B.; Lau, J.; Jensen, K. B.; Zubarev, R.; Levillain, E.; Becher, J. Synthesis of linear oligo-TTFs and their [2]rotaxanes with cyclobis(paraquat-p-phenylene), J. Materials Chem. 2000, 10, 2249-2258.
  53. 53. Budnik, B. A.; Haselmann, K. F.; Zubarev, R. A. Electron detachment dissociation of peptide di-anions: an electron-hole recombination phenomenon, Chem. Phys. Lett. 2001, 342, 299-302.
  54. 54. Tsybin, Yu. O.; Håkansson, P.; Budnik, B. A.; Haselmann, K. F.; Kjeldsen, F.; Gorshkov, M.; Zubarev, R. A. Improved Low-energy Injection Systems for High Rate Electron Capture Dissociation in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Rapid Commun. Mass Spectrom. 2001, 15, 1849-1854.
  55. 55. Olsen, J. V.;  Haselmann, K. F.; Nielsen, M. L.; Budnik, B. A.; Nielsen, P. E.; Zubarev, R. A. Comparison of Electron Capture Dissociation and Collisionally Activated Dissociation of Polycations of Peptide Nucleic Acids, Rapid Commun. Mass Spectrom. 2001, 15, 969-974.
  56. 56.  Becher, J.; Brimert, T.; Jeppesen, J. O.; Pedersen, J. Z.; Zubarev, R.; Bjørnholm, T.; Reitzel, N.; Jensen, T. R.; Kjaer, K.; Levillain, E. Tetrathiafulvaleno-annelated porphyrins, Angewandte Chemie – International Edition, 2001, 40, 2497-2500.
  57. 57. McLafferty, F. W.; Horn, D. M.; Breuker, K.; Ge, Y.; Lewis, M. A.; Cerda, B.; Zubarev, R. A.; Carpenter, B. K. Electron capture dissociation of gaseous multiply charged ions by Fourier-transform ion cyclotron resonance, J. Am. Soc. Mass Spectrom. 2001, 12, 245-249.
  58. 58. Haselmann, K. F.; Budnik, B. A.; Olsen, J. V.; Nielsen, M. L.; Reis, C. A.; Clausen, H.; Johnson, A. H.; Zubarev, R. A. Advantages of External Accumulation for Electron Capture Dissociation in Fourier Transform Mass Spectrometry, Anal. Chem. 2001; 73, 2998-3005.
  59. 59. Kjeldsen, F.; Budnik, B. A.; Haselmann, K. F.; Jensen, F.; Zubarev, R. A.  Dissociative Capture of Hot (3-13 eV) Electrons by Polypeptide Polycations: An Efficient Process Accompanied by Secondary Fragmentation. Chem. Phys. Lett. 2002, 356, 201-206.
  60. 60. Schwientek, T.; Bennett, E. P.; Flores, C.; Thacker, J.; Hollmann, M.; Reis, C. A.; Behrens, J.; Mandel, U.; Keck, B.; Schafer, M. A.; Haselmann, K.; Zubarev, R.; Roepstorff, P.; Burchell, J. M; Taylor-Papadimitriou, J.; Hollingsworth, M. A.; Clausen, H. Functional conservation of subfamilies of putative UDP-N-acetylgalactosamine : polypeptide N-acetylgalactosaminyltransferases in Drosophila, Caenorhabditis elegans, and mammals – One subfamily composed of l(2)35Aa is essential in Drosophila, J. Biol. Chem. 2002, 277, 22623-22638.
  61. 61.  Zubarev, R. A.; Haselmann, K. F.; Budnik, B. A.; Kjeldsen, K.; Jensen, F. Towards an Understanding of the Mechanism of Electron Capture Dissociation: a Historical Perspective, Eur. J. Mass Spectrom. 2002, 8, 337-349.
  62. 62.  Budnik, B. A.; Nielsen, M. L.; Olsen, J. V.; Haselmann, K. F.; Hörth, P.; Haehnel. W.; Zubarev, R. A. Can Relative Cleavage Frequencies in Peptides Provide Additional Sequence Information? Int. J. Mass Spectrom. 2002, 219, 283-294.
  63. 63.  Haselmann, K. F.; Budnik, B. A.; Kjeldsen, F.; Nielsen, M. L.; Olsen, J. V.; Zubarev, R.A.  Electronic excitation gives informative fragmentation of polypeptide cations and anions, Eur. J. Mass Spectrom, 2002, 8, 117-121.
  64. 64.  Polfer, N. C.; Haselmann, K. F.; Zubarev, R. A.; Langridge-Smith, P. R. R. Electron capture dissociation of polypeptides using a 3 Tesla Fourier transform ion cyclotron resonance mass spectrometer, Rapid Commun. Mass Spectrom. 2002, 16, 936-943.
  65. 65.  Balakin, A. A.; Dodonov, A. F.; Markin M. I.; Novikova L. I.; Soulimenkov, I. V.; Talroze, V. L.; Budnik, B. A.; Haselmann, K. F.; Zubarev, R. A. Polymer track membranes for extraction of ions from aqueous solutions at atmospheric pressure, Eur. J. Mass Spectrom. 2002, 8, 79-84.
  66. 66.  Budnik, B. A.; Tsybin, Y. O.; Håkansson, P.; Zubarev, R. A. Ionization energies of multiply protonated polypeptides obtained by tandem ionization in Fourier transform mass spectrometers, J. Mass Spectrom. 2002, 37, 1141-1144.
  67. 67.  Haselmann, K. F.; Polfer, N. C.; Budnik, B. A.; Kjeldsen, F.; Zubarev, R. A. Can the (M· – X) Region in Electron Capture Dissociation Provide Reliable Information on Amino Acid Composition of Polypeptides? Eur. J. Mass Spectrom. 2002, 8, 461-469.
  68. 68.  Niiranen, H; Budnik, B. A.; Zubarev, R. A; Auriola, S.; Lapinjoki, S. High-performance liquid chromatography–mass spectrometry and electron-capture dissociation tandem mass spectrometry of osteocalcin. Determination of γ-carboxyglutamic acid residues, J. Chromat. 2002, 962 95–103.
  69. 69.  Haselmann, K. F.; Jørgensen, T. J. D.; Budnik, B. A.; Jensen, F.; Zubarev, R. A. Electron Capture Dissociation of Weakly-bound Polypeptide Polycationic Complexes, Rapid Commun. Mass Spectrom. 2002, 16, 2260-2265.
  70. 70.  Zubarev, R. A. Electron Capture Dissociation of Peptides, in Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research, Silberring, J.; Ekman, R., Eds.; Wiley, 2002.
  71. 71.  Kjeldsen, F.; Haselmann, K. F.; Budnik, B. A.; Sørensen, E. S.; Zubarev, R. A. Complete Characterisation of Post-Translational Modification Sites in the Bovine Milk Protein PP3 by Tandem Mass Spectrometry with Electron Capture Dissociation as the Last Stage. Anal. Chem. 2003, 75, 2355-2361.
  72. 72.  Mirgorodskaya, O. M.; Haselmann, K. F.; Kjeldsen, F.; Roepstorff, P.; Zubarev, R. A. Towards the Standard-module Approach to Disulfide-linked Polypeptide Nanostructures. I. Methodological Prerequisites and Mass Spectrometric Characterization of the Test Two-loop Structure. Eur. J. Mass Spectrom. 2003, 9, 139-148.
  73. 73. Nielsen, M. L.; Budnik, B. A.; Haselmann, K. F.; Zubarev, R. A. Tandem MALDI/EI Ionization for Tandem Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of Polypeptides, Int. J. Mass Spectrom., 2003, 226, 181-187.
  74. 74.  Kjeldsen, F.; Sørensen, E.; Zubarev, R. A. Distinguishing of Ile/Leu Amino Acid Residues in the PP3 Protein by (Hot) Electron Capture Dissociation in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Anal. Chem. 2003, 75, 1267-1274.
  75. 75. Kjeldsen, F.; Zubarev, R. A. Secondary losses via γ-lactam formation in hot electron capture dissociation: a missing link to complete de novo sequencing of proteins? J. Am. Chem. Soc. 2003, 125, 6628-6629.
  76. 76.  Zubarev, R. A. Reactions of Polypeptide Ions with Electrons in the Gas Phase, Mass Spectrom. Rev. 2003, 22, 57-77.
  77. 77.  Cooper, H. J.; Håkansson, K.; Marshall, A. G.; Hudgins, R. R.; Haselmann, K. F.; Kjeldsen, F.; Budnik, B. A.; Polfer, N. C.; Zubarev, R. A. The Diagnostic Value of Amino Acid Side-chain Losses in Electron Capture Dissociation of Polyepeptides. Comment on: “Can the (M· – X) Region in Electron Capture Dissociation Provide Reliable Information on Amino Acid Composition of Polypeptides?” Eur. J. Mass Spectrom. 2002, 8, 461-469. Eur. J. Mass Spectrom. 2003, 9, 221-222.
  78. 78. Budnik, B. A.; Haselmann, K. F.; Elkin, Yu. N.; Gorbach, V. I.; Zubarev, R. A. Applications of Electron-Ion Dissociation Reactions for Analysis of Polycationic Chitooligosaccharides in Fourier Transform Mass Spectrometry, Anal. Chem. 2003, 75, 5994-6001.
  79. 79. Zubarev, R. A. Methods of Studying Gas-Phase Ions: Electron Capture Dissociation, in Encyclopedia of Mass Spectrometry, N. Nibbering, Ed.; Elsevier, v. 4, 2004.
  80. 80. Zubarev, R. A. Electron Capture Dissociation Tandem Mass Spectrometry, Curr. Opinions Biotech. 2004, 15, 12-16.
  81. 81.  Kjeldsen, F.; Zubarev, R. A. Top-down Approach to Characterization of Proteins, Encyclopedia Mass Spectrom. v. II. Elsevier, 2004.
  82. 82.  Adams, C.; Budnik, B. A.; Haselmann, K. F.; Kjeldsen, F.; Zubarev, R. A. Electron Capture Dissociation Distinguishes  a Single D-amino Acid in a Protein and Probes the Tertiary Structure, J. Am. Soc. Mass Spectrom. 2004, 15, 1087-1098.
  83. 83.  Savitski, M. M.; Ivonin, I. A.; Nielsen, M. L.; Tsybin, Yu. O.; Håkansson, P.;  Zubarev, R. A.  Shifted-basis Technique Improves Accuracy of Peak Position Determination in Fourier Transform Mass Spectrometry, J. Am. Soc. Mass Spectrom. 2004, 15, 457-461.
  84. 84.  Ramström, M.; Ivonin, I.; Johansson, A.; Askmark, H.; Markides, K. E.; Zubarev, R. A.; Håkansson, P.; Aquilonius. S.-M; Bergquist, J. Cerebrospinal fluid protein patterns in neurodegenerative disease revealed by liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry. Proteomics, 2004, 4, 4010-4018.
  85. 85.  Nielsen, M. L.; Savitski, M. M.; Kjeldsen, F.; Zubarev, R. A. Physicochemical Properties Determining the Detection Probability of Tryptic Peptides in Fourier Transform Mass Spectrometry. A Correlation Study. Anal. Chem. 2004, 76, 5872-5877.
  86. 86.  Al-Khalili, A.; Thomas, R.; Ehlerding, A.; Hellberg, F. Geppert, W. D.; Zhaunerchyk, V.; af Ugglas, M.; Larsson, M.; Uggerud, E.; Vedde, J.; Adlhart, C.; Semaniak, J.;  Kamin´ska, M.; Zubarev, R. A.; Kjeldsen, F.; Andersson, P. U.; Osterdahl, F.; Bednarska, V. A.; Paa´l, A. Dissociative recombination cross section and branching ratios of protonated dimethyl disulfide and N-methylacetamide. J. Chem. Phys. 2004, 121, 5700-5708.
  87. 87. Budnik, B. A.; Olsen, J. V.; Egorov, T. A.; Anisimova, V. E.; Galkina, T. G.; Musolyamov, A. K.; Grishin, E. V.; Zubarev, R. A. De novo sequencing of antimicrobial peptides isolated from the venom glands of the wolf spider Lycosa singoriensis, J. Mass Spectrom. 2004, 39, 193-201.
  88. 88.  Kjeldsen, F.; Silivra, O. A.; Ivonin, I. A.; Haselmann, K. F.; Gorshkov, M.;  Zubarev, R. A. Cα-C Backbone Fragmentation Dominates in Electron Detachment Dissociation of Gas-Phase Poly-Peptide Anions. Chem. – Eur. J. 2005, 11, 1803-1812.
  89. 89.  Silivra, O. A.; Kjeldsen, F.; Ivonin, I. A.; Zubarev, R. A. Electron Capture Dissociation in a Quadrupole Ion Trap: First Results. J. Am. Soc. Mass Spectrom. 2005, 16, 22-27.
  90. 90.  Nielsen, M. L.; Savitski, M. M.; Zubarev, R. A. Improving protein identification using complementary fragmentation techniques in Fourier transform mass spectrometry, Mol. Cell. Proteomics, 2005, 6, 835-845.
  91. 91.  Adams, C.; Zubarev, R. A. Distinguishing and Quantification of Peptides and Proteins Containing D-Amino Acids by Tandem Mass Spectrometry. Anal. Chem., 2005, 77, 4571-4580.
  92. 92.  Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. New Database-independent, Sequence-tag-based Scoring of Peptide MS/MS Data Validates Mowse Scores, Recovers Below-threshold Data, Singles out Modified Peptides and Assesses the Quality of MS/MS TechniquesMol. Cell. Proteomics, 2005, 4, 1180 – 1188.
  93. 93.  Zubarev, R. A.; Witt, M.; Baykut, G. Two-fold Efficiency Increase by Selective Excitation of Ions for Consecutive Activation by Ion-Electron Reactions and Vibrational Excitation in Tandem Fourier Transform Ion Cyclotron Resonance Mass Spectrometry, Anal. Chem. 2005, 77, 2992-2996.
  94. 94.  Haselmann,  K. F.; Nielsen, P. F.; Zubarev, R. A. Characterization of an N-acylated glucagon-like peptide-1 derivative by electron capture dissociation, J. Am. Soc. Mass Spectrom. 2005, 16, 548-552.
  95. 95.  Kocher, T.; Engstrom, A.; Zubarev, R. A. Fragmentation of peptides in MALDI in-source decay mediated by hydrogen radicals, Anal. Chem. 2005, 77, 172-177.
  96. 96.  Misharin A. S.; Silivra O. A.; Kjeldsen F.; Zubarev R. A. Dissociation of peptide ions by fast atom bombardment in a quadrupole ion trap, Rapid Commun. Mass Spectrom. 2005, 19, 2163–2171.
  97. 97. Savitski, M. M.; Nielsen, M. L.; Kjeldsen, F.; Zubarev, R. A. Proteomics-grade de novo sequencing approach, J. Proteome Res. 2005, 4, 2348-2354.
  98. 98. Patriksson, A;  Adams, C. M.; Kjeldsen, F.; Raber, J.;  van der Spoel, D.; Zubarev, R. A. Prediction of N-Cα Bond Cleavage Frequencies in Electron Capture Dissociation of Trp-cage Dications by Force-field Molecular Dynamics Simulations, Int. J. Mass Spectrom. 2005, 248, 124-135.
  99. 99. Fung, Y. M. E.; Kjeldsen, F.; Silivra, O. A.; Chan, T. W. D.; Zubarev, R. A. Facile Disulfide Bond Cleavage in Gaseous Peptide and Protein Cations by 157 nm Ultra-violet Photo-dissociation, Angew. Chem. Int. Ed. 2005, 44, 6399-6403.
  100. 100. Gorshkov, M. V.; Zubarev, R. A. On the accuracy of polypeptide masses measured in a linear ion trap, Rapid Commun. Mass Spectrom. 2005, 19, 3755-3758.
  101. 101. Kjeldsen, F.;  Adams, C. M.; Savitski, M. M.; Zubarev, R. A. Localization of Positive Charges in Gas-Phase Polypeptide Polycations by Tandem Mass Spectrometry, Int. J. Mass Spectrom. 2006, 252, 204-212.
  102. 102. Kocher, T.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. PhosTShunter: A fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier Transform tandem mass spectrometry data sets. J. Proteome Res. 2006, 5, 659-68.
  103. 103. Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A. ModifiComb: A Database-independent Proteomics Tool for Detecting Known Post-translational Modifications, Finding Novel Types of Modifications and Fingerprinting Complex Protein Mixtures. Mol. Cell. Proteomics, 2006, 5, 935-948.
  104. 104. Zubarev, R. A. Protein primary structure using orthogonal fragmentation techniques in Fourier transform mass spectrometry, Expert Rev. Proteomics, 2006, 3, 251-261.
  105. 105. Savitski, M. M.; Kjeldsen, F., Nielsen, M. L.; Zubarev, R. A. Complementary Sequence Preferences of Electron Capture Dissociation and Vibrational Excitation in Fragmentation of Polypeptide Poly-cations, Angew. Chem. Int. Ed. 2006, 45, 5301-5303.
  106. 106. Adams, C. M.; Kjeldsen, F.; Patriksson, A.; van der Spoel, D.; Gräslund, A.; Papadopoulos, E.; Zubarev, R. A. Probing Solution-Phase and Gas-Phase Structures of Trp-cage Cations by Chiral Substitution and Spectroscopic Techniques, Int. J. Mass Spectrom. 2006, 253, 263-273.
  107. Kjeldsen, F.; Silivra, O. A.; Zubarev, R. A. Zwitterionic States in Gas-Phase Polypeptide Ions Revealed by 157-nm Ultra-Violet Photodissociation. Chem. Eur. J. 2006, 12, 7720-7728.
  108. Gorshkov, A. V.; Tarasova, I. A.; Evreinov, V. V.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A.; Gorshkov, M. V. Liquid Chromatography at Critical Conditions: Towards a Comprehensive Approach to Sequence Dependent Retention Time Prediction, Anal. Chem. 2006, 78, 7770-7777.
  109. Misharin, A. S.; Zubarev, R. A. Coaxial multi-electrode cell (“O-trap”) for high-sensitivity detection at a multiple frequency in Fourier transform Ion Cyclotron Resonance Mass Spectrometry: main design and modeling results. Rapid Comun. Mass Spectrom. 2006, 20, 3223–3228.
  110. Nielsen, M. L.; Savitski, M. M.; Zubarev, R. A. Extent of modifications in human proteome samples and its effect on dynamic range of analysis in shotgun proteomics, Mol. Cell Proteomics, 2006, 5, 2384 – 2391.
  111. Zubarev, R. A. Revealing the proteome complexity by mass spectrometry, Lecture Notes in Computer Sci. 2006, 3909, 456-457.
  112. Zubarev, R. A. Electron Capture Dissociation and Other Ion-electron Fragmentation Reactions. In Principles of Mass Spectrometry Applied to Biomolecules, Laskin J., Lifshitz C., Eds.; Wiley, 2006, pp. 475-517.
  113. Savitski M. M.; Kjeldsen, F.; Nielsen, M. L.;  Zubarev, R. A. Hydrogen Rearrangement to and from Radical z Fragments in Electron Capture Dissociation of Peptides, J. Am. Soc. Mass Spectrom. 2007, 18, 113-120.
  114. Savitski, M. M.; Kjeldsen, F.; Nielsen, M. L.;  Garbuzynskiy, S. O.; Galzitskaya, O. V.; Surin, A. K.; Zubarev, R. A. Backbone carbonyl basicities relate gas-phase fragmentation of peptides and protein folding. Angew. Chem. Int. Ed. 2007, 46, 1481-1484.
  115. Zubarev, R. A.; Mann, M. On the proper use of mass accuracy in proteomics,
    Mol. Cell. Proteomics, 2007, 6, 377-381.
  116. Lerner, M.; Corcoran, M.; Cepeda, D.; Nielsen, M. L.; Zubarev, R. A.; Ponten, F.; Uhlen, M.; Hober, S.; Grander, D.; Sangfelt, O. The RBCC Gene RFP (Leu5) Encodes a Novel Transmembrane E3 Ubiquitin Ligase Involved in ERAD, Mol. Biol. Cell, 2007, 18, 1670-1682.
  117. Frank A. M.; Savitski, M. M.; Nielsen, M. L.; Zubarev, R. A.; Pevzner, P. A. De novo peptide sequencing and identification with precision mass spectrometry. J. Proteome Res. 2007, 6, 114-23.
  118. Savitski M. M.; Kjeldsen, F.; Nielsen, M. L.;  Zubarev, R. A. Relative Specificities of Water and Ammonia Losses from Backbone Fragments in Collision-Activated Dissociation, J. Prot. Res. 2007, 6, 2669-2673.
  119. Savitski, M. M.; Nielsen, M. L.;  Zubarev, R. A. Side-chain Losses in Electron Capture Dissociation Improve Peptide Identification, Anal. Chem. 2007, 79, 2296-2302.
  120. Kjeldsen, F.; Savitski M. M.; Nielsen, M. L.;  Shi, L.; Zubarev, R. A. On studying protein phosphorylation patterns using bottom-up LC-MS/MS: the case of human a-casein, Analyst, 2007, 132, 768-776.
  121. Fälth, M.; Savitski, M. M.; Nielsen, M. L.; Kjeldsen, F.; Andren, P. E.; Zubarev, R. A. SwedCAD, a Database of Annotated High-Mass Accuracy MS/MS Spectra of Tryptic Peptides, J. Prot. Res. 2007, 6, 4063-4067.
  122. 122. Van der Spoel, D.; Patriksson, A.; Adams, C. M.; Kjeldsen, F. Zubarev, R. A. A direct comparison of protein structure in the gas and solution phase the Trp-cage. J. Phys. Chem. B. 2007, 111, 13147-50.
  123. 123. Samgina, T. Yu.; Arternenko, K. A.; Gorshkov, V. A.; Lebedev, A. T.; Nielsen, M. L.; Savitski, M. M.; Zubarev, R. A. Electrospray ionization tandem mass spectrometry sequencing of novel skin peptides from Ranid frogs containing disulfide bridges.
  124. Eur. J. Mass Spectrom. 2007, 13, 155-163.
  125. 124. Kotlova, E. R.; Senik, S. V.; Kocher, T.; Shavarda, A. L.; Sinyutina, N. F.; Psurtseva N. V.; Zubarev, R. A. Glycosylceramides from Flammulina velutipes: Variety of molecular species, metabolism and involvement in fungal differentiation. Chem. Phys. Lipids, 2007, 149, S82-S82.
  126. 125. Bergquist, J.; Hakansson, P.; Sundqvist, B. U. R.; Zubarev, R. A. Mass spectrometry of proteins – Uppsala perspectives on past and present. Int J. Mass Spectrom. 2007, 268, 73-82.
  127. 126. Rand, K. D.; Adams, C. M.; Zubarev, R. A.; Jørgensen, T. J. Electron Capture Dissociation Proceeds with a Low Degree of Intramolecular Migration of Peptide Amide Hydrogens. J. Am. Chem. Soc. 2008, 130,1341-1349.
  128. 127. Savitski, M. M.; Fälth, M.; Fung, E. Y. M.; Adams, C. M.; Zubarev R. A. Bifurcating Fragmentation Behavior of Gas-Phase Tryptic Peptide Dications in Collisional Activation, J. Am. Soc. Mass Spectrom. 2008, 19, 1755-1763.
  129. 128. Zubarev, R. A.; Zubarev, A. R.; Savitski, M. M. Electron Capture/Transfer versus Collisionally Activated/Induced Dissociations: Solo or Duet? J. Am. Soc. Mass Spectrom. 2008, 19, 753-761.
  130. 129. Tarasova, I. A.; Gorshkov, A. V.; Evreinov, V. V.; Adams. C. A.; Zubarev, R. A.; Gorshkov, M. V. Applicability of the critical chromatography concept to proteomics problems: Experimental study of the dependence of peptide retention time on the sequence of amino acids in the chain, Polymer Sci. Ser. A 2008, 50, 309-321.
  131. 130. Fälth, M.; Savitski, M. M.; Nielsen, M. L.; Kjeldsen, F.; Andren P. E.; Zubarev, R. A. Analytical Utility of Small Neutral Losses from Reduced Species in Electron Capture Dissociation Studied Using SwedECD Database, Anal. Chem. 2008, 80, 8089-8094.
  132. 131. Zubarev, R. A. Electron Capture Dissociation LC/MS/MS for Bottom-Up Proteomics, in Mary S. Lipton and L. Pasa-Tolic (eds.), Methods in Molecular Biology, Mass Spectrometry of Peptides and Proteins, Vol. 492, 2008.
  133. 132. Zubarev, R. A.; McLuckey, S. A. Electron/ion and ion/ion interactions: Fundamentals, applications, tools, and methodologies – Foreword. Int. J. Mass Spectrom. 2008, 276, V-VI.
  134. 133. Lind, S. B.; Molin, M.; Savitski, M. M.; Emilsson, L.; Astrom, J.; Hedberg, L.; Adams, C.; Nielsen, M. L.; Engstrom, A.; Elfineh, L.; Andersson, E.; Zubarev, R. A.; Pettersson, U. Immunoaffinity enrichments followed by mass spectrometric detection for studying global protein tyrosine phosphorylation, J. Proteome Res. 2008, 7, 2897-2910.
  135. 134. Samgina, T. Y.; Artemenko, K. A.; Gorshkov, V. A.; Ogourtsov, S. V.; Zubarev, R. A. Lebedev, A. T. De novo sequencing of peptides secreted by the skin glands of the Caucasian Green Frog Rana ridibunda, Rapid Commun. Mass Spectrom. 2008, 22, 3517-3525.
  136. 135. Zubarev, R. A.; Nielsen,  M. L.; Savitski, M. M.; Kel-Margoulis, O.; Wingender, E.; Kel, A. Identification of dominant signaling pathways from proteomics expression data, J. Proteomics, 2008, 1, 89-96.
  137. 136. Ståhl, S.; Fung, Y.M.E.; Adams, C. M.; Lengqvist, J.; Mörk, B.; Stenerlöw, B.; Lewensohn, R.; Lehtiö, J.; Zubarev, R. A.; Viktorsson, K. Proteomics and Pathway Analysis Identifies JNK-signaling as Critical for High-LET Radiation-induced Apoptosis in Non-Small Lung Cancer Cells, Mol. Cell Proteomics, 2009, 8, 1117-1129.
  138. 137. Artemenko, K. A.; Zubarev, A. R.; Samgina, T. Yu.; Lebedev, A. T.; Savitski, M. M.; Zubarev, R. A. 2D Mass Mapping as a General Method of Data Representation in Comprehensive Analysis of Complex Molecular Mixtures, Anal. Chem. 2009, 81, 3738–3745.
  139. 138. Fung, E. Y. M.; Besson, T.; Lemaire, J.; Maitre, P.; Zubarev, R. A. Room-temperature Infrared Spectroscopy Combined with Mass Spectrometry Distinguishes
  140. Gas-Phase Protein Isomers, Angew. Chem. Int. Ed. 2009, 48, 8340-8342.
  141. 139. Fung, E. Y. M.; Adams, C. A.; Zubarev, R. A. Electron Ionization Dissociation of singly and multiply charged peptides, J. Am. Chem. Soc. 2009, 31, 9977-9985.
  142. 140. Kotlova, E. R.; Senik, S. V.; Kucher, T.; Shavarda, A. L.; Kiyashko, A. A.; Psurtseva, N. V.; Sinyutina, N. F.; Zubarev R. A. Alterations in the composition of membrane glycero-and sphingolipids in the course of Flammulina velutipes surface culture development, Microbiology, 2009, 78, 193-201.
  143. 141.  Yang, H.; Fung, Y. M.; Zubarev, A. R.; Zubarev, R. A.  Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples. J. Proteome Res. 2009, 8, 4615–4621.
  144. 142. Nyblom, H.; Bugliani, M.; Fung, Y. M. Eva; Boggi, U.; Zubarev, R. A.; Marchetti, P.; Bergsten, P. Apoptotic, regenerative and immune-related signaling in human islets from type 2 diabetes individuals, J. Proteome Res. 2009, 8, 5650-5656.
  145. 143. Marin-Vicente, C.; Zubarev, R. A. Search engine for proteomics, Fact or Fiction? G.I.T. Lab J, 2009, 11-12, 10-11.
  146. 144. Pridatchenko, M. L.; Tarasova, I. A.; Guryca, V.; Kononikhin, A. S.; Adams, C.;  Tolmachev, D. A.; Agapov, A. Yu.; Evreinov, V. V.; Popov, I. A.; Nikolaev, E. N.; Zubarev, R. A.; Gorshkov, A. V.; Masselon, C. D.; Gorshkov, M. V. Use of models of biomacromolecule separation in AMT database generation for shotgun proteomics, Biochemistry-Moscow, 2009, 74, 1195-1202.
  147. 145. Hessle, V.; Björk, P.; Sokolowski, M.; González de Valdivia, E.; Silverstein, R.; Artemenko, K.; Tyagi, A.; Maddalo, G.; Ilag, L.; Helbig, R.; Zubarev, R. A.; Visa, N. The Exosome Associates Cotranscriptionally with the Nascent Pre-mRNP through Interactions with Heterogeneous Nuclear Ribonucleoproteins, Molecular Biology of the Cell, 2009, 20, 3459–3470.
  148. 146. Yang, H.; Zubarev, R. A. Multiple soft ionization of gas-phase proteins and swift backbone dissociation in collisions with <100 eV electrons, Angew. Chem. Int. Edition, 2010, 49,1439-1441.
  149. 147. Yang, H.; Zubarev, R. A. Recognition of amino acid chirality in polypeptide ions by MS/MS, in Chiral Recognition of Amino Acids, Zehnacker-Rentien A., Ed., Taylor & Francis, 2010.
  150. 148. Goloborodko, A. A.; Mayerhofer, C.; Zubarev, R. A.; Tarasova, I. A.; Gorshkov, A. V.; Zubarev, R. A.; Gorshkov, M. V. Empirical approach to false discovery rate estimation in shotgun proteomics, Rapid Commun. Mass Spectrom. 2010, 24: 454–462.
  151. 149. Yang, H.; Zubarev, R. A. Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides, Electrophoresis, 2010, 31, 764–1772.
  152. 150. Hermansson, M.; Artemenko, K.; Ossipova, E.; Eriksson, H.; Lengqvist, J.; Makrygiannakis, D.; Catrina, A. I.; Nicholas, A. P.; Klareskog, L.; Savitski, M.; Zubarev, R. A.; Jakobsson, P.-J. Mass spectrometric analysis of rheumatoid arthritic synovial tissue identifies specific citrullination sites on fibrinogen, Proteomics: Clinical Application, 2010, 4, 511 – 518.
  153. 151. Zubarev, R. A.; Artemenko, K. A.; Zubarev, A. R.; Mayrhofer, C.; Yang, H.; Fung, E. Y. M. Early life relict feature in peptide mass distribution, Cent. Eur. J. Biol. 2010, 5, 190-196.
  154. 152. Samgina, T. Y.; Gorshkov, V. A.; Artemenko, K. A.; Kovalev, S. V.; Ogourtsov, S. V.; Zubarev, R. A.; Lebedev, A. T. Novel natural peptides from Hyla arborea schelkownikowi skin secretion, Rapid Commun Mass Spectrom. 2010, 24, 1749-1754.
  155. 153. Gorshkov M. V.; Good, D. M.; Lyutvinskiy, Y.; Yang, H.; Zubarev, R. A. Calibration Function for the Orbitrap FTMS Accounting for the Space Charge Effect, J Am Soc Mass Spectrom, 2010, 20, 1846-1851.
  156. 154. Good, D. M.; Marin-Vicente, C.; Zubarev, R. A. Are the Majority of a2-Ions Cyclic? PhysChemChemPhys, 2010, 12, 13372-13374.
  157. 155. Valitova, Y. N.; Kotlova, E. R.; Novikov, A. V.; Shavarda, A. L.; Artemenko, K. A.; Zubarev, R. A.; Minibayeva, F. V. Binding of Sterols Affects Membrane Functioning and Sphingolipid Composition in Wheat Roots, Biochemistry – Moscow, 2010, 75, 554-561.
  158. 156. Maddalo, G.; Shariatgorji, M.; Adams, C. M.; Fung, E.; Nilsson, U.; Zubarev, R. A.; Sedzik, J.; Ilag, L. L. Porcine P2 myelin protein primary structure and bound fatty acids determined by mass spectrometry, Anal. Bioanal. Chem. 2010, 397, 1903-1910.
  159. 157. Shi L.; Yang T-Z.; Zubarev, R. A. Rapid Purification and Identification of Osteopontin from Human Milk by HPLC Coupled to FT-ICR-MS, Chem. Res. Chinese Univ. 2010, 26, 17-22.
  160. 158. Marin-Vicente, C.; Guerrero-Valero, M.; Nielsen, M. L.; Savitski, M. Gomez-Fernandez, J.; Zubarev, R. A.; Corbalan-Garcia, S. ATP enhances neuronal differentiation of PC12 cells by activating PKCα interactions with cytoskeletal proteins. J. Proteome Res. 2011, 10, 529-540.
  161. 159.  Goloborod’ko, A. A.; Mayerhofer, C.; Zubarev, A. R.; Tarasovaa, I. A.; Gorshkov, A. V.; Zubarev, R. A.; Gorshkov, M. V. Alternative Methods for Verifying the Results of the Mass Spectrometric Identification of Peptides in Shotgun Proteomics, J. Anal. Chem. 2010, 65, 1462–1468.
  162. 160. Quéré, R.; Andradottir, S.; Brun, A. C. M.; Zubarev, R. A.; Karlsson, G.; Olsson, K.; Magnusson, M.; Cammenga, J.; Karlsson, S. High levels of the adhesion molecule CD44 on leukemic cells generate acute myeloid leukemia relapse after withdrawal of the initial transforming event, Leukemia, 2011, 25, 515-526.
  163. 161. Chornoguz, O.; Grmai, L.; Sinha, P.; Artemenko, K. A.; Zubarev, R. A.; Ostrand-Rosenberg, S. Proteomic Pathway Analysis Reveals Inflammation Increases Myeloid-Derived Suppressor Cell Resistance to Apoptosis, Mol. Cell Proteomics. First Published on December 29, 2010, doi: 10.1074/mcp.M110.002980.
  164. mcp.M110.002980.
  165. 162. Bakalkin, G.; Watanabe, H.; Jezierska, J.; Depoorter, C.; Verschuuren-Bemelmans, C.; Bazov, I.; Artemenko, K. A.; Yakovleva, T.; Dooijes, D.; Van de Warrenburg, B. P. C.; Zubarev, R. A.; Kremer, B.; Knapp, P. E.; Hauser, K. F.; Wijmenga, C.; Nyberg, F.; Sinke, R. J.; Verbeek, D. S.  Prodynorphin Mutations Cause the Neurodegenerative Disorder Spinocerebellar Ataxia Type 23,  Am. J. Human Genetics, 2010, 87, 593-603.
  166. 163. Misharin, A. S.; Zubarev, R. A.; Doroshenko, V. M. Fourier transform ion cyclotron resonance mass spectrometer with coaxial multi-electrode cell (’O-trap’): first experimental demonstration, Rapid Commun. Mass Spectrom.  2010, 24, 1931-1940.
  167. 164. Zubarev, R. A. Role of Stable Isotopes in Life -  Testing Isotopic Resonance Hypothesis, Genomics, Proteomics & Bioinformatics, 2011, 9, 15-20.
  168. 165. Goloborodko, A. A.; Gorshkov, M. V.; Good, D. M.; Zubarev, R. A. Sequence scrambling in shotgun proteomics is negligible, J. Am. Soc. Mass Spectrom. 2011, 22, 1121-1124.
  169. 166. Artemenko, K. A.; Lind, S. B.; Elfineh, L.; Mayrhofer, C.; Zubarev, R. A.; Bergquist, J.; Pettersson, U. Optimization of immunoaffinity enrichment and detection: toward a comprehensive characterization of the phosphotyrosine proteome of K562 cells by liquid chromatography-mass spectrometry, Analyst, 2011, 136, 1971-1978.
  170. 167. Scholz, B.; Sköld, K.; Kultima, K.; Fernandez, C.; Waldemarson, S. Savitski, M. M.; Söderquist, M.; Borén, M.; Stella, R.; Andrén, P.; Zubarev, R.; James, P. Impact of Temperature Dependent Sampling Procedures in Proteomics and Peptidomics – A Characterization of the Liver and Pancreas Post Mortem Degradome, Mol. Cell Proteomics. 2011, 10, DOI: 10.1074/mcp.M900229-MCP200.
  171. 168. Sinha, P.; Chornoguz, O.; Clements, V. C. Artemenko, K. A.; Zubarev, R. A.; Ostrand-Rosenberg, S. Myeloid-derived suppressor cells express the death receptor Fas and apoptose in response to T cell-expressed FasL, Blood, 2011, 20, 5381-5390.
  172. 169. Lind, S. B.; Artemenko, K. A.; Elfineh, L.; Mayrhofer, C.; Zubarev, R. A.; Bergquist, J.; Pettersson, U. Toward a comprehensive characterization of the phosphotyrosine proteome, Cell. Signalling, 2011, 23, 1387-1395.
  173. 170. Good, D. M.; Zubarev, R. A. Drug Target Identification from Protein Dynamics using Quantitative Pathway Analysis, J. Proteome Res. 2011, 10, 2679-2683.
  174. 171. Enyenihi, A. A.; Yang, H.; Ytterberg, A. J.; Lyutvinskiy, Y.; Zubarev, R. A. Heme binding in gas-phase holo-myoglobin cations: distal becomes proximal? J Am Soc Mass Spectrom. 2011, 22, 7651-7656.
  175. 172. Yang, H.; Lyutvinskiy, Y.; Soininen, H.; Zubarev, R. A. Alzheimer’s disease and mild cognitive impairment are associated with elevated levels of isoaspartyl residues in blood plasma proteins, J. Alzheimer’s Disease, 2011, 27, 113-118.
  176. 173. Samgina, T. Y.; Gorshkov, V. A.; Vorontsov,  Y. A.; Artemenko, K. A.; Zubarev, R. A.; Lebedev, A. T. Mass spectrometric study of bradykinin-related peptides (BRPs) from the skin secretion of Russian ranid frogs, Rapid Commun. Mass Spectrom. 2011, 25, 933-940.
  177. 174. Kjeldsen, F.; Zubarev, R. A. Effects of Peptide Backbone Amide-to-Ester Bond Substitution on the Cleavage Frequency in Electron Capture Dissociation and Collision-Activated Dissociation, J Am. Soc. Mass Spectrom. 2011, 22, 1441-1452.
  178. 175. Lei, S.; Shuying, L.; Zubarev, R. A. ECD Technology in Biological Mass Spectrometry, Progress in Chemistry, 2011, 23, 1710-1718.
  179. 176. Ledvina A. R.; Savitski M. M.; Zubarev A. R.; Good, D. M.; Coon, J. J.; Zubarev, R. A. Increased Throughput of Proteomics Analysis by Multiplexing High-Resolution Tandem Mass Spectra, Anal. Chem. 2011, 83, 7651-7656.
  180. 177. Quere, R.; Andradottir, S.; Brun, A. C. M.; Zubarev, R. A.; Karlsson, G.; Olsson, K.; Magnusson, M.; Cammenga, J.; Karlsson, S. High levels of the adhesion molecule CD44 on leukemic cells generate acute myeloid leukemia relapse after withdrawal of the initial transforming event, Leukemia 2011, 3, 515-526.
  181. 178. Samgina T. Yu; Gorshkov V. A.; Vorontsov Ye. A.; Artemenko, K. A.; Ogourtsov, S. V.; Zubarev, R. A.; Lebedev, A. T.  Investigation of skin secretory peptidome of Rana lessonae frog by mass spectrometry, J Anal Chem 2011, 66, 1298-1306.
  182. 179. Samgina, T. Yu.; Gorshkov, V. A.; Vorontsova, Ye. A.; Artemenko, K. A.; Ogourtsov, S. V.; Zubarev, R. A.; Lebedev, A. T. Mass Spectral Study of the Skin Peptide of Brown Frog Rana temporaria from Zvenigorod Population, J Anal Chem, 2011, 66, 1353–1360.
  183. 180. Cox, J.; Heeren, R. M. A.; James, P.; Jorrin-Novo, J. V.; Kolker, E.; Levander, F.; Morrice, N.; Picotti, P.; Righetti, P. G.; Sánchez, J-C.; Turck, C. W.; Zubarev, R. A.; Alexandre, B. M.; Corrales, F. J.; Marko-Varga, G.; O’Donovan, S.; O’Neil, S.; Prechl, J.; Simões, T.; Weckwerth, W.; Penque, D. Facing challenges in Proteomics today and in the coming decade: Report of Roundtable Discussions at the 4th EuPA Scientific Meeting, Portugal, Estoril 2010, J Proteomics, 2011, 75, 4-17.
  184. 181. Lindén, M.; Bergström Lind, S.; Mayrhofer, C.; Segersten, U.; Wester, K.; Lyutvinskiy, Y.; Zubarev, R. A.; Malmström, P-U.; Pettersson, U. Proteomic analysis of urinary biomarker candidates for nonmuscle invasive bladder cancer, Proteomics, 2012, 12, 135–144.
  185. 182. Zubarev, R. A.; Good, D. M.; Savitski, M. M. Radical a-ions in electron capture dissociation: on the origin of species, J Am. Soc. Mass Spectrom. 2012, DOI: 10.1007/s13361-012-0374-2.
  186. 183. Masforrol, Y.; Gil, J.; Gonzalez, L. J.; Perez-Riverol, Y.; Fernandez-de-Cossio, J.; Sanchez, A.; Betancourt, L. H.; Garay, H. E.; Cabrales, A.; Albericio, F.; Yang, H. Q.; Zubarev, R. A.; Besada, V.; Acosta, O. R. Introducing an Asp-Pro Linker in the Synthesis of Random One-Bead-One-Compound Hexapeptide Libraries Compatible with ESI-MS Analysis, ACS Combinatorial Sci, 2012, 14, 145-149.