| Among many kinds of analytical methods, mass spectrometry (MS) has been considered to be a widely universal method with both high selectivity and high sensitivity. In the past two to three decades, mass spectrometry has become the most core analysis techniques in the field of analytical chemistry, especially for the analysis of biological macromolecules. The application of mass spectrometry is very extensive including aerospace, geological, metallurgical, pharmaceutical, forensic, life science, food safety, environmental pollution, homeland security and other fields.The generation and progress of mass spectrometry was associated with the establishment and improvement of the modern theory of electromagnetism. Since the first cathode ray vacuum tube for measuring mass-to-charge ratio of electron invented by J. J. Thomson in1897, the mass spectrometer experienced a very rapid development during the past100years. The different types of samples, at different states and under different operating conditions, can be detected by a variety of ion sources and with the combination of different mass analyzers, plenty of sample chemical and structural information could be obtained. In21st century, one of the most important development directions of mass spectrometer is miniaturization and portability. The aim is to get rid of the restrictions of big volume, high weight of traditional mass spectrometer and carrying out the mass spectrometry analysis out of the laboratory to realize the real-time, on-site sample detection. Compared to other mass analyzers, quadrupole ion trap mass analyzer has become the optimal choice for mini and portable mass spectrometer because of its simple structure, small size, high working gas pressure, cheap cost and tandem Mass Spectrometry performance, and so on. Quadrupole ion trap mass spectrometry has become a research hotspot in mass spectrometry once again.In the development process of the ion trap, Paul put forward the theory of quadrupole ion trap in1953and commercialization ion trap mass spectrometer began from1987. The ion trap at that time was the three-dimensional (3D) structure, composed of two end cap electrodes and one ring electrode and the working surface of the electrode were hyperboloid. The trajectory of ions in the3D trap was confined at one point by the action of the voltage in the three-dimensional direction result in that the storage space and storage efficiency of the ions was limited severely. In addition, processing and assembly of the hyperboloid shape electrodes were also another problem of the three-dimensional ion trap. Linear ion trap (LIT) was developed by Thermo Corporation in2002and hyperboloid working surface of electrodes were used only in two directions on the radial and the plate electrodes were used in the axial direction in LIT. The trajectory of the ions in the LIT was confined at a line, and the ion storage space and storage efficiency of LIT was significantly improved. Rectilinear ion trap (RIT), as a further simplified version of the linear ion trap with hyperboloid shape electrodes, was designed and developed since2004. The structure and electrode properties of RIT further reduced requirements of the processing and assembly of the trap while ensuring the performance. A series of portable mass spectrometer based on RIT has been developed and investigated. However, there still are many problems with RIT including the precision electrode assembly, trap symmetry and other factors, which limits its commercial promotion.Tandem mass spectrometry capability is the one of the biggest advantages of quadrupole ion trap mass spectrometer and a multi-stage tandem mass spectrometry analysis can be achieved under a single ion trap mass analyzer. The Tandem mass spectrometry is a powerful analytical tool in biological protein and peptide sequencing as well as the chemical structure study of the biomolecules, which is always the hotspot in mass spectrometry field. The developed methods for tandem mass spectrometry in ion trap mass spectrometer mainly are collision-induced dissociation (CID) and electron capture dissociation (ECD) and electron transfer dissociation (ETD), among which CID technique are most common used.In this thesis, the main research area is the research of new types of ion trap mass analyzers and the dissociation methods for gas phase ions in the ion trap. The whole content is divided into two parts, the first part is about the research of new types of ion trap mass analyzers and a number of new linear ion trap with independent intellectual property rights was designed, manufactured and investigated. The second part is about a new type tandem mass spectrometry:the dipolar DC driven collision-induced dissociation and the design, setup and application were discussed. The major contribution and innovation of this thesis are as follows:1. Either for conventional3D ion trap or the linear ion trap developed recently, the electrodes was made of metal material, generally stainless steel. The fixing and electrical insulation maintaining between electrodes all needs additional insulating material, for which ceramic material is the most commonly used. The accuracy of processing and assembling of the ion trap requires not only the precision of the stainless steel electrodes, also high precision ceramic material. The gold plated zirconia ceramic electrodes were used to build rectilinear ion trap, named ceramic-based rectilinear ion trap (cRIT). Both end segments (2mm width) were uncovered for the reason of insulation. There is a hole on each uncovered segment, and the four electrodes were fixed to the two end-cap electrodes by eight M1×8machine screws through the holes. The x and y electrodes were insulated each other by the two end-caps. The two circular end cap electrodes were used to assemble the ion trap electrodes and to keep good concentricity with other electric components. The assembly of the entire well is completely done by hand and the overall mechanical tolerances of all cRIT parts were tightly controlled within～10μm. The cRIT have shown an alternative way to construct the rectilinear ion trap with no discount performance.2. The electric field is mainly quadrupole field. From the view of physics, a perfect quadrupole field will have the most perfect analysis performance, but a perfect quadrupole field is a fully enclosed structure, which is infeasible for ion injection and ejection. The advantages of RIT were simple structure, ease of processing and assembly. But too simple structure also led to the more complex electric field composition in the trap, holes for ion injection and slots for ion ejection all will increase the higher order field components. The geometric structure of the ion trap will directly determine the distribution of the electric field in the trap, compared to other geometry parameters, the field radius ratio, i.e.(xo/yo) is the most major factor. A series of cRITs with different field radius ratios were constructed for geometry optimization. Their performances were compared by theory calculation and experiment.3. The performance of the ion trap mass spectrometer depends on the electric field distribution in the trap, while the electric field distribution is determined by the ion trap electrode geometry and the voltage applied. For rectilinear ion trap (RIT), the electric field distribution is complex even ignoring the geometry defection. There are many higher order fields besides the quadrupole field, which directly affect the ion trajectories inside the trap and the performance of ion trap mass spectrometry. It is very difficult to describe the ion motion and the property of RIT mathematically, In this thesis, the stability diagrams of RITs with different geometries were mapped and their performances were compared. We investigated the stability diagram of different RITs by changing the proportion of trap electrodes. The results show that the performance of RIT such as mass resolution can be estimated by simply comparing their stability diagram. In addition, the incomplete stability diagrams were obtained for y-direction stretched RITs. And the performance of y-direction stretched RITs can be improved remarkably by modulating the quadrupolar-DC voltages according to the characteristics of the boundaries of its stability diagram.4. With respect to the sine-wave voltage driving technology in conventional ion trap, digital ion trap (DIT) is a new technique for the ion trap operating mode, and has shown many unique advantages. In DIT, digital square waveform was used to drive the ion trap and mass scan process was completed by scanning the frequency of the square waveform with fixed amplitude. In this thesis, the performance of RIT in the digital ion trap mode and geometry optimization was investigated and an in-depth research about the effect of the amplitude of the square waveform voltage, scan rate, and other factors for the trap capability. In addition, another advantage for the cRIT is that the film with special patterns can be manufactured on the surface of ceramic electrode field.5. A mesh-electrode linear ion trap (ME-LIT) was developed and its performance was primarily characterized in this thesis. In the conventional LIT mass analyzer, the trapped ions were mass-selected ejected out from the trap in radical direction by a slot on a trap electrode. The slot could significantly affect the field distribution in the ion trap region and distorted the mass analysis performance. To compensate the detrimental electric field effects due to the slot, the slot were usually designed and machined as small as possible and it also needed very high mechanical accuracy and symmetry for having higher mass resolving power and ion ejection efficiency. In this study, a linear ion trap was constructed with several mesh-electrodes. The mesh-electrode was built with a plate electrode with a "big" slot on it and the slot was covered with a mesh. The MELIT could significantly diminish the detrimental electric field effects, decrease the requirement of the mechanical accuracy and symmetry, and increase the ion ejection and detection efficiency because of its big size. The ME-LITs with different geometries were assembled and tested. The stability diagram was mapped, a mass resolution in excess of500was obtained and high efficiency tandem mass spectrometry was demonstrated. The ME-LIT was proved to be a qualified linear ion trap mass analyzer and has the potential to be used widely.6. The ion trap is the only one type mass analyzer in which the multi-stage tandem mass analysis can be carried out in a single device and therefore the study of the method for tandem mass spectrometry in the ion trap has always received great attention. In this thesis, the digital ion trap technology was combined with the ceramic-based rectilinear ion trap (cRIT) system. Rectangular waveform was used for ion trapping. A dipolar excitation waveform which was by dividing down the trapping rectangular waveform was used for the ion ejection. We found that the high efficient collision-induced dissociation (CID) procedure of gas phase ions in the ion trap could be obtained by simply manipulating the duty cycle of the dipole excitation waveform, it could significantly simplify the tandem mass spectrometry analysis method and procedure with ion trap, since the dipolar DC voltage could be easily produced and applied to one pair of electrodes, which was fully controlled by computer software and does not need any hardware modification.The whole thesis is divided into six chapters and its major contents are listed as follows:Chapter1:Introduction. This chapter provides an overview of the principles and development of mass spectrometry. Research and The quadrupole ion trap mass analyzer were highlights and discussed in detail. Based on these comments and summarize, the research direction and research ideas were raised.Chapter2:Research and investigation of the ceramic-based rectilinear ion trap (cRIT). This chapter described the design, assembly and performance of the cRITs. In addition, the method for stability diagram mapping was introduced and relationship between the performance and stability diagram were studied. Finally, the experimental results are summarized and discussed.Chapter3:Research and investigation of cRIT in the digital ion trap mode. The principle and current status of digital ion trap were introduced firstly. A discussion about the resolution of the rectilinear ion traps in digital ion trap mode including mass scan rate, the amplitude of trapping waveform and so on was concluded in detail. Finally, the experimental results are summarized and discussed.Chapter4:Research and investigation of mesh-electrode linear ion trap (ME-LIT). In this chapter, a novel type of linear ion trap mesh-electrode linear ion trap (ME-LIT) using mesh with larger area to replace conventional narrow slit for ion ejection, has been constructed and its preliminary performance were evaluated. The experimental results are summarized and discussed.Chapter5:Research and investigation of dipole DC driven collision-induced dissociation method (DDC driven CID). Dissociation method used for tandem Mass Spectrometry in the ion trap was firstly introduced. The principle and instrument setup of DDC driven CID method were described and the application of the method for organic molecule and peptide molecules were shown as well. In addition, the study of selective dissociation of sample leucine enkephalin by DDC driven CID method was introduced. Finally, the experimental results are summarized and discussed.Chapter6:Conclusion and looking forward. In this chapter, all major achievements of this dissertation were concluded. Meanwhile, some drawbacks and looking forwards in our current researches were pointed out and some latent methods for the improvement were also presented.
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