Saturn GC/MS Hardware

3.1 Introduction

3.2 Configuration

3.3 Ion Trap Assembly

3.4 Vacuum System

3.5 Electronics

3.6 3800/3900 GC

1
3-1 Introduction

Figure 3-1: Functional block diagram of the Saturn system

2
Introduction
The Saturn system is the combination of a GC, MS, and a powerful data system. In this section
we will cover the hardware requirements of each component as it relates to the technique of
GC/MS.

3
MS Assembly Level Hardware

Figure 3-2: Principal Components of Saturn GCMS

4
MS Assembly Level Hardware
The ion trap mass spectrometer is a stand-alone instrument, consisting of mechanical and
electrical assemblies. The ion trap assembly is housed in a heated vacuum manifold. High
vacuum is supplied via a turbo-molecular pump, backed-up by a mechanical roughing pump.
Power for both pumps is supplied from the mass spectrometer assembly.
The electronic assemblies on the Saturn Mass Spectrometer generate the electron beam used
for ionization, the RF fields required for mass analysis, and monitor the signal from the detector.
The gas chromatograph is connected to the mass spectrometer using a temperature-controlled
transfer line. This allows direct interfacing of the capillary GC column into the ion trap analyzer.

5
Air Flow

Turbo system
Two fans blow air directly on the turbo and power
board electronics for maximum cooling. This keeps
the turbo as cool as possible.

Diffusion System

Figure 3-3: Diffusion chassis air flow

6
Air Flow
The turbo chassis blows all of the air out the front of the instrument. This keeps the turbo as cool
as possible to prevent overheating. The front grill is ducted so the air does not blow directly on
the user.
The diffusion pump system blows air into and pulls air out of the chassis. This push-pull
technique keeps the diffusion pump cool without over cooling.

7
3.2 Configuration
2200
• 3800 with a turbo only MS
• SIS is standard
• Up to three injectors all GC options
• All MS options available
• 1 pg OFN 50:1

2100
• 3900 GC with a turbo or Diffusion MS
• SIS, CI, and MSMS available options
• One 1177 injector only
• 8400 only
• no chromatoprobe or multi-CI
• Turbo 1 pg OFN 20:1 Diff 5 pg OFN 20:1

2000
• Turbo MS only
• Upgrade for existing GC only
• GC options depend on customer’s GC
• SIS, CI, and MSMS available.
• Chromatoprobe and multi-CI available.
• No specs. The condition of the customer’s GC
is unknown

8
Configuration

All of the Saturns are the same. The specs change based on the GC configuration to promote
pricing. The diffusion pump spec is lowered to ease installation.

2200 system

2100 System

9
Cable Connections
2100

Figure 3-4: 2100 Cable connections

2200

Figure 3-5: 2200 Cable connections

10
Cable Connections

The 3900 and 3800 use the same start cable to the MS.
The 3900 uses a crossover Ethernet cable connected to the built-in Ethernet card in the Dell PC.
The 3800 uses a coax Ethernet cable connected to a second Ethernet card installed in a PCI slot
in the Dell PC.
The Saturn 2100/2200 both use an IEEE or GPIB cable connected to a National Instruments
IEEE PCI board in the Dell PC.

11
3.3 Ion Trap Assembly

The ion trap consists of the following components:

Figure 3-6: Ion trap assembly

12
Ion Trap Assembly
The components in the ion trap assembly provide a chamber where ionization and mass
analysis of components eluting from the GC takes place.

13
Filament Assembly
• Two filaments and a repeller plate, filaments are
mounted side-by-side, with each the same distance
from the entrance hole of the lens.
• Only one filament is used at a time.
• The Alignment tool is used to set the proper distance
from the xferline hole to the flange
• Each filament lasts about 6 months
• Filament lifetime is application dependant

Figure 3-7: Exploded view of the filament assembly

14
Filament Assembly
The filament assembly is mounted on the trap oven.
Two filaments are mounted on the filament assembly as a convenience to the user. When one
burns out, the other one is available without shutting down the vacuum to replace it. The
switching of filaments is carried out in the software. Power is supplied to the filaments via three
wires attached to the lower manifold board. These are the same filaments that are used on the
Saturn 3, but they have extra wires attached.
A filament is simply a length of rhenium (Re) wire. A current of approximately 2-3 amps is
passed across the filament. The current heats the filament causing it to emit electrons.
The typical electron flow or emission current is in the range of 5-100 uA. The repeller is
located behind the filaments and is maintained at a dc potential of approximately -11.5 V in EI
mode and –10.5 in CI mode. Electrons emitted from a filament are repelled by the negative
potential and accelerated toward the lens assembly.

15
Lens and Gate Assemblies
• The lens and gate assemblies are built into the
filament end cap.
• Function is to focus the beam of electrons and
control the flow of electrons into the trap.

Figure 3-8: Exploded view showing the lens and gate

16
Lens and Gate Assemblies
The lens assembly is located between the filament assembly and the electron gate in the filament
electrode of the ion trap. The lens consists of a metal disk with a central tube that extends into
the electron gate. The lens is held at ground potential; it focuses the electrons emitted from the
filament into the cavity of the ion trap. The lens is part of the trap oven.
The electron gate is located beneath the lens assembly, inside the filament electrode. It is
insulated from the filament electrode by anodizing the outer surface.
The electron gate is a cylindrical electrode that controls the entry of electrons into the ion trap
cavity. When electrons are not needed for ionization, the electron gate is maintained at a –150 V
potential. This repels electrons emitted from the filament from entering the trap. When electrons
are required in the ion trap cavity, the potential on the electron gate is changed to +150 V.
electrons are accelerated into the trap. This voltage is supplied to the gate via the gate conductor
that makes a spring connection with the lower manifold board.

17
Ion Trap Electrodes
• Three stainless steel electrodes.
- Filament end cap
- Exit end cap
- Ring electrode

Chrome

SilcoSteel

Figure 3-9: Three ion trap electrodes

18
Ion Trap Electrodes
The three ion trap electrodes are the critical hardware components of the MS. Their inner
surfaces, when assembled, create a hyperbolic geometry. Precision machining is used to ensure
the exact geometry. The surface of the electrodes is finished with chrome or silcosteel coating to
minimize any activity.
Care must be taken to prevent damage to the ion trap electrode surfaces as scratches or other
imperfections can lead to active sites.
The RF voltage is connected to the ring electrode. The axial modulation or any other
supplemental voltage are connected to the end caps.

19
Electron Multiplier
• Positioned next to the multiplier end cap.
• Housed in a convenient assembly to allow easy
installation or removal.

A Exit End Cap F Multiplier Contacts

B Electron Multiplier Track G Multiplier High Voltage Pin
C Multiplier Signal Pin H Transfer Line Alignment
D EM Grid I Transfer Line Entrance Hole
E Electron Multiplier Mount

Figure 3-10: Electron multiplier assembly

20
Electron Multiplier
The cone shaped section of the multiplier assembly is made of glass. The inside of the glass cone
has a lead oxide-based coating.
The electron multiplier assembly has been pre-aligned and housed into a mounting bracket.
This allows easy installation and removal, as the multiplier is a consumable item and will
requiring changing on an average of sixteen months.
High voltage is applied to the upper part of the cone with an increasing positive voltage
gradient down to the end of the cone. Electrons are generated on the multiplier surface and
collected at the anode at the base of the cone. This signal is then transferred to the electrometer
circuit on the lower manifold board.

21
3.4 Turbo Vacuum System

Six principal components in the vacuum system.

- Vacuum manifold
- Turbomolecular pump
- Foreline pump
- Vent Inlet Valve
- Calibration gas valve
- Cl reagent gas valve

Figure 3-11: Block diagram of vacuum system

22
Turbo Vacuum System
The goal in a GC/MS system is to place as much as possible of the compounds eluting from the
GC into the trap without exceeding the storage capacity of the MS. Typically, the gas flow into a
mass spectrometer is limited to less than 1.5 mL/min. This can be accomplished using a narrow
bore (0.25 or 0.32 mm ID) capillary column directly into the source.
The goal within the MS is to keep the pressure low enough so that the mean free path of
molecules is large enough that they move independently at velocities controlled by their
molecular weights and temperatures. Under these conditions, the mean free path is greater than
the dimensions of the enclosure (of the trap) and molecular flow occurs.
Molecular flow, also known as conductance, is defined as the flow of a gas through a pipe in
which the mean free path of gas molecules is large compared to the dimensions of the pipe. In
other words, there is no viscosity effect, which is defined as internal friction, or alteration in
velocity of a given ion as a result of the contribution of all the ions in the vicinity (based on their
charges or molecular weights).

23
Turbo Vacuum Manifold
• Ion trap assembly is enclosed in a heated vacuum
manifold.
- Viton® 0-ring makes an airtight seal between the
manifold and the turbomolecular pump.
- Viton® Quad-ring between the top of the
manifold and the ion trap makes an airtight seal.
- Heater is controlled via the data system.
• The RF feedthrough passes through the manifold
bottom. The other Electrical feedthroughs pass
through the top flange.

A Pneumatics Exhaust Tube D Turbomolecular Cable

B Transfer Line E Vacuum Hose
C Clamping Screws (4 places) F Vacuum Hose Elbow

Figure 3-12: Vacuum Manifold

24
Turbo Vacuum Manifold
The manifold temperature can be set from 80 – 120° C. On initial setup or after the system has
been shut down and the ion trap vented to the atmosphere, we recommend an initial manifold
temperature of 120° C for the rapid removal of water vapor. After this period, a reduction in
manifold temperature to 40° C is sufficient for the majority of applications.

A stick on surface heater heats the manifold. The thermocouple sensor mounts directly on top of
the heater to keep the heater from overheating and burning out. A piece of insulation is glued to
the bottom and two sides. The manifold has to be removed before the heater and insulation can
be replaced.

25
Turbomolecular Pump
• Under normal conditions, pump provides a vacuum
of approximately 10^5 to 10^6 Torr.
• Air cooled and thermostat protected.
• Rated at 70 L/s.

Figure 3-13: Turbomolecular pump assembly

26
Turbomolecular Pump
A turbomolecular pump is actually a high rpm gas turbine. It contains a computer
balanced rotating shaft with attached blades supported by ceramic bearings.
Molecules move through the blade system and are forced to exhaust.
These pumps have the benefits of a high capacity in a compact design, clean
vacuum, and immediate start-up / shut-down.
The pump will fail if it suffers worn bearings, poor lubrication or poor cooling.
If the temperature of the pump housing near the bearing exceeds 65° C, the speed
of the pump will be decreased. If, after the pump speed is decreased, the
temperature of the pump housing near the bearing does not fall below 65° C, the
pump controller will shut down the pump.
If the pump is below 80% of its full speed, the magnitude of the signal sent by
the controller to the power control board is not sufficient to cause the power
control board to send a TURBO OK signal to the SAP board. As a result, the
filament, electron multiplier, CI reagent gas valve, and calibration gas valve
cannot be turned on. If this is the case, there probably exists a leak in the system
that must be found and fixed for the system to be fully operational.

27
Foreline Pump
• This roughing pump establishes the vacuum
necessary for proper operation of the turbo pump.
• The pump is rated at 90 L/min.
• Connects to turbo pump via 2.1 meters of 0.75 inch
ID reinforced Tygon® tubing.
• oil sight glass
• Switch to change between 115 V and 230V operation

Voltage switch is
under this cover
A Foreline
B Clamping Ring
C Seal
D Inlet
E Gas Ballast Valve
F Drain Plug
G Oil Level Sight Glass
H Filler Plug
I Exhaust

Figure 3-14: Mechanical pump

28
Foreline Pump
The Foreline pump is sometimes referred to as the roughing pump, as it provides a rough
vacuum for the turbo or diffusion pump.
A rotary-vane pump usually contains a single cylinder with two cycles, intake and
exhaust. On the intake cycle, the valve opens and input vapor is compressed. Then, upon
opening the exhaust valve, the vapor is compressed and discharged to the exit and the oil
reservoir. There is a safety valve which prevents oil vapor from reaching the analyzer
(analyzer is at a lower pressure).
You should be warned that a large percentage of sample resides in the oil reservoir; the
waste oil should be treated as a hazardous material. The oil should be changed every three to
four months.
In general, these pumps have a rugged design requiring low maintenance. The principal
failure is due to long use or failing to replace the oil.
The pump is typically turns on and off with the power switch on the MS.
The pump can be switched from 230V (default) to 115V operation by changing the
switch under the motor cover.

29
3.5 Diffusion Vacuum System

Eight principal components in the vacuum system.

- Vacuum manifold
- Peltier Baffle
- Diffusion pump
- Foreline pump
- Thermocouple gauge
- Vent Inlet Valve
- Calibration gas valve
- Cl reagent gas valve

Figure 3-15: Diffusion Vacuum System

30
Diffusion Vacuum System

The diffusion pump is an alternative vacuum pump to the turbomolecular pump. It is less
costly to replace, has a longer life span, and can be operated in ambient temperatures up to
35 °C. However, servicing the instrument does take slightly longer because the diffusion
pump must be fully cooled and the Peltier baffle warmed up to room temperature before
breaking vacuum. This takes ½ hour to start up or shutdown.
The diffusion pump vacuum system removes air, carrier gas, adsorbed water vapor, and
analytes from the mass spectrometer ion trap assembly.

31
Diffusion Vacuum Manifold
• One piece manifold
• Only the front half is heated
• The pump is shipped installed with covers over
the pump to prevent the fluid from leaking into
the manifold

A Manifold B Peltier Baffle C Diffusion Pump D Inlet Seal E Inlet Clamp

F Analyzer Assembly G Pneumatics Manifold H RF Coil

Figure 3-16: Diffusion Vacuum Manifold

32
Diffusion Vacuum Manifold
The vacuum manifold is a stainless steel box that maintains the ion trap assembly in a
vacuum. Carrier gas is fed into the ion trap via the transfer line, and calibration gas and
Chemical Ionization gases are fed into the ion trap via the pneumatics assembly. The
vacuum manifold is evacuated and maintained at vacuum of approximately 1 x 10-5 Torr
(1.3 x 10-3 Pa) by a diffusion pump. A Peltier baffle is incorporated in the manifold to
minimize background contamination caused by the back streaming of pump vapors. The
manifold can be heated to 120 C for bakeout. Normal operation is 40 C.

33
Diffusion Pump
• Under normal conditions, pump provides a vacuum of
approximately 10^5 to 10^6 Torr.
• Air cooled and thermostat protected.
• Rated at 65 L/s.
• No Moving parts
• Filled with 40 cc Santovac-5 silicon pump fluid.
• Heater is 90 V (115V) or 135 V (230V)
• A diffusion pump creates a cloud of silcon fluid above
the inlet to the manifold

Figure 3-17: Diffusion pump

34
Diffusion pump

The ion trap assembly requires a vacuum of approximately 1 x 10-5 Torr for the generation
and detection of ions. The Varian AX65 air-cooled diffusion pump with a pumping speed of
30 l/s for air and 65 l/s for helium provides this.
The pump features two safety devices. The first is an over temperature switch that prevents
catastrophic pump failure and subsequent ion trap contamination from over heating
problems, such as a cooling fan failure or a blocked air inlet. The second feature is a sight
glass that allows inspection of the diffusion pump fluid level and condition without breaking
vacuum. This reduces periodic maintenance time, and helps prevent the pump being run
without fluid.
The heater is in the bottom of the pump, which heats the fluid till it evaporates. The vapor
rises and is cooled near the top causing it to fall and remove molecules as it returns to the
bottom.

35
Peltier Baffle
• Factory assembled and leaked checked, only
replaced as a unit in the field.
• Each wire is a different size so it can only be
plugged together correctly.
• 40 C differential between cold side and hot
side.
• Extremely long lifetime.
• The Diff pump is shut down if this stops
drawing current or the fan cooling it stops
drawing current.

Figure 3-18: Peltier Baffle

36
Peltier Baffle

The Peltier baffle is a cooled line of sight baffle that reduces back streaming of vacuum
pump vapors into the vacuum manifold. The design consists of a one-piece baffle that is
cooled by a thermoelectric cooling element (TEC). The TEC is essentially an electronic
heat pump based on the Peltier effect. A voltage is applied to the TEC, causing heat to be
pumped from the cold side of the TEC to the hot side. The cold side of the TEC draws heat
from the baffle, thereby cooling it, and the hot side of the TEC pushes heat into the heat
sink. The heat sink is cooled by forced air convection.
The TEC is activated when the system is started, and remains on until it is switched off
during the shutdown procedure

37
 Thermocouple Gauge
• Monitors the roughing vacuum and shuts
down the Diff pump if the vacuum rises
above 500 mTorr for more than 30 seconds.
• Very long lifetime

• Connected to the diffusion pump controller

board

Thermocouple
gauge

Figure 3-19: Thermocouple gauge

38
Thermocouple Gauge
A thermocouple gauge is a simple, rugged, vacuum gauge that is used to measure vacuum
pressures in the 2 Torr to 1 x 10-3 Torr range. The gauge’s main purpose is to enable the
diffusion pump controller to detect gross leaks and foreline pump failure.
The thermocouple gauge is active whenever the diffusion pump controller is active. It is
monitored during start up to ensure the vacuum system has been pumped down to the
diffusion pump’s required operational pressure. Once the diffusion pump is operational, the
thermocouple gauge is monitored to ensure the operational pressure is maintained. If the
pressure drops below 500 mTorr for more than 30 seconds the diffusion pump is shut down.

39
Vent Valve
• Lever opened valve.
• Allows vacuum manifold to be vented to air
through a fritted restrictor.
Cl Reagent Gas Valve
• Metering needle valve and a solenoid-operated valve.
- Solenoid valve allows Cl reagent gas into the
vacuum manifold.
- Needle valve is used to precisely adjust the Cl
reagent gas flow.
• Cl reagent gas valve is turned on and off through the
data system.

CI Gas Needle Valve

Vent Lever

Figure 3-20: Vent Lever and CI needle valve

40
Vent Valve

The vent valve is a manually operated valve that connects to atmosphere via the pneumatics
manifold. You open and close the vent valve via a toggle arm, which is accessible from the
front of the instrument. The air enters through a 2 micron frit which slow the air flow to
protect the turbo and filter out particles.

Cl Reagent Gas Valve

Two solenoid valves control the flow of CI reagent gas into the manifold. First, the shutoff
valve near the rear panel opens to permit reagent gas flow into the instrument through a
fitting. When this valve is open, the foreline pump removes a portion of the CI gas to
prevent CI gas surges (pressure pulses) in the ion trap. The gas then flows through the
shutoff valve through metering and solenoid-operated valves before entering the vacuum
manifold. With the CI gas solenoid open, the CI needle valve determines the split ratio of
the reagent flow between the manifold and foreline pump.
You turn the CI reagent gas valve on and off via the data system from the Instrument
Control Page or Acquisition, you adjust the flow rate of the reagent gas into the manifold by
means of the metering valve.

41
Calibration Gas Valve
• Permits calibration gas to enter the manifold
• Metering needle valve and a solenoid-operated
valve.
- Flow of calibration gas into the manifold is set
manually with the needle valve.
- Solenoid valve is opened and closed via the
data system.
• Calibration compound is perfluorotributylamine
(PFTBA).
• Calibration Vial sealed with an o-ring.

Cal Gas Needle Valve

Figure 3-21: Calibration gas valve and vial

42
Calibration Gas Valve

The calibration-gas-valve assembly consists of a metering needle valve, an ON/OFF

solenoid-operated valve, and a glass vial containing the calibration liquid. The assembly sits
directly behind the instrument’s door. The needle valve controls calibration gas flow into
the vacuum manifold through the solenoid valve.
The calibration compound is perfluorotributylamine (PFTBA) or C12F27N, also known as
fluorocarbon-43 (FC-43). A small glass vial attached to the valve assembly holds the
compound. You set the flow of calibration gas into the manifold manually via a needle
valve. The data system controls the opening and closing of the solenoid-operated valve.

43
Transfer Line
• 2.5 x 16 cm stainless steel tube that directly couples
the GC with the MS.
• Purpose of the transfer line is to keep the GC column
warm as it enters the MS.
- Because the transfer line is connected to the
vacuum, it does not need to be as hot as the
column oven.
- Maximum operating temperature is 420°C.
- Transfer line should not be heated above the
maximum temperature specified for the capillary
column.

Transfer Line

A Spring B Boot C Tie Wrap D Washer E Transfer Line Tip

F O-Ring G Heat Exchanger H Nose I E-Ring J Ferrule K Nut

Figure 3-22: Transfer line assembly

44
Transfer Line
A stainless-steel-tube transfer line directly couples the GC to the mass spectrometer. The
transfer line keeps the GC column warm as the column enters the mass spectrometer. The
transfer line is 12 cm (5 in.) long, and has a diameter of 4.1 cm (1.6 in.). One end enters a
hole in the right side of the GC before passing into the GC oven. The other end enters the
vacuum manifold with the transfer-line tip inserted into the ion trap.
The body of the transfer line consists of a stainless-steel weldment fitted with a center
tube, a heat exchanger, and a boot. The heat exchanger is an aluminum cylinder that
contains a cartridge heater and a thermocouple as the temperature sensor. The temperature
sensor measures the temperature of the tube. The cartridge heater heats the cylinder, which
in turn distributes heat evenly throughout the length of the transfer line tube. The boot of
the transfer line, which mates to the GC, prevents hot air leakage from the GC Oven.

45
Transferline Installation
• The transferline is designed for easy removal
and installation after the MS is vented.
• The Nose clip holds the transferline in place and
unclips to release the transferline.
• The alignment tool is used to hold the
transferline still, while tightening or loosening
the column nut.

A Heating Cable H O-ring

B Boot I Transfer Line Tip
C Nut J Heating Cable Slot
D Ferrule K Nose Clip
E Transfer Line/Alignment Tool L Bayonet Mount
F Nose M Analyzer Assembly Tongue
G Nose Hole N Analyzer Assembly Lock-Down Tabs

Figure 3-23: Transferline Installation

46
Transferline Installation

A bayonet mount feature secures the transfer line. Before you remove the trap, push gently
on the bayonet mount as you twist it counterclockwise and pull the mount out. Make sure
the transfer line extends out from the trap.
NOTE: Failing to remove the transfer line before removing the trap may damage the trap heater
post.

The power board supplies power to the cartridge heater via a transfer line heater cable. The
heater cable projects out from one end of the transfer line. It then plugs into a soft-shell
connector on the top of the power board panel.
You set the transfer line temperature from the Instrument Control Page. The maximum
temperature that the transfer line can sustain is 350 °C; the minimum temperature depends
on the GC oven and trap temperatures. In general, you can set the transfer line temperature
as much as 30 °C below the maximum column operating temperature and not observe
adverse chromatographic effects (e.g., retention time shifts or peak broadening). The cooler
the transferline is operated, the less degradation of the column will occur. The transferline
heats by turning the heater full on and then off. The normal duty cycle is about 50%. If the
transferline has a bad column installed or some contamination in it, a square wave may be
observed in the chromatogram during a blank run. Normal operation masks this small shift
in baseline. Normally a few hundred counts.

47
Multi-CI Assembly
• Allows three different CI reagents to enter the
vacuum manifold
• Works with either liquid or gas reagents
• Controlled by the GC external events
• Mounting instructions with pictures are in the
hardware help file.

Schematic Diagram of the MCI Module

Figure 3-24: Multi-CI assembly and Schematic

48
Multi-CI Assembly

The muilti-CI assembly allows for up to three different CI reagents to be introduced into the
MS without changing or readjusting the gas flows. The reagents can all be adjusted and
then introduced when needed. They can even be mixed or introduced in the same run or
consecutive runs.
The CI reagents are turned on by the GC’s external events. This can be connected to a 3800
or a 3400 with a small voltage adapter board. The insructions for installation are in the
hardware help manual, located on the windows desktop.
The adjustment of the CI reagents flow is done from the Manual Control screen of the
Saturn System Control Module. However, for the correct Channel of the MCI Module to be
selected for adjustments, the GCMS method should have the correct Channel selected in the
GC Sample Delivery section of the Method.

49
3.5 Saturn Electronics
The electronic assemblies consists of the following:
• Power input subsystem and turbomolecular (or
diffusion) pump controller
• Power board
• Scan acquisition processor/waveform (SAP/Wave)
board
• Manifold electronics assembly
• RF generator board
The electronics functions have been distributed
throughout the spectrometer to minimize cable lengths
between critical components. The SAP/Wave and
power boards reside in an electronics enclosure that is
separated from the analyzer section by a sheet metal
bulkhead. The manifold electronics are enclosed
directly above the analyzer. The RF generator attaches
to the rear of the RF coil assembly.

50
Saturn Electronics

The Saturn system does not have a transformer, thus allowing it to have a much smaller
footprint. The switching power supply board has two switches to change it from 115 V
operation to 230 V operation. The turbo and diffusion controllers also need to be switched.
The trap, transferline, and manifold heaters are all line voltage heaters and need to match the
voltage configuration of the instrument. The fans are DC voltages.

51
Turbo Electronic Diagram

Figure 3-25: Turbo Electronics

52
Turbo Electronics
The turbo controller is a independent system. It receives a start/stop signal from the MS and
then performs its duties. It outputs a 0-10V signal to the MS to report the turbo speed. The
controller’s transformer is used to supply a small power supply board called the jump start
board which is mounted on the turbo controller. This board is used to supply the switching
power supply with an initial 15V supply to start the chips on the board.

53
Diffusion Electronic Diagram

Figure 3-26: Diffusion Electronics

54
Diffusion Electronics
The diffusion pump controller controls all of the components used to operate the pump. The
Peltier baffle and cooling fan are monitored for current draw. If the current draw stops, the
diffusion pump is turned off. The MS must be turned off and back on to reset the controller.
The thermocouple gauge is monitored for vacuum. If the foreline pump stops, or a vacuum
leak develops, the diff pump is turned off to protect the fluid. The MS must be turned off
and back on to reset the fault. The diff pump is monitored for current draw and resistance.
If the current stops the pump is turned off. If the heater has the wrong resistance, it maybe
the wrong heater and the pump is turned off.
There is a bimetal strip attached to the side of the pump, if the switch opens the pump is too
hot and power is shut off. The pump can overheat from being in too hot an environment,
(above 35C) or if the cooling airflow is blocked.
The pump is maintained at operating temperature by putting a constant amount of power
into the pump and allowing the airflow to cool the pump.

55
Power Control Board
The power control board supplies power to all electronics components
except the turbo and diff controllers.
• Protected by a 5A, Non-Time-Delay, fuse.
• The -15V and +15V dc power supplies, which supply the voltages to
the analog circuits on the power board and the manifold electronics
assembly.
• The +20V and -20V dc power supplies, which supply the voltages to
the SAP/Wave and RF generator board’s analog circuitry.
• The +24 Vdc power supply supplies power for the solenoid valves,
electronics compartment fan and the electron multiplier power
supply.
• The +55 Vdc power supply, which supplies unregulated +55 Vdc
voltage to the RF generator board.
• The 180-volt power supply that supplies voltage to the ion trap
electron gate circuit and the ion gauge.
• The trap and ion gauge filament control circuits
• Three heater control circuits the manifold, trap and transfer line
heaters.
• Three solenoid control circuits, which turn the calibration gas, CI
reagent gas, and CI shutoff valve solenoids on and off.
• Mounted on the top edge of the power board are 15 monitor LEDs.
When illuminated, these lights indicate that the voltages are at their
proper levels.
• During normal operation all LEDs except the +/-180 volts should be
on. The +/-180 volts only turns on when the filaments are on.

56
Power Control Board
The following circuits reside on the board:
The trap and ion gauge filament control circuits, which provide current to heat the filament
and regulate the emission current from the filament. You set the trap filament emission
current between 5 and 100 uA via the data system.
Three heater control circuits that provide feedback control for the manifold, trap and transfer
line heaters. The trap heater uses a proportional integral (PI) control circuit. Because there
is an integrator component in this controller, removing power from the circuit will produce a
lengthy stabilization time, e.g., up to two hours (dependent on the temperature set point).
Three solenoid control circuits, which turn the calibration gas, CI reagent gas, and CI
shutoff valve solenoids on and off.
The electron energy control circuits, which controls the dc bias on both the ion trap and ion
gauge filaments.
The diagnostic multiplexer circuit, which routes the voltage output of various components,
and circuits on the power control board to the SAP/Wave board. You can access these
voltage outputs through the diagnostic pages.
Mounted on the top edge of the power board are 15 monitor LEDs. When illuminated, these
lights indicate that the voltages of the various circuits on the power board are at their proper
levels, and that there are no faults. During normal operation all LEDs except the +/-180
volts should be on. The +/- 180 volts only turns on when the filaments are on.

57
RF Generator Assembly
• The assembly consists of an RF generator
circuit board.
• RF detector circuit board
• RF coil
• A shielded housing beneath the vacuum
manifold encloses the coil and RF detector
circuit board
• The RF generator circuit board is attached to
the back of the shielded housing.

Figure 3-27: RF Generator and coil

58
RF Generator
The RF generator assembly consists of an RF generator circuit board, an RF detector circuit
board, and the RF coil. A shielded housing beneath the vacuum manifold encloses the coil
and RF detector circuit board. The RF generator circuit board is attached to the back of the
shielded housing.

The RF generator circuit board receives an analog signal from the SAP/Wave circuit board
that is proportional to the current mass position in the scan, which is in turn proportional to
the desired RF voltage applied to the ion trap. The RF detector circuit board sends a signal
proportional to the actual amount of RF voltage applied to the ion trap to the RF generator
board. The RF generator board compares the desired and actual amount of the RF voltage
and adjusts the gain of an RF amplifier to cause the actual RF voltage to equal the desired
RF voltage. Since the high voltage required at the ion trap exceeds the capabilities of
conventional electronic amplifiers, a resonant LC circuit consisting of the RF coil and the
ion trap capacitance is used. At resonance, the RF voltage at the ion trap end of the coil is
about 100 times that at the RF generator circuit end of the coil.

59
The Manifold Electronics Assembly
• Two boards supply the trap components
• The upper manifold board connects to the
multiplier high voltage and ion gauge.
• The lower manifold board supplies the
filaments, gate, AM voltage, and multiplier
signal.
• Connections are made to the trap via glass
sealed feedthroughs on the manifold
flange.

Figure 3-28: Manifold Electronics

60
The Manifold Electronics Assembly
Two boards reside in the enclosure directly atop the Analyzer flange. The following
circuitry, which is critical to the functioning of the ion trap or that must be in close
proximity to the trap, resides on these boards.
The electron multiplier power supply, which supplies high voltage (-800 to -3000 Vdc) to
the cathode of the electron multiplier.
The integrator circuit, which receives the amplified ion current from the anode of the
electron multiplier, converts the current into voltage and passes the voltage on to the
SAP/Waveboard.
The trap filament selection relay.
The electron gate control that controls the gate polarity.
The axial-modulation low and high frequency transformers.
The ion gauge support circuitry, which includes filament On/Off and selection relays and a
log amplifier for gauge read-back signal conditioning.

61
Scan Acquisition Processor /
Waveform Generator Board
• Controlled by an 80186 processor and on board
ROM boot code.
• A second set of control software is downloaded and
stored in RAM when communication is established
with the PC
• Controls the scan function
• Generates waveforms and Axial Modulation Voltages
• Collects the mass spectrum and transfers it to the PC
• Reads and measures analog and digital signals

Figure 3-29: SAP Board

62
Scan Acquisition Processor/Waveform Generator Board
The scan acquisition processor/waveform generator (SAP/Wave) board is a real-time control
and acquisition microcomputer that makes use of an 80C186 microprocessor. The
SAP/Wave board communicates with the data system via an IEEE-488 interface board
installed in the data system computer bus. The SAP/ Waveboard performs the following
functions:
Interprets instrument commands from the data system and produces a sequence of analog
and digital signals that control operation of circuits on other Saturn GC/MS boards.
Filters, integrates and digitizes the ion current signal and transmits the spectra to the data
system.
Generates axial modulation waveforms, including waveforms used by SECI, MS/MS and
SIS options.

Upon power-up, the 80C186 processor runs a ROM resident program that initializes the
board. The program permits the processor to receive information through the IEEE-488
interface. When you start up the Saturn data system, operating information is downloaded
to the SAP/Wave board’s RAM memory. The SAP/Wave board then performs its
operations in response to the commands sent through the IEEE-488 interface.

When a mass spectrum is acquired, the data system downloads parameters such as electron
multiplier voltage, scan range and time, ionization mode, etc. The SAP/Wave board uses
this information to create a scan over the desired mass range. During the scan, ion current
data is accumulated and, at the end of the desired scan time, sent to the data system for
further processing and display.

The waveform generator is capable of generating waveforms over a wide range of

frequencies and amplitudes. The data system produces a digital version of the desired time
domain waveform, and downloads the resulting binary file RAM. At the appropriate time,
the data is clocked out of the RAM into a waveform reconstruction DAC. The DAC output
is then filtered to remove undesirable frequencies. The Saturn GC/MS uses the waveform
generator in chemical-ionization (SECI), MS/MS, or SIS applications; as well as in normal
axial modulation.

Characteristics of the waveform generator include the following:

Dual-port RAM (256 Kbytes) to provide memory for single or multiple digitized waveforms
A selectable frequency generation clock (625 KHz, 1.25 MHz, or 2.5 MHz and a 15-bit
variable length counter to control timing
A 12-bit DAC, low pass filter and amplifier to reconstruct waveforms
A variable operational frequency range that depends on whether you are using the high
frequency transformer (12 to 500 KHz) or low frequency transformer (200 Hz to 1.25 KHz)
Application of the waveform output to the endcap electrodes of the ion trap is done via the
two transformers located in the manifold electronics assembly.

63
Section 3.6 3800/3900 GC
• The GC needs to be properly configured to
work with the MS.
• EFC needs to be set to Vacuum.
• Column flow must be between .75 – 1.5
mL/min.
• The column needs to be installed and
properly conditioned.

64
3800/3900 GC
A 3800 GC can have up to three injectors. Two injectors can be connected to the MS by the
quick switch valve. GC detectors can be installed on the GC allowing system control to
collect data from the GC detectors and the MS at the same time.

The 3900 GC cannot have any detectors installed. It has a limited number of options.

65
Configuring the EFC

• The 3800 EFC is configured from the GC front

panel setup screen.
• The 3900 EFC is configured from the setup
button on the 3900 module window in system
control.
• For both GCs the outlet of the EFC needs to be
set to vacuum.

Figure 3-30: EFC configuration

66
Configuring the EFC
The EFC calculations change based on the column dimensions and the outlet of the
column. GC detectors are at atmospheric pressure, whereas the MS is a vacuum. Choosing
the wrong outlet in the EFC setup will cause the flow calculation to be wrong.

67
Column
• The capillary column shipped with the system is
30 m x 250 um, 0.25 um film
CP-sil 8 CBMS
• The column should be installed into the injector
3.4 cm for the 1177 and the column should
extend 1 mm past the end of the transfer line.
• The column is shipped uninstalled and needs to
be condition

68
Column
Column stationary phases can be chosen by the analyst depending on the sample.
Generally, a stationary phase which provides adequate resolution in a short
analysis time is recommended. This requires matching the polarity of the sample
to the polarity of the stationary phase. A relatively non-polar column such as a
CP-sil 8 CBMS can be used for greater than 75% of common GC/MS
applications. The Saturn system ships with a 30 m x 0.25 mm ID, 0.25 m film
thickness, CP-sil 8 analytical column.
Columns should never be heated without gas flow through it. When columns
are heated to elevated temperatures, they bleed stationary phase.
When installing a column, it is especially important that the column is cut
squarely and that the cut is wiped clean with solvent (methanol). A jagged
column edge will cause flow disturbances. A square cut is also imperative for
making a seal within the SPI injector insert. It is recommended that the nut and
ferrule are slipped over the end of the column before column cutting. This ensures
that any ferrule shavings that fall into the end of the column will be cut off.

69
Column Conditioning

1. Install column in GC and Purge with helium before

connecting to MS.
2. Temperature program column (start at 50 C, then 10
degrees/min, up to 300 C, hold for 30 min.)
3. Cool it down and connect to MS
4. Heat up Ion Trap + Manifold only (Column and Transferline
cold)
5. When Ion Trap is heated up, heat Transferline to 170
Degrees Celsius.
6. When Transferline reaches170 C, condition column again.
(Step 2).

70
Column Conditioning
Never elevate the column oven temperature without first ensuring there is flow through the
column. Set the carrier gas flow to 1 mL/min. You can check for flow by placing the end of
the column into a small beaker of solvent.
Column bleed is seen as normal background in the mass spectrum. The bleed is caused by
polymer degradation, a breakdown of the stationary phase. The amount of normal column
bleed will increase with film thickness, column diameter, and length. Generally, polar
columns have higher column bleed than non-polar columns. Column bleed becomes
excessive when the column is damaged or contaminated which is noticed as high signals at
m/z 207 and 281 (larger than the hydrocarbon background.)

71