Addressing the influence of charged plasma effects in the Penning traps on mass accuracy measurements by Fourier transform ion cyclotron resonance mass spectrometer
04 / 2004 - 03 / 2007
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)
In the rapidly developing field of proteomics, where a systematic analysis of proteins expressed in the cells of different living organisms is envisaged, FT ICR spectrometry plays a unique role. It provides a tool for direct measurements of molecular masses of proteins and peptides (small proteins or products of protein cleavage). Combined with high end database queries this technique drastically enhances the protein identification capabilities in complex mixtures. The probability of unambiguous protein identification is directly proportional to the experimentally obtained mass measurement accuracy. For the majority of peptides 1/10 to the power 6 mass accuracy is enough for such identification. By using the FT ICR technique mass accuracies up to 1/10 to the power 9 have been demonstrated on separate ion doublets by accurately measuring the cyclotron frequency of the ions stored in the Penning trap of the FT ICR. The current understanding of the processes taking place inside the Penning trap of the FT ICR spectrometer dictates that the main source of the errors in determining the cyclotron frequency is an interaction of clouds of different m/z ions with each other and ion-ion interaction inside these clouds. In addition, thermal electrons can be introduced into the Penning trap for structural analysis of the macromolecules. These electrons and the following ion-electron reactions have a strong effect of the ion-ion interactions. These interactions show great similarities with reactions occurring in magnetically confined charged plasmas. For that reason we propose to use computational methods developed in the field of plasma physics to describe and model the ion-ion and ion-electron interactions inside the charged plasma captured in the Penning trap of the FT ICR. To have a large dynamic range in the mass spectrum (the ration of maximum to minimum numbers of ions of different m/z in the trap) as many as possible ions should be trapped. Because of strong ion-ion interactions between ions rotating in the cell after excitation the actual cyclotron frequencies are shifted from the natural cyclotron frequencies W= B*z/m. This shift for particular m/z ions depends strongly on the number of ions in the cell and on the relative positions of different m/z ion clouds. These positions depend strongly on the excitation procedure. Ions are excited to their cyclotron orbits from the center of the trap where they are located after being trapped. In this state they experience strong Coulomb interaction, which causes coupling of their motion at the beginning of the excitation event. This coupling causes large differences in mass spectra obtained with different modes of RF-excitation. Both groups were trying to address the problem of improving mass accuracy measurements and attempts were made to understand the sources of mass errors in FT ICR measurements. The main conclusion made from earlier studies is that only direct modeling of charged plasma effects causing cyclotron frequency shifts could provide answers. In this collaboration we intend to systematically investigate the problems described above by combining FT ICR experiments from both groups with "in-silico" computer experiments.