TECHNICAL REPORT ON THE PAUL TRAP MASS SPECTROMETER DEVELOPED IN THE MASS SPECTROMETRY LABORATORY S. Renuka Prasad, S. Sevugarajan, Vikram A. Sarurkar, Jiss Paul, Dnyaneshwar Gorde DEPARTMENT OF INSTRUMENTATION INDIAN INSTITUTE OF SCIENCE BANGALORE 560 012 March 2003 Mass Spectrometry Laboratory, IISc 31 COPYRIGHT 2003 BY MASS SPECTROMETRY LABORATORY DEPARTMENT OF INSTRUMENTATION INDIAN INSTITUTE OF SCIENCE BANGALORE –560 012 INDIA. Mass Spectrometry Laboratory, IISc 2 Preface This report provides technical details of a Paul trap mass spectrometer fabricated in our laboratory. The report has two motivations. First, it aims to consolidate and put together at this point of time, the status of our efforts. This will help us in making a “road map” for future developments. Secondly, this report hopes to be a primer, an introduction, for future generation of students who enter the laboratory and wish to make a quick entry into the experiments going on in the lab. In addition, I think this report will also be of interest to groups of aspiring ion trappers in the country who have been enthused and encouraged by our progress to “get into” the area of ion trap mass spectrometry. They have often asked if this is an “expensive” area of research. To this latter group I would like to say that our modest success has been possible with a “shoe-string” budget and an abundance of enthusiasm of dedicated young students who contributed bits and pieces of their time. March 2003 Mass Spectrometry Laboratory, IISc A. G. Menon 3 Mass Spectrometry Laboratory, IISc 4 Contents Page no. 1. Introduction………………………………………………………….7 2. Ion trap mass spectrometry………………………………………….8 3. Technical specifications…………………………………………….16 4. Performance characteristics………………………………………..25 Appendix 1 Circuit diagrams of electronic circuits…………………………….33 Appendix 2 Technical specifications of DAQ, PCI-MIO-16-E-1………………41 References……………………………………………………………….51 Mass Spectrometry Laboratory, IISc 5 Mass Spectrometry Laboratory, IISc 6 1 Introduction The motivation of this technical report is to describe the design and provide fabrication details of the Paul trap mass spectrometer that has been built in our laboratory. This technical report gives both the theory of ion trapping in Paul trap mass spectrometers and the technical specifications of mechanical assembly, vacuum chamber and other electronic subsystems associated with our laboratory’s Paul trap mass spectrometer. Section 2 gives the theory of the ion trap mass spectrometry including development of equations of ion motion and the conditions required for the ions to have stable trajectories inside the trap. Section 3 provides the technical specifications of our trap electrodes, electronic subsystems including constant current source, gating power supply, extraction power supply, high voltage dc power supply, RF signal generator as well as the vacuum system and graphical user interface are presented. Section 4 presents a few mass spectra to demonstrate the performance our mass spectrometer. Appendix 1 gives the detailed orcad layouts of all the electronic circuits associated with the Paul trap mass spectrometer and the technical data related to the National Instruments data acquisition device PCI-MIO-16-E-1 is given in Appendix 2. At the end of the report a few important and pertinent references are provided. Mass Spectrometry Laboratory, IISc 7 2 Ion trap mass spectrometry 2.1 Motion of ions The Paul trap mass spectrometer consists of a 3-electrode geometry mass analyzer with a hyperboloid of one sheet forming the central ring electrode and hyperboloid of two sheets forming the two-endcap electrodes (March and Hughes, 1989). In an ideal Paul trap, the potential distribution inside the trap is quadratic and the field varies linearly. The potential distribution has both spherical and rotational symmetry due to the geometry of the ion trap. Legendre polynomials are used repersenting such potential distributions inside the ion trap. If Pn is the Legendre polynomial of order n, then the potential distribution inside the trap in terms of spherical co-ordinates are given by (Brown and Gabrielse, 1986; Beaty, 1986) ∞ ρn n=0 ron φ ( ρ ,θ ,ϕ ) = φo ∑ An Pn (cos θ ) (2.1) (1.1) where ro = radius of the ion trap and φo is a time dependent potential given by φo = U o + Vo cos Ωt (2.2) where Vo = zero-to-peak voltage of the RF potential Uo = magnitude of the dc potential. An = dimensionless weight factors for different terms. The various terms corresponding to n = 0,1,2,3…etc. represent the multipole components of the potential. In case of pure quadrupolar ion trap only the term corresponding to n = 2 is non-zero. Therefore the potential distribution in a pure quadrupole ion trap in terms of cylindrical co-ordinates r and z can be written as φ ( r , z ) = A2 z 2 − r2 2 (2.3) where A2 is the weight of quadrupole component and has a value of –2 for pure quadrupolar potential distribution. The differential equation that governs the motion of a single ion can be obtained from (Landau, 1976) ρ dρ (r , z ) e = − ∇φ (r, z ) 2 m dt Mass Spectrometry Laboratory, IISc (2.4) 8 ρ where ρ is the position vector and ρ2 = r2 + z2. Substituting equation (2.3) in equation (2.4) we get κe d 2u = [U o + Vo cosΩt ]u 2 dt mro2 (2.5) where κ = -2 when u refers to the radial, r, direction and κ = 4 when u refers to the axial, z, direction. Equation (2.5) can be rewritten in the canonical form of the Mathieu equation as d 2u + (a u − 2q u cos 2ξ )u = 0 dξ 2 (2.6) with the substitutions ξ = Ωt/2 and a z = − 2a r = q z = 2q r = − 8eU o mro2 Ω 2 (2.7) . 4eVo . mro2 Ω 2 (2.8) The parameters au and qu are referred to as Mathieu parameters. The solution to the equation (2.6) (McLachlan, 1947) is given by u = Au U e (ξ ) + Bu U o (ξ ) (2.9) where Au and Bu are arbitrary constants and U e (ξ ) = U o (ξ ) = ∞ ∑C 2 n ,u cos(2n + β u )ξ (2.10) ∑C 2 n ,u sin(2n + β u )ξ (2.11) n = −∞ ∞ n = −∞ If we define ωu,n as the angular frequency of order n for motion in direction u (= r,z) it can be shown that 1 2 ω u , n = n + β u Ω 0≤n≤∞ Ωt Θ ξ = 2 (2.12) when n = 0 the fundamental frequency ωu,0 in either r or z direction is given by ωu is referred to as the secular frequency of the ion in the respective direction. Mass Spectrometry Laboratory, IISc 9 ωu = 1 βuΩ 2 (2.13) Substituting equation (2.10) and (2.11) into equation (2.9) and solving for C2n,u co-efficients, we get recursion formulae for C2n,u co-efficients. On elimination of C2n,u co-efficients we get the continuous fraction expression for βu in terms of au and qu as (March, 1992; March and Hughes, 1989) β u2 = a u + + q u2 (β u + 2) − a u − q u2 2 (β u + 4) − a u − 2 (β u q u2 + 6 ) − a u − ... 2 q 2u (β u − 2) − a u − q u2 2 (β u − 4) − a u − 2 (β u q u2 − 6 ) − a u − ... 2 (2.14) Stable regions of ion trajectories are characterized by values of au and qu for which βu lies between 0 and 1. Fig. 2.1 Mathieu stability plot. Mass Spectrometry Laboratory, IISc 10 Fig. 2.1 shows the condition under which ions will be stable inside an trap. The lines along which the βz remains constant are known as the iso-βz lines, similarly the lines along which βr remains constant are known as iso-βr lines. Let us now take a closer look at Fig. 2.1 to see how it could be of help from the point of view of the Paul trap mass spectrometer. What the stability plot implies is that all au- qu values lying outside the area bounded by βz = 0 to 1 and βr = 0 to 1 will have unstable trajectories. A choice of an au-qu can be translated to dc voltage (Uo) and RF amplitude (V0) values by substitution in equation (2.7) and (2.8) above (for a given mass, frequency and ro ). Similarly, any point chosen within the stable region will indicate stable trajectories at the computed Uo and Vo values (again for a given mass, frequency and ro ). This provides us with a very simple technique to operate the instrument as a mass spectrometer. Let us choose to operate the mass spectrometer with Uo = 0 volts. What this means is that the "operating line" lies along the au = 0 axis. Along this line, the βz = 1 curve crosses this axis at a qu value of 0.908 (referred to in literature as qcut-off). If we re-write equation (2.8) so that we may use commonly used units (i.e.: m in amu, Vo in volts, ro in cms, and Ω in MHz) it takes the form qz = 0.0978Vo mro2 Ω 2 (2.15) For qz = 0.908, ro =0.7cm and Ω = 1MHz, equation (2.16) gives a relationship between mass and Vo as m = 0.2198Vo(0-p) (2.16) Equation (2.16) provides us with the relationship, which can be used by the mass spectroscopists in interpreting the intensity-voltage histogram as a mass spectrum. In ideal Paul traps the ion trajectories can be calculated from equation (2.6). The form of ion trajectory in an r-z plane resembles Lissajous patterns composed of two frequency components ωr,0 and ωz,0 with a superimposed micromotion of frequency Ω/2π due to the RF drive frequency (Dawson, 1976). Consequently, in z direction, the motion of ion can be represented by z=Z+Γ (2.17) where Γ is the displacement due to micromotion and Z is the displacement due to macromotion (which is the secular motion of the ions). When Γ << Z (that is z ≅ Z), it can be shown that the acceleration due to RF drive d2Γ/dξ2, averaged over a period of the RF drive is equal to zero and the acceleration of the secular motion d2z/dξ2 averaged over the same period is given by Mass Spectrometry Laboratory, IISc 11 1 2 d 2z = − + a qu z u 2 dξ 2 (2.18) which, when written in terms of time, becomes d 2z 1 2 Ω2 a qu z = − + u 2 4 dt 2 Ωt Θ ξ = 2 (2.19) Equation (2.19) corresponds to simple harmonic motion of the ions and if ω0 is used to refer to the ion secular frequency, then d 2z = − ω 02 z dt 2 (2.20) Comparing equation (2.13) and (2.19) it turns out that 1 β z = a u + q u2 2 1/ 2 (2.21) The expression (2.21) is valid for qz values less than 0.4. This approximation is known as Dehmelt or adiabatic approximation (Wuerker et al., 1959; Dawson, 1976). In practice, however, several geometrical and constructional imperfections introduce non-linearities in the field distribution. The real trap potential deviates from the ideal one due to truncation of the electrodes, deviations from the hyperbolic shape, possible misalignments, space charge of the stored ion cloud and existence of aperture for admitting electrons as well as for the collection of destabilized ion. The fundamental properties of the ion motion within the idea Paul trap is hence altered due to the introduction of higher order terms in the quadrupolar field, thus exhibiting effects differing considerably from those of the linear trap. Some of these effects are as follows: the non-linearity of the RF field in the axial and radial direction, perturbation in ion secular frequencies (the characteristic frequency with which the ions oscillate inside the trap) and coupling between axial and radial motion. The experimental conditions in practical traps appear as non-linear parameters in the restoring term in the equation of ion motion. These higher order contributions can be visualized as “perturbations” to the ion motion in a pure quadrupolar field. The equation of ion motion in axial and radial directions incorporating the experimental and practical constraints resembles the well-studied Duffings equation. Mass Spectrometry Laboratory, IISc 12 2.2 Block diagram of the Paul trap mass spectrometer The block diagram of a Paul trap mass spectrometer is given in Fig. 2.2. It consists of a three-electrode geometry mass analyzer, an electron gun and a detector. The electronic circuits include an electrode gun supply, an RF power source, a dc high voltage detector power supply and a interface card to enable PC control of the instrument. In our mass spectrometer the analyte gas molecules are ionized in situ by electron bombardment. Electrons are produced by thermionic emission when a rhenium filament is heated by a constant current source. An extraction electrode in combination with the gating electrode focuses ions into the central cavity of the trap. The gating electrode is used to gate the electron beam into the ion trap cavity. When positive potential is applied to the gating electrode the electron beam is allowed into the ion trap cavity, and when negative potential is applied the electron beam is blocked. The electron beam gating control block consists of positive and negative voltage power supplies. A high voltage pulsing circuit connects the two power supplies alternately to the gating electrode, thereby allowing the electron beam in or blocking it. The high voltage RF supply supplies a 1MHz, 2kVp-p RF potential for producing the confining field. The RF power supply is based on a crystal oscillator for high frequency stability. A high-Q LC tuned circuit at the output couples the output of the supply to the ion trap. The electrometer amplifier having a gain in about of 106 amplifies output from the electron multiplier detector. It also has a fast response time to faithfully amplify the fast rising mass peaks. 2.3 Timing diagram In order to obtain the mass spectrum of an analyte gas the different electronic subsystems related to electron gun and amplitude of the RF potential needs to be co-ordinated. The timing diagram for a simple scan in a typical experiment is shown in Fig. 2.3. At the start of the experiment, an ionization pulse is applied to the gating electrode. This allows the electron beam in the trap and ionizes the analyte gas molecules inside. The RF potential at this instant is held at a value such that the lowest mass of interest is trapped. After this ionization phase the ions are allowed to cool in the cooling period. After the cooling period the RF is ramped to generate the mass spectrum and electron multiplier detector detects the ejected ions. The mass spectrum from each experiment is then averaged to get a better S/N ratio. Mass Spectrometry Laboratory, IISc 13 Fig. 2.2 Block diagram of a Paul trap mass spectrometer Mass Spectrometry Laboratory, IISc 14 . Ionization Cooling Ramping time time time Figure 2.3: Timing diagram of Paul trap mass spectrometer Mass Spectrometry Laboratory, IISc 15 3 Technical specifications and circuit description 3.1 Mass analyzer The hyperbolic profile of the endcap and ring electrode is given by (Knight,1983) r2 z2 − = −1 ro2 z o2 r2 z2 − =1 ro2 z o2 (end cap) (ring electrode) (3.1) (3.2) In an ideal trap the radius of the central ring electrode ro and half the distance between the two closest points of end-cap electrodes zo are related by the expression ro2 = 2z02. The radius of the ring electrode r0 in our machine is 7mm and z0 (= r0/√2) works out to 4.95mm. The electrodes are fabricated from austenitic stainless steel flanges whose diameter is 88.9mm (3.5”) and the surfaces are machined at the center of the flange using a CNC lathe. The truncation of the electrodes has been made at 3ro. For achieving the required axial distance between the tips of the end cap electrodes as 9.9mm (=2zo) appropriate Teflon spacers have been used between the electrodes. The endcap electrode which faces the filament side has a 1mm diameter hole at it’s center for admitting electrons into the trap for ionizing the neutral analyte gas molecules. The other endcap electrode, which faces the electron multiplier, has a 3mm hole at its center for collecting the destabilized ions. 3.2 Electron gun The electron gun consists of a filament, an extraction electrode and a gating electrode. Our filament has a triple filament assembly and is a spare of the filament of the thermal ion source of a written-off AEI-MS702 mass spectrometer. We use both rhenium and tungsten filaments. The extraction electrode, gating electrode and the filament are all electrically isolated and mounted on one-endcap electrode. Mass Spectrometry Laboratory, IISc 16 3.3 Detector The electron multiplier used in our machine is an ETP’s electron multiplier (model number AEM 5000A). It provides an amplification of about 106 for a bias voltage of –2.5kV. 3.4 Mounting flange The Paul trap mass spectrometer including the mass analyzer, electron gun and electron multiplier are mounted on CF100 stainless steel flange. Provision has been made on this flange for attaching two needle valves for admitting sample gases. Vacuum feed throughs have been made locally using Teflon and stainless steel welding rods. First, Teflon cylinders were tight fitted into the flange and then 2mm stainless steel welding rods are pierced into the Teflon. Two 5-pin feed throughs and three single-pin feed throughs have been used. These feed throughs were tested to withstand a pressure of 10-6torr. 3.5 Vacuum The mechanical assembly of the Paul trap is positioned in a vacuum chamber. Vacuum sealing of the demountable flange is done using a neoprene O-ring. The vacuum is maintained at 10-6 torr with a help of a diffusion pump/ LN2 trap backed by a rotary pump. Pirani and Penning gauges are used for measuring the pressure. 3.6 Electronics The Paul trap mass spectrometer requires the following power supplies for its operation: Constant current source: A current source that can deliver a current from 0A to 8A to the filament to generate the electrons. Typical value of current used in our experiments is about 4A. Filament bias supply: The filament bias supply is a voltage source capable of outputting 0 to –150V/10mA. It is a variable supply, on which current source floats. Typical value set in our experiments is about –14.5V. Extraction electrode supply: This supply is capable of delivering a variable output voltage from 0 to 130V/10mA. This range of voltage will give flexibility to the experimenter to optimize the extraction voltage for his experiments. In our experiments, the extraction electrode is biased at 30V. Gating electrode supply: This supply is capable of delivering a switched ±150V to the gating electrode. The switching of the gating electrode enables control on Mass Spectrometry Laboratory, IISc 17 the entry of electrons into the trap. This switching is done through a pulsing circuit. RF power supply: This variable RF generator outputs 1.5kVp-p at a frequency of 1MHz for analyzing masses up to 150amu. High voltage dc power supply: This supply is capable of delivering 0 to – 3kV/1mA dc voltage for biasing the electron multiplier. This switched mode power supply is kept at –2.5kV in our experiments. Electrometer amplifier: Electrometer amplifier is required for further amplifying the ion signal obtained from the electron multiplier. The gain of this amplifier is about 106. The description of these circuits will be discussed in the following sections. For ionization of the sample gas molecules, we require sufficient number of electrons with sufficient energy. These electrons are produced by an electron gun. An electron gun assembly used by us consists of a filament, an extraction electrode and a gating electrode as shown in Fig. 3.1. Figure 3.1: Electron gun assembly Electrons are produced by thermionic emission from a filament with high work function. The number of electrons produced is function of the temperature of the filament and thus passing larger current through the filament results in higher filament temperature as well as higher electron emission. Since it is desirable to have a constant electron current the instrumentation need to maintain a constant filament temperature. To a good approximation this is achieved by passing a constant current through the filament. The appropriate electronics for passing a constant current through the filament must take into consideration the variation of filament resistance with temperature (both tungsten and rhenium, the filament material used in our experiments, have positive temperature coefficient). The simplest approximation to a current source is using a voltage source V and a series resistor R connected to a load RL as shown in Fig. 3.2. Mass Spectrometry Laboratory, IISc 18 Here as long as RL<<R the current is nearly constant because any small variation in the RL will not seriously affect the combined resistance. But this resistor current source has several drawbacks. For good approximation to a constant current through RL we must use large voltages, with high power dissipation on resistor R. In addition, the current is not easily programmable. Fig. 3.2: Resistor current source An alternative scheme is to use a transistor based constant current source. The basic concept of the current source is shown in Fig. 3.3. This circuit works by applying VB to the base of transistor (with VB > 0.6, so that the transistor will be in active region). Here the power dissipation will depend on the VCE of the transistor and, consequently, a proper choice of VCC can reduce the power dissipation. Further, programming of the current source can be achieved by controlling VB. Fig. 3.3: Basic transistor current source In the present work we have configured a constant current source, which sources current to a load returned to ground. An error amplifier is used to maintain the base bias of the transistor as a constant for a given load current. The basic concept of this circuit is shown in Fig. 3.4. The feedback is obtained from a small current sensing resistor Rs, which is connected in series with the load RL. The error amplifier will compare the voltage across the sensing resistor Rs with Vref, the reference voltage. By varying the Vref we can program the current source. Mass Spectrometry Laboratory, IISc 19 Figure 3.4: Variable constant current source We will next focus on achieving requisite electron energy. This is achieved by floating the filament constant current source with respect to the extraction electrode. The final energy attained by the ion is a combination of this floating voltage, extraction electrode bias as well as the RF amplitude of the ring electrode during the ionization period. We have provided a wide range of voltage from 0V to –150V in order to give variable energy to electrons. Referring to the Fig. 3.1 we should focus the electrons in to the trap to ionize the sample molecules with the help of an extraction electrode is used for this purpose. For focusing the electrons a positive dc voltage is required to be applied to the extraction electrode. This will accelerate as well as focus the electrons in to the trap. Normally the applied dc voltage is of the order of +14.5V. The voltage source used is of voltage series pass voltage regulator. Detailed constant current source circuit diagram is given in Appendix 1. The second electrode in the electron gun assembly is called the gating electrode. This electrode is used to gate the electrons for user-determined times into the trap. This allows the user to control the ionization time and hence the number of ions being produced inside the trap. This timing will lead to the need for a pulsing circuit. This pulsing circuit will give positive or negative dc voltage to the gating electrode to pass or block the electrons. From experiments it was determined that a voltage of +/-150V would be required to accelerate or block the electrons. The basic block diagram of the pulsing circuit is shown in Fig. 3.5. The pulsing circuit should respond to the input pulse. The switching time of the circuit should be minimized to shut the electrons quickly. This circuit is interfaced with the computer where we can determine the pulsing time in terms of ionization time and cooling time using LABVIEW software and interfacing card. The switching device switches the positive or negative supplies to the gating electrode. The switching device used in the circuit is transistor. The isolator will electrically isolate the circuit with computer. Mass Spectrometry Laboratory, IISc 20 Figure 3.5: Basic pulsing circuit The voltage sources mentioned in the above systems uses a series pass voltage regulator which gives a very good output voltage regulation. The basic block diagram of the regulator is shown in the Fig 3.6. A series regulator places the regulating element (series pass control device) in series with the load, and it is the voltage across the regulating element that is varied to adjust the load voltage. A feedback voltage from output is fed to the comparator. This compares the feedback voltage with a reference voltage and the difference signal controls the series pass device. The series pass control device used in the circuit is a transistor and the comparator is based on an operational amplifier. The feedback circuit is a simple resistive voltage divider. The pulsing circuit diagram is given in detail in Appendix 1. Figure 3.6: Basic series pass regulator 2.3 RF power supply For trapping the ions inside the trap RF supply is used to produce a quadrupolar potential distribution inside the trap. RF quadrupolar field causes mass selective trapping of the ions inside the Paul trap. The voltage of the RF power supply can varied up to 1.5kVp-p at 1MHz in order to have a wide mass range with sufficient trapping strength. The basic concept of the RF generator is shown in Fig. 3.7. Mass Spectrometry Laboratory, IISc 21 Figure 3.7: RF generator Since the output voltage of the RF generator should be variable, we use a modulator along with a crystal oscillator that will give 1MHz square wave. This is applied to amplitude modulator, which modulates the amplitude of the 1MHz signal according to the modulating voltage. Finally the modulated signal is applied to a power amplifier, which amplifies the signal as well as tunes the signal with the help of a tank circuit (primary coil) to get a perfect 1MHz sine wave. By proper coupling of this primary RF signal with a secondary tank circuit we can generate the required RF voltage, which will be applied to the trap. The important point to be noted while implementing the RF supply is that we should take into consideration of various capacitance like trap capacitance, cable capacitance etc. Hence, it is better to have a tunable inductance in the secondary to compensate the capacitance change so that the tank circuit will tune to 1MHz. This will ensure maximum coupling between the primary and secondary of the tank circuits. The full circuit diagram of RF generator is given in Appendix 1. High voltage dc power supply An electron multiplier is used to detect the ions ejected out from the trap. In our laboratory we use ETP’s electron multiplier model number AEM 5000A, which works on the principle of secondary emission and amplifies the input ion signal by an amount of up to 107 depending on the dc voltage applied across it. A high negative voltage of order of 3kV is required for the operation of the electron multiplier. This voltage should be regulated and free from ripple as this ripple might get coupled to the output. Using linear techniques it is rather difficult to get a well regulated –3kV power supply. Hence a switched mode power supply techniques are employed to get a regulated –3kV power supply. The detailed circuit diagram of -3kv dc power supply is given in page 38 and 39 of Appendix 1. As shown in the circuit MOSFET IRF840 is used as a series pass element, as a switch, in this case. When the MOSFET is ON energy is stored in an inductor connected to the MOSFET. When the MOSFET switches OFF, the energy stored in the inductor is transferred to another inductor through the ferrite Mass Spectrometry Laboratory, IISc 22 core. The output current is rectified and filtered to give a smooth –3kV DC. The turn’s ratio of the two inductors ensures the steeping up of the voltage. A PIC micro controller is used to control the whole operation of the circuit. It also provides the functions like shutting down the circuit, in event of output overload or overheating of the MOSFET. A serial link is also provided for digitally controlling the output voltage. The MOSFET switching frequency is 50kHz, which ensures easy filtering of the output voltage even by small value capacitors. Electrometer Amplifier An electrometer amplifier is employed for amplifying the signal from the electron multiplier. An electrometer amplifier consists of a trans-impedance amplifier, a current to voltage converter stage, followed by one or two voltage amplification stages. The transimpedance amplifier stage is built around LF351 OpAmp. The feedback resistor sets the current conversion factor to 1V/µA. The bandwidth of the amplifier is limited to 200kHz and the response time of the amplifier is about 5.6µs. Two voltage amplifier stages follow the transimpedance amplifier stage. Each of the voltage amplifier stage has a gain of about 34, thereby giving an overall gain in excess of 1000. Each of the OpAmp is provided with separate supply filtering and decoupling network on the supply pins to minimize the noise. The PCB for the electrometer amplifier is designed with due consideration to noise reduction and is provided with ground planes on both the sides. The decoupling capacitors are kept as close as possible to the supply pins and the signal traces are made as short as they can be. Finally the board is mounted in a metal box to shield the amplifier circuit from radiated noise. The detailed circuit layout is shown in Appendix 1. Graphical User Interface (GUI) A user friendly Graphical interface between the computer and the mass spectrometer has been developed by using National instrument’s LABVIEW software and PCI-MIO-16-E-1 data acquisition device (DAQ). National instrument’s PCI-MIO-16-E-1 data acquisition device (DAQ) generates the required analog and digital signals according to the user’s specification (such as sampling rate, amplitude, timing sequence, etc.,) given in the LABVIEW program. The DAQ that we have in our lab has 16 analog input channels, two 12-bit analog to digital converters with the sampling rate of 1.25 mega samples/sec. The detailed specification of the hardware is given in Appendix 2. Mass Spectrometry Laboratory, IISc 23 Generation of gating pulse and control signal The gating pulse is generated with the help of general-purpose timing signal connections available in the DAQ. The pulse is obtained by programming the GPCTR1 counter/timer through the software. The counter output’s a pulse depending on the total experimental time and the pulse duration depends on the ionization time. The software calculates the total experimental time internally, which is the addition of ionization time, cooling time and ramping time that are set by the user in the program. The control signal for controlling the output amplitude of the RF signal source is generated by digital to analog converter present in the DAQ. The DAQ hardware consists of two digital to analog converters, DAC0 and DAC1. We have used DAC0 for our purpose. The software generates the digitized data and downloads the data to the DAC0 through the computer and DAC0 generates the corresponding analog output. Through the software user can set the ionization time, cooling time, ramping time, initial RF voltage, voltage at ionization period, voltage at cooling period and maximum RF voltage. Acquisition and calibration of mass spectrum The electrometer amplifier’s output is given to channel0 of the ADC present in the DAQ. The analog signal obtained from the electrometer amplifier is converted to digital data’s through the ADC and is displayed in the oscilloscope block available in the front panel of the program. To obtain a better S/N ratio the signal is continuously averaged and is displayed in averaged mass oscilloscope block available in the front panel of the program. For the purpose of displaying the calibrated the obtained averaged mass spectrum we use XY plotter block available in the software. A small amplitude RF signal obtained from the feedback of RF generator is digitized by using channel1 of the ADC in DAQ and this voltage data serves as the input for X terminal of the plotter block. The scale of the X-axis is calibrated in terms of amu by using the Equation (2.16) and by substituting the digitized voltage data obtained from Channel1 for V. The signal for Y input is averaged mass spectrum. The user has the flexibility of zooming the axis of oscilloscope and XY plotter blocks. The program also has the option of restarting the averaging whenever the user changes any of the experiment parameters. Mass Spectrometry Laboratory, IISc 24 4. Performance characteristic 4.1 Mechanical assembly The three trap electrodes, electron gun assembly, extraction electrode, gating electrode and the electron multiplier are supported by three stainless steel pillars. These pillars are mounted on a 6” diameter stainless steel flange. The required electrical isolation is done by using Teflon washers/spacers. The electrical connections from different power supplies are taken into vacuum chamber by Teflon feed through’s that are fitted to the stainless steel flange. The flange has a provision for attaching two needle valve for inletting the analyte gasses. The output of the electron multiplier is taken out to the electrometer amplifier through a stainless steel wire through one of the feed through in the flange. To have a better S/N an electromagnetic shielding is provided to the stainless steel wire by using a stainless steel wire mesh around the wire. The trap electrodes and the entire mechanical assembly are shown in Fig. 4.1and 4.2 respectively. 4.2 Electronics All electronic subsystems were tested for having achieved the desired performance. These test included checking for achieving the required specification and also for their load and line regulation. The final performance of these subsystems will be seen in the quality of the mass spectra obtained. We show below, as an example, the switching characteristics of the pulsing circuit. Fig.4.3 shows the rise and fall time for a ±150V pulse. It may bee seen that the rise time is about 16µs and the fall time is of the order of 270µs. Although the fall time is large, it does not affect the performance of the mass spectrometer. The photograph of the chassis housing the electronic subsystem is shown in Fig. 4.4. Mass Spectrometry Laboratory, IISc 25 Fig. 4.1 Endcap and ring electrodes used in our laboratory Paul trap mass spectrometer Mass Spectrometry Laboratory, IISc 26 Fig. 4.2 Full view of our laboratory Paul trap Mass Spectrometry Laboratory, IISc 27 Fig. 4.3 Switching characteristic of the pulsing circuit. Fig. 4.4 Chassis housing all the electronic subsystem Mass Spectrometry Laboratory, IISc 28 4.3 GUI A snap shot of the GUI developed using LABVIEW is given in Fig.4.5. The user can vary any experimental parameter by setting appropriate values for that particular parameter in the front panel of the GUI. The following section gives the explanation of different functions of the software according to the numerals marked in the front panel. 1. Using six controls, user can set ramping time, cooling time, ionization time, maximum RF voltage, RF voltage at cooling and RF voltage at ionization. 2. This chart shows the typical analog control signal generated by the software. 3. This oscilloscope has the function of displaying the raw ion signal data obtained from the electrometer amplifier. 4. The time averaged uncalibrated mass spectrum will be displayed in this scope. 5. The final calibrated mass spectrum can be obtained from this XY recorder. 6. Adjustments for varying the scales of the oscilloscopes. 7. Display indicating how many cycles of averaging has been done. User can also restart the averaging by pressing “RESET AVERAGING” button. 4.4 Mass spectra The Mass spectrometer has to be operated in the following sequence for obtaining the mass spectrum. 1. Switch ON the rotary pump and open the backing and the butterfly valves. 2. When the pressure reading in the Pirani Gauge meter reaches around 5x10-3torr, the diffusion pump should be switched ON. The user has to wait till the pressure indicated by the Penning gauge meter reaches 1x10-6torr. 3. All the electronic subsystems except the current source and RF generator are switched ON. 4. Current source and the RF generator are next turned ON after starting the control program in which all the experimental parameters are set. 5. The RF signal and the electrometer amplifier output, which is the mass spectrum, are fed into a 100MHz analog oscilloscope. The two signals are superposed and the RF voltage corresponding to the peaks in the mass spectrum are calculated for the purpose of mass calibration. 6. The Electrometer amplifier output is also fed to a 100MHz Digital scope for the purpose of averaging to have better S/N ratio. Typical Mass spectrum of two samples – Benzene and Xylene are shown in Fig. 4.5 and 4.6. It may be seen that the resolution obtained is reasonable through out the range. Mass Spectrometry Laboratory, IISc 29 2 5 1 4 3 6 7 Fig. 4.5 Front panel of the control program Mass Spectrometry Laboratory, IISc 31 30 Mass Spectrometry Laboratory, IISc 31 Mass Spectrometry Laboratory, IISc 32 Appendix 1 Mass Spectrometry Laboratory, IISc 31 Mass Spectrometry Laboratory, IISc 31 34 Mass Spectrometry Laboratory, IISc 35 Mass Spectrometry Laboratory, IISc 36 Mass Spectrometry Laboratory, IISc 37 Mass Spectrometry Laboratory, IISc 38 Mass Spectrometry Laboratory, IISc 39 Mass Spectrometry Laboratory, IISc 40 Appendix 2 Mass Spectrometry Laboratory, IISc 31 Specifications This appendix lists the specifications of PCI-MIO-16E-1 device. These specifications are typical at 25 °C unless otherwise noted. Analog Input Input Characteristics Number of channels PCI-MIO-16E-1 .............................. 16 single-ended or 8 differential (software-selectable per channel) Type of ADC.......................................... Successive approximation Resolution .............................................. 12 bits, 1 in 4,096 Max sampling rate (single-channel)1 PCI-MIO-16E-1 .............................. 1.25 MS/s Relative accuracy ................................... ±0.5 LSB typ dithered, ±1.5 LSB max undithered Analog Output Output Characteristics Number of DAC................................2 Resolution...............................................12 bits, 1 in 4,096 Type of DAC ..........................................Double-buffered, multiplying FIFO buffer size PCI-MIO-16E-1....................................2,048 samples Data transfers ..........................................DMA, interrupts, programmed I/O DMA modes ...........................................Scatter gather (single transfer, demand transfer) Dynamic Characteristics Mass Spectrometry Laboratory, IISc 42 Settling time for full-scale step...............3 µs to ±0.5 LSB accuracy Slew rate .................................................20 V/µs Noise.......................................................200 µVrms, DC to 1 MHz Glitch energy (at midscale transition) Magnitude Reglitching disabled.................±20 mV Reglitching enabled..................±4 mV Duration...........................................1.5 µs Stability Offset temperature coefficient ................±50 µV/°C Gain temperature coefficient Internal reference.............................±25 ppm/°C External reference............................±25 ppm/°C Digital I/O Number of channels................................8 input/output Compatibility ..........................................TTL/CMOS Timing I/O Number of channels ............................... 2 up/down counter/timers, 1 frequency scaler Resolution Counter/timers ................................ 24 bits Frequency scaler ............................. 4 bits Compatibility ......................................... TTL/CMOS Base clocks available Counter/timers ................................ 20 MHz, 100 kHz Frequency scaler ............................. 10 MHz, 100 kHz Mass Spectrometry Laboratory, IISc 43 Base clock accuracy ............................... ±0.01% Max source frequency............................ 20 MHz Min source pulse duration ..................... 10 ns, edge-detect mode Min gate pulse duration ......................... 10 ns, edge-detect mode Data transfers .........................................DMA, interrupts, programmed I/O DMA modes........................................... Scatter gather Triggers Analog Trigger Source PCI-MIO-16E-1...............................ACH<0..15>, external trigger (PFI0/TRIG1) Level .......................................................± full-scale, internal; ±10 V, external Slope .......................................................Positive or negative (software selectable) Resolution...............................................8 bits, 1 in 256 Hysteresis................................................Programmable Bandwidth (–3 dB) PCI-MIO-16E-...................................2 MHz internal, 7 MHz external External input (PFI0/TRIG1) Impedance........................................10 k. Coupling ..........................................DC Protection.........................................–0.5 to VCC + 0.5 V when configured as a digital signal, ±35 V when configured as an analog trigger signal or disabled, ±35 V powered off Digital Trigger Compatibility ..........................................TTL Mass Spectrometry Laboratory, IISc 44 Response .................................................Rising or falling edge Pulse width .............................................10 ns min RTSI Trigger lines ........................................... 7 Calibration Recommended warm-up time ................ 15 min Calibration interval ................................ 1 year External calibration reference ................ >6 and <10 V Onboard calibration reference Level ............................................... 5.000 V (±3.5 mV) (over full operating temperature, actual value stored in EEPROM) Temperature coefficient .................. ±5 ppm/°C max Long-term stability ......................... ±15 ppm/ Bus Interface Type .......................................................Master, slave Power Requirement +5 VDC (±5%) PCI-MIO-16E-1................................... 1.1 A Power available at I/O connector ........... 4.65 to 5.25 VDC at 1 A Physical Dimensions (not including connectors) .................... 17.5 by 10.6 cm (6.9 by 4.2 in) I/O connector PCI-MIO-16E-1.............................. 68-pin male SCSI-II type Hardware Overview Mass Spectrometry Laboratory, IISc 45 Figure 3-1 shows a block diagram for the PCI-MIO-16E-1 Figure 3-1. PCI-MIO-16E-1 Block Diagram I/O Connector Mass Spectrometry Laboratory, IISc 46 Mass Spectrometry Laboratory, IISc 47 Mass Spectrometry Laboratory, IISc 48 Mass Spectrometry Laboratory, IISc 49 Mass Spectrometry Laboratory, IISc 50 Beaty, E.C. (1986) Calculated electrostatic properties of ion traps. Phys. Rev.A, Vol. 33, 3645-3656. Brown, L.S. and Gabrielse, G. (1986) Geonium theory: Physics of single electron or ion in a Penning trap. Rev. Mod. Phys., Vol. 58, 233-311. Dawson, P.H. (1976) Quadrupole Mass Spectrometry and it’s Application, Elsevier, Amsterdam. Knight, R.D. (1983) The general form of the quadrupole ion trap potential. Int. J. Mass Spectrom. Ion Physics, Vol. 51, 127-131. Landau, L.D. and Lifshitz, E.M. (1976) Mechanics, Third Edition, Pergamon, UK. McLachlan, N.W. (1947) Theory and applications of Mathieu functions, Calarendon press, UK. March, R.E. (1992) Ion trap Mass Spectrometry. Int. J. Mass Spectrom. Ion Processes, Vol. 118/119, 72-135. March, R.E. and Hughes, R.J. (1989) Quadrupole Storage Mass Spectrometry, Wiley-Interscience Publications, New York. Wuerker, R.F., Shelton, H., and Langmuir, R.V. (1959) Electrodynamic containment of charged particles. J.Appl.Phys, Vol. 30 342-349. Mass Spectrometry Laboratory, IISc 31