Q-Exactive-GC Operating Manual
Q-Exactive-GC Operating Manual
Q-Exactive-GC Operating Manual
Mass Spectrometer
Operating Manual
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Technical Documentation
Thermo Fisher Scientific
2215 Grand Avenue Parkway
United States
Chapter 7 Troubleshooting.....................................................................7-1
Safety Guidelines for Troubleshooting ........................... 7-2
Fault Table..................................................................... 7-3
Main Power Failure........................................................ 7-4
Vacuum Leak ................................................................. 7-5
Failure of UHV Chamber Heating Control ................... 7-7
Turbomolecular Pump is Not Running ......................... 7-8
Index......................................................................................... I-1
Contents
Typographical Conventions
This section describes typographical conventions that have been
established for Thermo Fisher Scientific manuals.
Signal Word
Make sure that you follow the precautionary statements presented in
this manual. The special notices appear different from the main flow of
text:
Viewpoint Orientation
The expressions left and right used in this manual always refer to the
viewpoint of a person that is facing the front side of the instrument.
Data Input
Throughout this manual, the following conventions indicate data input
and output with the computer:
• For brevity, expressions such as “choose File > Directories” are used
rather than “pull down the File menu and choose Directories.”
• Any button that you click on the screen is represented in bold face
letters. For example, “click Close”.
Topic Headings
The following headings are used to show the organization of topics
within a chapter:
Reference Documentation
This Q Exactive GC Operating Manual represents the Original
Operating Instructions. In addition to this manual, Thermo Fisher
Scientific provides other documents for the Q Exactive GC mass
spectrometer that are not part of the Original Operating Instructions.
Reference documentation for the Q Exactive GC mass spectrometers
includes the following:
You can access PDF files of the documents listed above and of this
manual from the data system computer. The software also provides
Help.
Go to Start > All Programs > Thermo Exactive Series > Manuals.
• Forepump
• Turbomolecular pumps
Contents
- Computer equipment
- Spare parts
• Printed manual
Contents
General Description
Q Exactive GC mass spectrometers are stand-alone Orbitrap™
instruments with an extractable ion source for gas chromatography
(GC) mass spectrometry (MS) high-throughput applications. The
instruments are designed to be placed on a bench in the laboratory. This
chapter describes the principal components of Q Exactive GC systems
and their respective functions.
The ions are transferred into the C-Trap through three stages of
differential pumping. See “Ion Optics” on page 3-12 for details. In the
C-Trap, the ions are accumulated and their energy is dampened using a
bath gas (nitrogen). The ions are then injected through three further
stages of differential pumping using a lens system (Z-lens) into the
Orbitrap analyzer where mass spectra are acquired by image current
detection. The vacuum inside the Orbitrap analyzer is maintained below
1E-9 mbar. See “Orbitrap Analyzer” on page 3-19 for details.
Ions are passed through the C-Trap into the HCD cell. The HCD cell
adds a Higher Energy Collision Induced Dissociation capability to the
instrument. In combination with the quadrupole mass filter this allows
MS/MS experiments or all-ion fragmentation (AIF) in case of a broad
range of selected mass-to-charge ratios. After the ions have been
fragmented in the HCD cell, the HCD cell voltages are ramped up and
the ions are transferred back into the C-Trap from where they are
injected into the Orbitrap analyzer for detection. See page 3-22 for a
description of the HCD cell.
Control Elements
Q Exactive GC mass spectrometers are mainly operated from the
desktop computer (data system). LEDs at the front side of the
instrument give general information about the system status. Switches
and ports for other devices of the GC/MS system are located at the
power panel on the left side of the instrument. The mains inlet and the
Ethernet port are located at the rear side of the instrument. This section
describes the control elements for important system functions.
NOTICE The system status LEDs give a quick overview of the general
system status; they do not have any function for the safety status of the
instrument. Before performing any maintenance on the instrument,
make sure that the main power circuit breaker switch (labeled Main
Power) is in the Off (O) position and that the power cords of mass
spectrometer and forepump are disconnected. It is not sufficient that the
Power LED is off because it might be defective. All system status LEDs
are off, when the electronics service switch is in the Service Mode
position. ▲
Power Panel
Figure 3-3 shows the rear side of the instrument. Visible are the power
panel, power column, forevacuum port, and ventilation slots.
Power Column
The main power circuit breaker switch (labeled Main Power) is located on
the power panel at the left side of the mass spectrometer. See Figure 3-4.
In the Off (O) position, the circuit breaker removes all power to the
mass spectrometer, including the vacuum pumps. In the On (|) position,
power is supplied to the mass spectrometer. In the standard operational
mode, the circuit breaker is kept in the On (|) position.
NOTICE The service mode switch does not disable the EI/CI
electronics. The EI/CI electronics have a separate switch on the rear.
The EI/CI electronics are powered through the power column and will
not have power when the main circuit breaker is in the OFF position. ▲
USB Port
Main Power switch Electronics service switch Output Input System Reset Syringe Pump Port
(Not Used on
Q Exactive GC)
Both switches contain circuit breakers that protect the electrical wiring
of the instrument from an overloaded (overcurrent) condition when it is
exposed to more electrical current than it is designed to handle. In case
of a thermal overload they interrupt the power supply to the instrument.
After cooling down (and removal of the overload), the circuit breakers
close and both switches can be used again. If you cannot reset the
instrument to the operating mode despite repeated attempts, the circuit
breaker inside the switch is blown. In this case, call a Thermo Fisher
Scientific field service engineer to replace it.
Peripheral Control
• The Ready Out port allows the mass spectrometer to provide ready
status through contact closure for an external receiving device.
The contact closure signals are transmitted through a trigger cable that
connects the respective port to the external device. A suitable plug
connector (P/N 2087270) for the peripheral control output connection
is provided with the Installation Kit. See “User I/O Connections” on
page 5-16 for specifications of the peripheral control output connection
ports.
The contact closure signals are transmitted through a trigger cable that
connects the respective port to the external device. A suitable plug
connector (P/N 2098690) for the peripheral control input connection is
provided with the Installation Kit. See “User I/O Connections” on
page 5-16 for specifications of the peripheral control input connection
ports.
The reset button is also located on the power panel. When you press the
reset button, the instrument software is reloaded from the data system.
See “Resetting the System” on page 6-13 for information on resetting
the mass spectrometer.
The USB port allows the internal computer to communicate with other
devices of the GC/MS system. Do not connect any device to this port
other than dedicated Thermo Fisher Scientific devices.
Power Column
The power column at the rear side of the instrument provides external
connections for mains supply, gas, and Ethernet communication. See
Figure 3-5.
Ethernet connector
Located at the top left side is the Ethernet port for connecting the mass
spectrometer to the data system computer.
The power connector for the mains supply is located below the two
power outlets. The Q Exactive GC instrument is designed to operate at
a nominal voltage of 230 V AC, 50/60 Hz. Line voltages can vary
between a minimum of 207 V AC and a maximum of 253 V AC.
Connect the power cord of the instrument to a wall receptacle that is
fused with 15 A or 16 A.
Above the gas ports, a ground bolt provides a protected earth connection
for the ground wires of other devices of the GC/MS system.
The ports for nitrogen gas allow connecting a Teflon™ hose from the gas
supply of the laboratory to the instrument. (See also “Gas Supply” on
page 3-27.) The required gas pressure is 800 ± 30 kPa (8 ± 0.3 bar,
116 ± 4 psi).
Vacuum Gauges
Ion Optics
Figure 3-6 shows the schematic view of the Q Exactive GC mass
spectrometers. With the exception of the quadrupole, voltages for the
elements of the ion optics are provided by the ion optic supply
DC board (See page 3-30.) and the ion optics supply RF board. (See
page 3-30.) The quadrupole voltages are supplied by a dedicated PCB.
See page 3-30.
Transfer Multipole
Orbitrap Transfer
Mass Analyzer Filament Ion Volume Line
Repeller
There are three types of ion sources available for the Q Exactive GC: an
electron ionization (EI) source, a chemical ionization (CI) source that
enables that enables positive ion chemical ionization (PCI) and negative
ion chemical ionization (NCI), and a combination EI/PCI/NCI source.
All available ion sources include an ion volume, repeller, source lenses,
an RF lens, and dual filaments and are programmable from 50 °C to
350 °C. Figure 3-7 provides images of the three available ion volumes.
The ion source parts are contained in an ion source cartridge. See
Figure 3-8.
Lens 1
Repeller
Repeller Ion Cartridge Sleeve
Nut
Lens 2
Ion Volume
Locking Ring EI Ion Volume
Ion Volume-Repeller
Repeller Insulator
Spring
The injection flatapole is a square array of flat metal electrodes that acts
as an ion focusing and as an ion pre-filtering device (Figure 3-9). An
RF voltage that is applied to the electrodes (injection flatapole RF) gives
rise to an electric field that focuses the ions along the axis of the lens. A
DC offset voltage is applied to the injection flatapole (injection
flatapole DC).
The inter-flatapole lens is a metal plate with a small hole through which
the ion beam can pass. A DC potential is applied to the lens to aid in
ion transmission. The lens also acts as a vacuum baffle between the
source and analyzer ion optics chambers.
The bent flatapole always acts as an ion transmission device. It guides the
ions through a 90° arc from the injection flatapole to the quadrupole
and removes the neutral gas jet and passing through the injection
flatapole. Because of the bent shape of the flatapole, the neutral particles
cannot follow the bent path of the flatapole. The region around the bent
flatapole is pumped by the interstage inlet IS1 of the source TMP.
The quad exit lens focuses the ions coming from the quadrupole into the
transfer multipole.
The split lens is used to start and stop the injection of ions into the mass
analyzer. It provides a high deflection voltage most of the time so that
ions are deflected into a baffle except when they are to be allowed into
the C-Trap. The fast switching of the ion beam ensures the precise
determination of the ion injection time that is required for Automatic
Gain Control (AGC).
In a quadrupole rod assembly, rods opposite each other in the array are
connected electrically. Thus, the four rods can be considered as two pairs
of two rods each. RF and DC voltages are applied to the rods and these
voltages are ramped during the scan. Voltages of the same amplitude and
sign are applied to the rods of each pair. However, the voltages applied
to the different rod pairs are equal in amplitude but opposite in sign. See
Figure 3-11.
RF voltage
+ DC
Figure 3-11. Polarity of the RF and DC voltages applied to the rods of the
quadrupole mass filter
RF voltage
6700 V P/P
500 V DC voltage
Voltage (V)
In the mass spectrometer, the rods of the quadrupole are supplied with a
variable ratio of RF voltage and DC voltage (Figure 3-12). For each
injection, controlled by the split lens, the quad RF amplitude and
DC voltage are set to fixed values. Under these conditions, only ions of a
certain range of m/z ratios are maintained within bounded oscillations as
their velocity carries them through the mass filter. At the same time, all
other ions undergo unbounded oscillations. These ions strike one of the
rod surfaces, become neutralized, and are pumped away, or they are
ejected from the rod assembly.
Orbitrap Analyzer
The heart of the Orbitrap™ analyzer is an axially-symmetrical mass
analyzer. It consists of a spindle-shape central electrode surrounded by a
pair of bell-shaped outer electrodes. See Figure 3-13. The Orbitrap
analyzer employs electric fields to capture and confine ions.
Figure 3-13. Schematic of Orbitrap cell and example of stable ion trajectory
Owing to the fast pulsing of ions from the C-Trap, ions of each
mass-to-charge ratio arrive at the entrance of the Orbitrap analyzer as
short packets that are only a few millimeters long. For each
mass-to-charge population, this corresponds to a spread of flight times
of only a few hundred nanoseconds for mass-to-charge ratios of a few
hundred Daltons per charge. Such durations are considerably shorter
than a half-period of axial ion oscillation in the C-Trap. When ions are
injected into the Orbitrap analyzer at a position offset from its equator
(See Figure 3-14.), these packets start coherent axial oscillations without
the need for any additional excitation cycle.
The evolution of an ion packet during the increase of the electric field is
shown schematically in Figure 3-14. When the injected ions approach
the opposite electrode for the first time, the increased electric field
(owing to the change of the voltage on the central electrode) contracts
the radius of the ion cloud by a few percent. The applied voltages are
Measuring Principle
In the mass analyzer shown in Figure 3-13 on page 3-19, stable ion
trajectories combine rotation around an axial central electrode with
harmonic oscillations along it. The frequency w of these harmonic
oscillations along the z-axis depends only on the ion’s mass-to-charge
ratio m/z and the instrumental constant k:
z
= m- k
---
Two split halves of the outer electrode of the Orbitrap analyzer detect
the image current produced by the oscillating ions. By Fast Fourier
Transformation (FFT) of the amplified image current, the instrument
obtains the frequencies of these axial oscillations and therefore the
mass-to-charge ratios of the ions.
Ion Detection
During ion detection, the central electrode and the additional electrode,
which deflects ions during injection and compensates electric field
imperfections during the measurement (See Figure 3-14 on page 3-20.),
are maintained at very stable voltages so that no mass drift can take
place. The outer electrode is split in half at z=0, allowing the ion image
current in the axial direction to be collected. The image current on each
half of the outer electrode is differentially amplified and then undergoes
analog-to-digital conversion before processing using the fast Fourier
transform algorithm.
a period of only 50–100 oscillations. After this, the ion packet of a given
m/z assumes the shape of a thin ring, with ions uniformly distributed
along its circumference. See Figure 3-15. Because of this angular and
radial smearing, radial and rotational frequencies cannot appear in the
measured spectrum. Meanwhile, axial oscillations will persist, with axial
thickness of the ion ring remaining small compared with the axial
amplitude. Moving from one half outer electrode to the other, this ring
will induce opposite currents on these halves, thus creating a signal to be
detected by differential amplification.
HCD Cell
The HCD cell consists of a straight multipole mounted inside a metal
tube, which is connected in direct line-of-sight to the C-Trap. It is
supplied with a collision gas to provide increased gas pressure inside the
multipole. The C-Trap is directly attached to the HCD cell, so part of
the collision gas flows into the C-Trap to serve as bath gas. See “Gas
Supply” on page 3-27 for details. The ion optic supply DC board
provides all RF and DC voltages necessary for operating the HCD cell.
(See page 3-30.)
The spectra of fragments generated in the HCD cell and detected in the
Orbitrap analyzer are comparable to the typical fragmentations patterns
obtained on triple-quadrupole instruments. Refer to the QuickStart
Guide for your instrument for more information.
Vacuum System
The vacuum manifold encloses the ion source interface, ion guides,
C-Trap, and the Orbitrap analyzer. The vacuum manifold consists of
thick-walled aluminum chambers with machined flanges on the front,
sides, and bottom, and various electrical feedthroughs and gas inlets.
The vacuum manifold is divided into three chambers. The region inside
the first chamber is evacuated by a rotary-vane pump (forepump). The
region inside the second chamber, called the source chamber, is
evacuated by a turbomolecular pump (source TMP). The region inside
the third chamber, called the analyzer chamber, is evacuated by another
turbomolecular pump (analyzer TMP). Figure 3-16 shows a schematic
overview of the vacuum system, Table 3-4 shows the vacuum regions of
the mass spectrometer.
Ion Gauge 2 (IKR 270) Ion Gauge 1 (IKR 251) Vent Valve (N2) Pirani Gauge (TPR 280)
HV = High Vacuum
FV = Forevacuum
See page 3-11 for information about the vacuum gauges in the
Q Exactive GC mass spectrometer.
Turbomolecular Pumps
Two turbomolecular pumps (TMPs) provide the vacuum for the mass
spectrometer. The TMPs are controlled by individual controllers and
powered by +24 V DC (480 W) power supplies. Power for the TMPs is
turned off by the main power circuit breaker switch, but not by the
electronics service switch. The TMPs are air cooled by fans that are
mounted in fan inserts on the bottom of the instrument.
Pump controllers provide power to and control of the TMPs. The status
of each TMP (such as temperature or rotational speed) is sent from the
TMP controller to the vacuum control board. See page 3-31.
Analyzer TMP
• An 20 L/s interstage inlet (IS1) about half way down the rotor stack,
which evacuates the region between Z-lens and Orbitrap analyzer.
• A 250 L/s high-vacuum (HV) inlet at the top of the rotor stack,
which evacuates the UHV (Orbitrap analyzer) chamber.
The interstage inlet IS1 of the source TMP provides the forevacuum for
the analyzer TMP.
Vent Valve
and the manifold is vented with nitrogen. See Figure 3-16 on page 3-23
and Figure 3-17 on page 3-27. The vent valve closes after power is
restored to the instrument.
System Bakeout
After the system has been open to the atmosphere (for example, during
maintenance work or a power outage), the vacuum deteriorates due to
contaminations of the inner parts of the vacuum system caused by
moisture. These contaminations must be removed by heating the
vacuum system by a system bakeout. See “Baking Out the System” on
page 8-11 for instructions on performing a system bakeout.
Bakeout Devices
Bakeout Control
NOTICE Individual printed circuit boards also have devices for checking
the actual temperature. ▲
Cooling Fans
Six fans provide cooling for the Q Exactive GC mass spectrometers. On
the right instrument side, a fan insert with four fans cools the electronic
boards. On the left instrument side, a second insert with two fans cools
the analyzer chamber and the analyzer TMP. From the rear of the mass
spectrometer, air is drawn in through fan filters. The exhaust air is
expelled from the ventilation slots on the sides of the mass spectrometer.
The vacuum control board monitors all fans within the instrument.
During a system bakeout, it switches off one of the two fans below the
analyzer TMP. In case of a fan failure, the board triggers an alert in the
Tune software. In case of a failure of the fans below the analyzer TMP,
no bakeout procedure is possible.
Gas Supply
Q Exactive GC mass spectrometers require ultra high-purity
(>99.999%) nitrogen for the collision gas (bath gas) of the C-Trap and
for the collision gas for the HCD cell. Nitrogen is also used to vent the
vacuum manifold with the vent valve if the system is shut down. The
required pressure is 800 ± 30 kPa (8 ± 0.3 bar, 116 ± 4 psi). The vented
vacuum manifold is protected against overpressure by pressure relief
valves and a glass manifold cover over the ion source. Figure 3-6 shows a
schematic of the gas supply in the instrument.
Nitrogen
HCD Cell
Vacuum Manifold
Vent Valve
Pressure Regulator
CI Gases
Calibration Gas
The gas flow from the left nitrogen port is directed through Teflon™
tubing to the vent valve
The gas flow from the right nitrogen port is directed through Teflon
tubing to a pressure regulator, which keeps the gas pressure to C-Trap
and HCD cell constant. From the regulator, the collision gas is led to
the HCD cell next to the C-Trap (flow rate: ~0.5 mL/min). In the
Q Exactive GC mass spectrometers, an electronic pressure regulator sets
the nitrogen pressure according to the operating mode of the instrument
and the chosen user setting. The nitrogen gas leaking from the
HCD cell is used for ion trapping and cooling in the C-Trap.
Preamplifier
The preamplifier board is a broadband amplifier with high-resistive
differential inputs. It converts the image current, which is induced by
the ions oscillating in the Orbitrap analyzer, to a proportional output
voltage. The preamplifier interfaces through coaxial cables directly to
the data acquisition board, which also provides the electric power for the
preamplifier. After analog-to-digital conversion on the data acquisition
board, the output voltage undergoes further Fourier transformation on
the internal computer.
Source Board
In the Q Exactive GC system, the source board controls the CI gas flow
valves.
The source board distributes power to the ion gauges and the nitrogen
gas valves—including the vent valve. Two connections to the I/O board
allow the source board to communicate with other devices of the
GC/MS system.
The system status LEDs on the front side of the instrument (See
Figure 3-2 on page 3-5.) are controlled by the source board. The
displayed status information partially comes from other boards. The
board communicates through the SPI bus.
Quadrupole Board
The quadrupole board (quad board) supplies RF voltages and
DC voltages for the quadrupole. See “Quadrupole Mass Filter” on
page 3-15. Set values and readbacks of voltages, currents, and
temperatures are communicated through the SPI bus.
FT Adapter Board
The FT adapter board links the internal computer to the various system
components. Its main function is the control of scan events within the
instrument. The board contains a micro controller, an FPGA (Field
Programmable Gate Array), and serial port connectors.
SPI Bus
On the vacuum control board, analog signals from vacuum gauges are
converted to digital signals and passed to the internal computer through
a USB connection. TMPs are attached to a serial port connector and
this is connected by the signal lines to the vacuum control board. (See
“Vacuum System” on page 3-23.)
C-Trap RF Board
The C-Trap RF board operates the C-Trap with four phases of
RF voltage (Main RF) and three pulsed DC voltages (PUSH, PULL,
and OFFSET). It allows simultaneous switching off the RF and pulsing
of each C-Trap electrode. See “Orbitrap Analyzer” on page 3-19 for
further information. The board also provides the entrance voltage and
the exit voltage to the C-Trap. The board communicates with the other
boards through the SPI bus.
CE HV Supply Board
The central electrode high-voltage supply board provides five voltages
for the ion optics of Q Exactive GC mass spectrometers:
For positive ions, the CE voltages are negative and the DE voltages are
positive. The maximum CE voltage is 5 kV and the maximum
DE voltage is 1.25 kV. See “Orbitrap Analyzer” on page 3-19 for further
information.
The board communicates through the SPI bus. A Peltier element on the
rear side of the board serves as means of heat dissipation.
CE Pulser Board
The central electrode pulser board switches the injection and
measurement voltages for the central electrode and the deflector
electrode of the Orbitrap analyzer. Resistor-capacitor circuits on the
board convert the switching pulse into a smooth transition between the
voltages. Furthermore, the board switches the polarity of the central
Orbitrap electrode.
I/O Board
The input/output (I/O) board provides the interfaces for data exchange
between the Q Exactive GC mass spectrometer and other devices of the
GC/MS system. It contains a reset switch, four relay outputs and a
digital inlet port. (See “Peripheral Control” on page 3-7.) It is connected
to the FT adapter board and to the source board.
Contents
! CAUTION Points out a hazardous situation that can lead to minor or medium
injury if not avoided.
! WARNING Points out a hazardous situation that can lead to severe injury or death
if not avoided.
! DANGER Points out a hazardous situation that will lead to severe injury or death
if not avoided.
Rating Plate
To correctly identify the instrument when communicating with Thermo
Fisher Scientific, always have the information from the rating plate
available. The rating plate is attached to the power column at the rear
side of the instrument. See Figure 4-1.
Intended Use
Q Exactive GC mass spectrometers are stand-alone Orbitrap™
instruments with an ExtractaBrite™ removable ion source for gas
chromatography (GC) mass spectrometry (MS) high-throughput
applications.
• Electrical Connections
• General Operation
Permitted Materials
Q Exactive GC mass spectrometers are designed to be operated with the
following materials:
• Nitrogen gas: Used for the C-Trap bath gas and HCD collision gas
NOTICE Use only the forepump oil indicated on the name plate and
pump. In case other oils are used, the manufacturer (Oerlikon Leybold
Vacuum) rejects all responsibility should any trouble occur. ▲
In Case of Emergency
❖ To shut down the system in case of emergency
! WARNING Electric Current. Electric shock hazard. Do not use the electronics
service switch to shut down the instrument. The electric components of
the vacuum system will still be connected to the electric power supply
and the pumps will remain running.
Figure 4-2. Power panel, showing main power circuit breaker switch and reset button
Power Panel
Residual Hazards
Users of Q Exactive GC mass spectrometers must pay attention to the
following residual hazards.
! CAUTION Hot Surface. Touching parts of the forepump might cause burns. The
forepump in function is hot and some surfaces could reach a
temperature higher than 70 °C (158 °F). Switch off the pump and let it
cool down before any intervention or take appropriate precautions.
Always wear heat protective gloves when working on a pump that is
“still warm from operation”.
! CAUTION Hot Surface. Touching hot parts of the ion source interface might
cause severe burns. During operation of the mass spectrometer, the
ExtractaBrite removable ion source might reach temperatures of up to
350 °C, while the GC column transfer line might reach temperatures of
up to 400 °C. To let the ion source interface cool down, set the ion
source and transfer line temperatures to 25 °C. Wait until the ion
source has cooled down to room temperature (for approximately
60 minutes) before you begin working on it. Do not leave the
instrument unattended when the covers and front door are removed,
exposing the hot source parts. Hot ion source parts might ignite
combustible material. Keep combustible materials away from the ion
source mount.
Eye Protection
The type of eye protection required depends on the hazard. For most
situations, safety glasses with side shields are adequate. Where there is a
risk of splashing chemicals, goggles are required.
Protective Clothing
Gloves
Contents
Instrument Dimensions
The Q Exactive GC system always includes the TRACE 1310 GC and
has maximum dimensions of h 95 cm (37 in.), w 91 cm (36 in.),
l 148 cm (58 in.). Figure 5-1 shows a schematic view of the instrument
with important instrument dimensions.
95
Top View
148
91
! CAUTION Only workbenches with at least four legs provide sufficient stability for
the Q Exactive GC mass spectrometer. The workbench top must be
dry and clean (free of grease). Thermo Fisher Scientific recommends
using a workbench with a skidproof top.
Minimum Clearance
Allow at least 15 cm (6 in.) of clear space behind the system for proper
air circulation and for clearance of the gas lines and electrical
connections. This also provides sufficient space for accessing the fan
filters on the rear side of the mass spectrometer. In addition, allow at
least 92 cm (36 in.) of vertical clearance between the top of the mass
spectrometer and any shelves above it.
NOTICE Avoid blocking the ventilation slots at the rear side of the mass
spectrometer. Items might fall behind the instrument, inhibit airflow,
and cause the system to overheat. Depending on the circumstances,
either the Tune software will switch off the instrument and display an
error message or the turbomolecular pump control will shut down the
instrument and vent it. ▲
NOTICE Before moving the instrument from one place to another, all
participating personnel must carefully read and follow the instructions
given in this manual. ▲
! CAUTION Heavy Load. Because of its weight of about 220 kg, handling the
instrument alone might cause muscle strain and back injury. Lifting
and moving the instrument requires the effort of at least six persons to
keep the individual load within acceptable limits (maximum 40 kg for
men or 15 kg for women for a duration of 5 seconds). The carriers
must be trained in how to carry loads properly (for example, by rising
from the knees with a straight back). Thermo Fisher Scientific
recommends using a pallet jack to lift the mass spectrometer to the
height of the workbench.
The following instructions assume that the instrument has been moved
to the installation site with a pallet jack and the top cover of the
transport crate has been removed.
1. Gather six persons and appoint one person that takes command and
gives instructions to the remaining people.
2. Lift the instrument to the height of the working bench by using the
pallet jack.
3. Remove the four clamps that fix the instrument to the transport
pallet. See Figure 5-2.
4. Each lifting device consists of a folded metal sheet with holes and a
twice bent tube. It comes with four hexagon screws, four washers,
and two clamps. Mount each device onto the handles at one
instrument side:
1
3
4
2
toward mass
spectrometer
The ends of the lifting devices must be aligned flush with each other
as shown in Figure 5-4. Red circles in the figure indicate the
positions of the diamond-shaped holes in the lifting devices.
Transport pallet
Mass spectrometer
Lifting devices
! CAUTION Top Heavy Load. The mass spectrometer might tip over while being
moved in the laboratory and cause bodily injury or instrument damage.
The instrument’s center of gravity is at the top of the front side: the
instrument has a tendency to tilt forward. When lifting the instrument,
support the top of the instrument and keep the tilt angle below 5°;
never exceed 10°.
7. The rear pair of the four support points for the instrument consists
of wheels. Thus, only two persons are necessary for moving the
instrument into its final position on a bench, while holding the two
front handles. See Figure 5-2 on page 5-5 for information about the
position of the support points.
Push down the spring (safety catch) of the handle by using a screw
driver and shove the handle into its housing.
Laboratory Conditions
This section gives an overview of important requirements for the
laboratory where the Exactive Series mass spectrometer is placed. For
details, refer to the Exactive Series Preinstallation Requirements Guide.
! WARNING Electric Current. Electric shock hazard. Wrong usage of these ports
might endanger personnel. Read and understand the Operating
Manual to prevent risk of harm to the operator and to protect
equipment against damage. To ensure that the instrument is free from
all electric current, always disconnect the power cords of mass
spectrometer and forepump before attempting any type of maintenance.
NOTICE Do not connect other gases than nitrogen to the nitrogen inlets
of the Q Exactive GC mass spectrometer! This might affect instrument
performance. The maximum pressure for the gas inlet is 830 kPa
(8.3 bar, 120 psi). ▲
Laboratory Temperature
The mass spectrometer is designed to operate at a laboratory room
temperature between 15 and 26 °C (59 and 78 °F).
NOTICE Do not put the mass spectrometer under an air duct, near
windows, or near heating and cooling sources. Temperature fluctuations
of 1 °C or more over a 10 minutes period can affect instrument
performance. ▲
Humidity
The relative humidity of the operating environment must be between
40 and 70%, with no condensation. It is recommended that your
laboratory be equipped with a temperature/humidity monitor to ensure
that your laboratory is always within the required temperature and
humidity specifications.
Vibration
Floors must be free of vibration caused, for example, by equipment in
adjoining locations.
2. Insert the opposite end of the Teflon tubing into the press-in fitting
of the y-piece that is attached to the gas ports at the rear side of the
instrument. See Figure 5-6. To connect the tubing, align the Teflon
tubing with the opening in the fitting and firmly push the tubing
into the fitting until the tubing is secure.
NOTICE If air is not properly purged from gas supply lines, the
instrument leak check will report an oxygen leak until the air is
removed. ▲
Y-piece
! WARNING Moving Parts and High Voltage. Risk of injury or electric shock. The
interior of the instrument contains parts that are moving or that are at
high voltages. When opening the instrument housing is necessary, call a
Thermo Fisher Scientific field service engineer.
Screws
! WARNING Fire Hazard. Some CI gases, such as methane and isobutane, are
flammable. Make sure these gases are properly exhausted and all gas
fittings on the system are leak-free. Check for leaks by pressurizing the
gas lines, shutting off the gas supply, and ensuring that the pressure
does not drop. If you have an electronic leak detector available, use it to
detect leaks as well. Consult your local Environmental and Safety
Regulations for information about how to properly exhaust fumes from
your laboratory.
Output Specifications
1 of 4 outputs
Input Specifications
Location and function of the Start In input are described on page 3-8.
Figure 5-10 shows the circuit diagram and Table 5-2 lists the
specifications of the peripheral control output.
Contents
! CAUTION Hot Surface. The external surface of the ion source housing can
become hot enough to burn your skin. Avoid touching the ion source
housing when the mass spectrometer is in operation. Allow the ion
source to cool to room temperature (approximately 60 minutes) before
touching the ExtractaBrite removable ion source.
! CAUTION Hot Surface. Touching hot parts of the ion source interface might
cause severe burns. During operation of the mass spectrometer, the
ExtractaBrite removable ion source might reach temperatures of up to
350 °C, while the GC column transfer line might reach temperatures of
up to 400 °C. To let the ion source interface cool down, set the ion
source and transfer line temperatures to 25 °C. Wait until the ion
source has cooled down to room temperature (for approximately
60 minutes) before you begin working on it. Do not leave the
instrument unattended when the covers and front door are removed,
exposing the hot source parts. Hot ion source parts might ignite
combustible material. Keep combustible materials away from the ion
source mount.
You can check the current pressure values in the Vacuum / Bakeout
window of the Tune software. To display the Tune software window,
choose Start > Programs > Thermo Exactive Series > Tune. The
Instrument status LED in the toolbar (see image in margin) turns green
when the vacuum levels are sufficient for operating your Exactive Series
system. If the LED is not green, you might have an air leak; see
“Vacuum Leak” on page 7-5 for instructions.
2. To select another disk drive so that you can determine its disk space,
click Directory.
If necessary, you can free space on the hard disk by deleting obsolete files
and by moving files from the hard disk drive to a backup medium. First,
copy files to the backup medium. After you have copied the files, you
can delete them from the hard disk.
You need to optimize the tune parameters (or change the Tune Method)
whenever you change the type of experiment. Refer to the QuickStart
Guide for a procedure for optimizing the tune parameters for your
experiment.
4. Place the electronics service switch, located on the power panel (See
Figure 3-4 on page 3-7.), in the Service Mode position.
5. Put the main power circuit breaker switch of the mass spectrometer
in the Off position.
6. Shut down the TRACE 1310 GC. See the GC user documentation
for instructions.
NOTICE The data system must be running before you start up the
instrument. The instrument will not operate until software is received
from the data system. ▲
5. Make sure that the main power circuit breaker switch is in the
Off (O) position and that the electronics service switch is in the
Service Mode position.
6. Place the main power circuit breaker switch in the On (|) position.
When you place the main power circuit breaker switch in the On (|)
position, the forepump and the turbomolecular pumps are started.
All LEDs on the mass spectrometer front panel are off.
a. After the main switch is switched On, the pumps of the mass
spectrometer are run up. To monitor the vacuum readings in the
Tune software, it is necessary to switch on the electronics switch,
too. The Pirani gauge (see “Vacuum Gauges” on page 3-11)
monitors the pressure at the forepump. Within a short time, a
significant pressure decrease must be observed. The quality of
If the pressure exceeds 1E-4 mbar for more than 10 seconds, the
ion gauge is switched off. After five minutes, the ion gauge is
switched on again. After three failed attempts, it is only possible
to switch on Ion Gauge 1 manually in the Tune software.
If the pressure exceeds 1E-4 mbar for more than 10 seconds, the
ion gauge is switched off. After five minutes, the ion gauge is
switched on again. After three failed attempts, it is only possible
to switch on Ion Gauge 2 manually in the Tune software.
e. The Vacuum LED on the system panel turns green when all the
following conditions are met:
• In the Tune software, all LEDs are green. (The Ion Gauge 1
is allowed to be off ).
1. Operation of the system with excessive air and water in the vacuum
manifold can cause reduced sensitivity and tuning problems. Before
you begin data acquisition with your Q Exactive GC system, you
need to bake out the system for at least twelve hours plus a cooling
period of three hours. See “Baking Out the System” on page 8-11.
3. Make sure that the gas pressure is within the operational limits:
See also “Before Operating the System” on page 6-3 for additional
information.
The Q Exactive GC mass spectrometer, the GC, and the autosampler (if
present) have been installed by a Thermo Fisher Scientific field service
engineer.
1. Ensure that mass spectrometer and data system computer are both
powered on and the mass spectrometer is in Standby condition. See
page 6-6 for instructions about placing the instrument to Standby
condition.
2. To reset the mass spectrometer, press the Reset button located on the
power panel. See Figure 3-4 on page 3-7. Make sure the Status LED
is extinguished before releasing the Reset button. When you press
the Reset button, the following occurs:
NOTICE If resetting the system does not resolve the failure: Put the
electronics switch in the Service Mode position for about one minute.
Afterwards, place the electronics service switch back in the Operating
Mode position. ▲
The split and purge valves of the selected channel are automatically
closed, and the channel is pressurized with carrier gas to the leak
check set point.
The system monitors the pressure for one minute. If the pressure
does not drop more than the maximum allowed sensitivity value,
then the leak check will pass. If the leak check does not pass, use the
leak detector to find and fix any leaks.
To flowmeter
NOTICE For the most reproducible results, you should conduct a more
detailed column evaluation. However, the following steps, while
recommended, are not required. ▲
7. Remove the clear plastic component, including its fittings, from the
oven and set them aside.
4. Place the ion source cartridge on the source holder and set aside.
Figure 6-2. Storing the Ion Source Cartridge in the Source Holder
Figure 6-3. Attaching the Source Plug to the Source Plug Holder
6. Attach the source exchange tool to the source plug in the source plug
holder.
Figure 6-4. Attaching the Source Plug to the Source Exchange Tool
7. Twist the plug until it aligns securely in the grooves in the source
exchange tool and remove the plug from the holder
Alignment Grooves
Figure 6-5. Attaching the Source Plug to the Source Exchange Tool
NOTICE IMPORTANT Use compressed air to blow all the dust off the
source plug before inserting it into the mass spectrometer. ▲
8. Once the ion source temperature has dropped below 200 °C, insert
the barrel end of the source exchange tool into the vacuum interlock
Figure 6-6. Inserting the Source Plug into the Vacuum Interlock
13. Wait for oven and transfer line temperatures to drop below 50 °C to
avoid burns before proceeding to touch the column and nut.
14. Use the GC transfer line handle to slide the GC transfer line away
from the MS transfer line.
GC Transfer
Line Handle
NOTICE Monitor the foreline pressure when removing the column and
nut to confirm that the source plug is properly sealing the transfer line.
If the pressure exceeds 3 mbar, the leak is excessive, and the source plug
should be reseated or inspected for damage. If the turbomolecular pump
is forced off by the vacuum protection and the pump speed drops below
80% speed, cycling power will not restart the turbomolecular pump.
The pump speed must further drop below 25% before cycling the power
to reset the pump and allow it to spin up to 100%. Be careful not to
have the circuit breaker off for more than 5 seconds or there is a risk that
the system will vent and must be pumped down overnight. ▲
16. Unwind an appropriate column length to insert into the transfer line
along the front of the instrument. Leaving about an inch gap
between the column and the left side of the front panel will usually
give you an appropriate length of column for installation.
Column Gap
Figure 6-10. Inserting the New Column through the GC Transfer Line
18. Carefully extend the column out the front to allow application of
the nut and ferrule.
Column
19. Insert the column through the nut and ferrule (flat side of the nut
faces the MS).
Figure 6-12. Inserting the Column through the Nut and Ferrule
20. Use a scoring wafer to score and then remove the last 10 mm of
column to provide a clean, well-cut end.
21. Wipe the column with an alcohol soaked-wipe after inserting
through the ferrule.
22. Carefully push the column back into the GC transfer line while
keeping the nut and ferrule on the column.
23. Insert the column into the MS transfer line and tighten the nut until
the column just resists sliding through the ferrule.
24. Loosen the nut ¼ turn and push the column into the MS transfer
line until it just touches the source plug.
25. Pull the column ½ to 1 mm away from the source plug and tighten
the nut ½ turn.
NOTICE To avoid forcing the column into the source plug when
tightening the nut, the column can be pulled back approximately 1 mm
before tightening the nut. ▲
26. Ensure the column and nut are correctly installed in the MS transfer
line.
27. Pull the GC transfer line handle to the left to close it.
33. Using the source holder, place the ion source on the
insertion/removal tool and install the ion source using the vacuum
interlock.
34. In Tune Instrument Control – EI/CI source, set the:
a. MS transfer line temp to the method temperature.
b. Ion source temp to the method temperature.
35. In Tune, place the instrument in the On state.
36. Leak check at the nut with tetrafluoroethane spray and tighten with
a 1/4” wrench as needed. Perform leak checking by scanning in full
scan and looking for +CF3 (68.99466) and +CH2CF3 (83.01031)
peaks while spraying potential leak spots with tetrafluoroethane
(dusting spray or refrigerant R-134A).)
37. Confirm the GC transfer line is covering the nut to prevent a cold
zone on the column.
38. If vacuum compensation was set to Off for any reason (such as
conditioning a new column), set vacuum compensation to On.
39. On the GC, set the Oven to On.
40. On the GC, in the Auxiliary Temperature Control, set Transfer Line
1 and Transfer Line 2 to On.
41. If necessary, reinsert the ion source to assure good electrical contacts
using the insertion/removal tool and vacuum interlock once all
temperatures have stabilized for 30 minutes and the source has
thermally expanded.
42. Replace the vacuum interlock knob and evacuate the inlet valve
chamber to remove the remaining air between the ball valve and
interlock plug.
43. Confirm there are no leaks before beginning any tuning or analyses.
Contents
! WARNING High Voltage. High voltages capable of creating an electric shock are
used in the instrument. Do not remove protective covers from PCBs.
Opening the instrument housing is only allowed for maintenance
purposes by Thermo Fisher Scientific personnel. To ensure that the
instrument is free from all electric current, always disconnect the power
cords of mass spectrometer and forepump before attempting any type of
maintenance.
! CAUTION Hot Surface. Touching hot parts of the ion source interface might
cause severe burns. During operation of the mass spectrometer, the
ExtractaBrite removable ion source might reach temperatures of up to
350 °C, while the GC column transfer line might reach temperatures of
up to 400 °C. To let the ion source interface cool down, set the ion
source and transfer line temperatures to 25 °C. Wait until the ion
source has cooled down to room temperature (for approximately
60 minutes) before you begin working on it. Do not leave the
instrument unattended when the covers and front door are removed,
exposing the hot source parts. Hot ion source parts might ignite
combustible material. Keep combustible materials away from the ion
source mount.
! CAUTION Hot Surface. Touching hot parts of the forepump might cause burns.
The forepump in function is hot and some surfaces could reach a
temperature higher than 70 °C (158 °F). Switch off the pump and let it
cool down before any intervention or take appropriate precautions.
Always wear heat protective gloves when working on a pump that is
“still warm from operation”.
Fault Table
If malfunctions on the mass spectrometer occur, you will find possible
causes and instructions for repair in Table 7-1.
If the log file of the data system shows a reboot of the system and the
pressure reading in the Tune software shows a bad vacuum, this
indicates that the system was vented. In case of frequent but short power
failures we recommend installing an uninterruptible power supply
(UPS). If main power failures occur frequently while the system is not
attended (for example, in the night), we recommend installing a power
fail detector.
Vacuum Leak
For proper performance, your Q Exactive GC system must operate at
acceptable vacuum levels. You can check the current pressure values in
the Vacuum / Bakeout window of the Tune software window.
1. To display the Tune software window, choose Start > Programs >
Thermo Exactive Series > Tune. The Instrument status LED in the
toolbar (see image in margin) turns green when the vacuum levels of
the instrument are sufficient for operating your Q Exactive GC
system.
If the pressure remains high, the system might have an air leak. See
below for instructions.
2. Make a visual inspection of the vacuum system and vacuum lines for
leaks.
3. Check each fitting and flange on the system for tightness, and
tighten the fittings or flanges that are loose.
4. Ensure that the o-rings and the cover plates of the vacuum manifold
are properly positioned.
5. Ensure the MS transfer line nut is secure. A leak can develop at this
seal when the GC transfer line temperature is reduced significantly.
7. Ensure that the glass cover of the ion source is properly seated on the
o-ring if source maintenance has been performed with the covers off
If you cannot find the location of the leak or tighten the leak yourself,
contact your Thermo Fisher Scientific field service engineer.
In case of a failure of the UHV chamber heating control, shut down the
mass spectrometer as described on page 6-7. To prevent permanent
damage to components of the Q Exactive GC mass spectrometer,
Thermo Fisher Scientific recommends calling a Thermo Fisher
Scientific field service engineer.
Contents
! WARNING High Voltage. High voltages capable of causing an electric shock are
used in the instrument. Do not remove protective covers from PCBs.
Opening the instrument housing is only allowed for maintenance
purposes by Thermo Fisher Scientific personnel. To ensure that the
instrument is free from all electric current, always disconnect the power
cords of mass spectrometer and forepump before attempting any type of
maintenance.
! CAUTION Hot Surface. Touching parts of the forepump might cause burns. The
forepump in function is hot and some surfaces could reach a
temperature higher than 70 °C (158 °F). Switch off the pump and let it
cool down before any intervention or take appropriate precautions.
Always wear heat protective gloves when working on a pump that is
“still warm from operation”. Take note of the warning labels on the
pump.
! CAUTION Hot Surface. Touching hot parts of the ion source interface might
cause severe burns. During operation of the mass spectrometer, the
ExtractaBrite removable ion source might reach temperatures of up to
350 °C, while the GC column transfer line might reach temperatures of
up to 400 °C. To let the ion source interface cool down, set the ion
source and transfer line temperatures to 25 °C. Wait until the ion
source has cooled down to room temperature (for approximately
60 minutes) before you begin working on it. Do not leave the
instrument unattended when the covers and front door are removed,
exposing the hot source parts. Hot ion source parts might ignite
combustible material. Keep combustible materials away from the ion
source mount.
- Proceed methodically
- Dirty tools can contaminate your system. Keep the tools clean
and use them exclusively for maintenance and service work at
the mass spectrometer.
Returning Parts
To protect our employees, we ask you for some special precautions when
returning parts to the factory for exchange or repair. Your signature on
Health and Safety Form confirms that the returned parts have been
de-contaminated and are free of hazardous materials. See “Safety Advice
for Possible Contamination” on page 8-52 for further information.
NOTICE Prevent any liquids from entering the inside of the instrument.
Leaking liquids might get into contact with electronic components and
cause a short circuit. ▲
3. Search for leaks in the gas line, for example, by using a conventional
thermal conductivity-based leak detector, such as is widely used to
check leaks in gas chromatography equipment.
5. When you cannot find a leak in the gas line, we recommend calling
a Thermo Fisher Scientific field service engineer to check for gas
leaks within the instrument.
Pumps Maintenance
This section only outlines the maintenance procedures for the forepump
and the turbomolecular pumps (TMPs) of the mass spectrometer. The
manuals of the pump manufacturers give detailed advice regarding
safety, operation, maintenance, and installation. Note the warnings and
precautions contained in these manuals!
The foreline (roughing) pump is usually located on the floor behind the
Q Exactive GC instrument and occasionally requires maintenance. It
establishes the vacuum needed to run the turbomolecular pump inside
the instrument. Typically, the foreline pump oil needs to be replaced
every four months. However, depending on your sample type and
frequency of use, your maintenance interval will be different. Refer to
the foreline pump documentation for information. The forepump
requires several maintenance procedures to be performed by the user.
Table 8-2 outlines the maintenance schedule for the forepump as
recommended by the pump manufacturer. To simplify the maintenance
work, the pump manufacturer recommends combining several jobs. For
maintenance instructions, refer to the forepump manual.
! CAUTION Hot Surface. Touching hot parts of the forepump might cause burns.
The forepump in function is hot and some surfaces could reach a
temperature higher than 70 °C (158 °F) for GC/MS systems. Switch off
the pump and let it cool down before any intervention or take
appropriate precautions. Always wear heat protective gloves when
working on a pump that is “still warm from operation”. Take note of
the warning labels on the pump.
! CAUTION Hot Liquid. Touching hot forepump oil might cause burns. Always
wear protective gloves and protective goggles when you handle the
forepump oil.
! CAUTION Hazardous Chemicals. The forepump oil might cause skin or eye
irritation and it might contain toxic, carcinogenic, mutagenic, or
corrosive/irritant chemicals. Avoid exposure to potentially harmful
materials. Always wear protective clothing, gloves, and safety glasses
when you handle the forepump oil.
Forepump oil and exhaust filters are available from Thermo Fisher
Scientific (see Chapter 9: “Replaceable Parts”). If you want to order
other spare parts, contact the pump manufacturer (Edwards for GC/MS
systems).
This topic outlines the maintenance work for the TMPs. These
procedures require removing the housing of the instrument and partially
disassembling it. Therefore, a Thermo Fisher Scientific field service
engineer must be called if servicing is required. See also page 8-53.
Bakeout is mandatory after the system has been vented for maintenance
or service work in the analyzer region. You should bake out an
instrument that has been vented for at least twelve hours (12 hours)
before you can start using it again.
If the system has vented during a power failure and it not at the correct
pressure and you need to use the system within 24 hours, it is necessary
to bake out the system to attain the operating vacuum. See “Starting Up
the System after a Shutdown” on page 6-9.
NOTICE Before you start the bakeout, ensure that the pumps are up and
running at their operating speed. If you have just switched on the mass
spectrometer, this will take about 10 minutes. See “Starting Up the
Instrument” on page 6-9. To check the pump speed, open the
Instrument Status window of the Tune software and expand the
Vacuum System node of the Instrument tree. ▲
3. Enter the desired baking duration (in hours) into the spin box. The
available range is 4 to 100 hours.
4. Click Bake out. A dialog box shows the duration of the baking
procedure. See Figure 8-2. Click Yes to confirm the message.
5. The dialog box disappears and the baking procedure starts. The
instrument indicates the active bakeout procedure by a flashing
Vacuum LED. (See Figure 3-2 on page 3-5.) Additionally, the Tune
software displays a corresponding message box. See Figure 8-3.
6. The baking of the instrument stops after the preset duration. The
Vacuum LED keeps flashing until the cooling and stabilization time
(of about 3 hours) is finished.
! CAUTION Hot Surface. Touching hot parts of the instrument immediately after a
bakeout might cause burns. If you abort a system bakeout, parts of the
instrument can be hot. Allow the instrument to cool for at least three
hours before you start operating it again.
NOTICE Avoid blocking the ventilation slots at the rear of the mass
spectrometer. Items might fall behind the instrument, inhibit airflow,
and cause the system to overheat. Depending on the circumstances,
either the Tune software will switch off the instrument and display an
error message or the turbomolecular pump control will shut down the
instrument and vent it. ▲
1. Each fan filter bracket is mounted on hinges. Insert a finger into the
recess in the instrument frame and pull at the fan filter bracket to
open it. See Figure 8-4 and Figure 8-5.
2. Remove each fan filter from the rear of the mass spectrometer by
pulling it out of the filter bracket. See Figure 8-5.
If the fan filters are covered with dust, proceed as described in “Cleaning
the Fan Filters” below. Replacements for the fan filters are available from
Thermo Fisher Scientific (see Chapter 9: “Replaceable Parts”).
4. Squeeze the water from the fan filters and allow them to air dry.
Figure 8-6. Locating the Vacuum Interlock Knob and Evacuate Button
2. Get the source exchange tool that shipped with your instrument. It
is used to remove and insert the ion source cartridge through the
vacuum interlock. The tool has a large black handle on one end and
a stainless steel barrel at the other. On the black handle is a diagram
describing how to insert and remove the ion source cartridge from
the instrument using the tool. The stainless steel barrel is cut with a
track and the black handle moves up and over the track, depending
on whether you are removing or installing an ion source cartridge.
Alignment
Left Track Groove
Handle of Barrel
Right Track
of Barrel
Usage Diagram
Figure 8-7. Locating the Vacuum Interlock Knob and Evacuate Button
3. Grasp the handle of the source exchange tool in one hand and use
your other hand to pull the metal barrel out and away from the
handle so that tool is fully extended.
4. Attach the source exchange tool to the front of the instrument.
a. With your hand around the stainless steel barrel, twist the tool
until the alignment groove at the end of the barrel aligns with
the left screw around the slot vacated by the vacuum interlock
knob.
b. Twist and push the stainless steel barrel to the right until it clicks
into place under the screw at the top of the slot.
NOTICE If the evacuate light flashes for only a short time then returns
to a solid light without the Ready to Open light turning green, there is a
leak in the VPI seal. The source removal tool connection should be
checked or field service contacted. ▲
6. Twist, then loosen the top part of the vacuum interlock handle to
allow the entire handle to swing up and down. This handle controls
the interior ball valve, which seals the vacuum chamber.
7. Swing the handle down and then twist the top of it in the opposite
direction to lock it into place.
NOTICE If more than 60 seconds have passed since the Ready to Open
indicator light has come on, it will turn off. You should press the
Evacuate button and wait until the Ready to Open light is lit again
before opening the valve. Do not open the valve if the Ready to Open
light is not on. This may indicate a leak in the valve region. When a leak
is detected during the evacuate sequence, the amber evacuate LED will
flash on and off. ▲
9. Slowly push the ion cartridge tool into the instrument. Because you
are removing the ion volume in this step, you will go down the right
side of the metal track on the barrel
10. Once the tool is all the way in (when the groove at the end of the
barrel is covered by the black handle) twist the handle to the left to
engage the ion source cartridge and move it onto the end of the
barrel. You are essentially disconnecting the ion source cartridge
from the ion source block and moving it onto the tool.
11. Pull the tool toward you and down the left side of the metal track on
the barrel. As you keep pulling it toward you, more and more of the
barrel will be exposed. You may encounter resistance while removing
the source. To release the source from the spring contacts make
small repeated rotations (vibrations) of the handle to the left and
right quickly.
12. Once you reach the end of the track (when the back line at the end
of the barrel is uncovered by the black handle), twist the handle to
the left to lock it into place.
Figure 8-13. Locking the Tool in Place. Note: Tool is Rotated Left.
13. Pull the vacuum interlock handle down to close the interior ball
valve.
14. Twist the end of the vacuum interlock handle and flip the swing
handle up so that it rests next to the vacuum interlock knob
location. Then twist the end again to hold it in place.
15. Replace the plug in the VPI to prevent accidental venting and
excessive leaks.
! CAUTION Hot Surface. Touching hot parts of the ion source interface might
cause severe burns. During operation of the mass spectrometer, the ion
source can reach temperatures up to 350 °C. Wait until the ion source
has cooled down to room temperature before you begin working on it.
18. Hold the handle of the source exchange tool with one hand and use
the other hand to pull the barrel toward you and into the handle.
Ion Source
Cartridge
19. Invert the source exchange tool so that the barrel is pointed toward
the floor.
20. Slide the source holder, which is in the Q Exactive GC toolkit, onto
the end of the ion source cartridge. The opening of the source
holder is designed to accommodate the handles of the ion volume.
Wing of Ion
Volume
Filament Hole
Source Holder
Ion Volume
Handles Fit Here
21. Twist the holder to disengage the ion source cartridge from the tool.
NOTICE The repeller locking nut is now loose on the repeller spring. Be
careful not to tip the source or the components will fall out. ▲
22. Set the ion source cartridge and holder on a clean surface
.
! CAUTION Hot Surface. The ion source parts might be hot, so use caution when
handling.
23. Let the ion source cartridge cool down before removing it from the
source holder.
24. Disassemble the ion source cartridge by removing the locking ring
first, then the repeller spring, then the nut, insulator, and repeller
(which comes out in one piece), ion volume, lens 1, lens 2, and lens
3/RF lens.
NOTICE IMPORTANT Many nitrile and latex gloves not certified for
clean room use contain silicone mold releasing agents that will
contaminate the instrument. For this reason, clean room gloves are
strongly recommended when handling the ion source cartridge. We
recommend Cardinal Health CP100 Nitrile Cleanroom Gloves. ▲
Lens 1
Repeller
Repeller Ion Cartridge Sleeve
Nut
Lens 2
Ion Volume
Locking Ring Ion Volume
Ion Volume-Repeller
Repeller Insulator
Spring
3. Align the long tooth of lens 3/RF lens with the notch on the bottom
of the sleeve and drop the lens into the sleeve.
Figure 8-21. Inserting Lens 3/RF Lens into the Source Sleeve
4. Place lens 2 on top of lens 3/RF lens with the small hole facing
down. It should fit snugly and sit evenly on top of lens 3/RF lens.
Small Hole of
Lens 2
5. With the longer teeth of lens 1 facing down toward lens 2, align the
larger metal section of lens 1 with the sleeve window and let it fall
into place.
Larger Metal
Section Longer Teeth
of Lens 1
Sleeve
Window
6. Insert the ion volume with the handles fitting into the notches of the
sleeve. Make sure the ion volume is firmly seated into the gap on
lens 1. You may need to rotate lens 1 slightly to make the ion
volume fit correctly.
Handles Fit
Here Ion Volume
Handles
Lens 1 Gap
Figure 8-24. Inserting the Ion Volume into the Source Sleeve
NOTICE The ion volume handles are different sizes and will only fit into
the sleeve one way. ▲
9. Insert the large flat end of the repeller so that it rests on top of the
ion volume.
Large Flat
End of
Repeller
Repeller
Spring
11. Place the locking ring on top of the repeller spring so that the
repeller protrudes through the center hole on the locking ring. The
hooks on the sleeve fit between the larger gaps on the locking ring.
Larger Gaps on
Locking Ring
Hooks on Sleeve
NOTICE Do not twist and lock the locking ring on the sleeve at this
time. ▲
NOTICE If you try to attach the ion source cartridge to the tool by
inverting it, the components will likely fall, so make sure you are
working over a table. Otherwise, you may have to stop and clean the
components again. ▲
2. Look for a small vertical 3mm line engraved on the end of the
barrel. This line always matches up with the picture on the handle.
There is a similar engraved line on the sleeve of the ion source
cartridge. This line matches up with the filament.
Engraved
Line on
Barrel
Engraved
Line on
Sleeve
Figure 8-28. Aligning the Tool with the Ion Source Cartridge
3. Position the engraved line on the tool with the open end of the hook
on the sleeve. There is a pin the source exchange tool that will latch
under the hook.
4. Push the ion source cartridge up into the barrel of the tool and twist
it until the engraved lines are aligned. The ion source cartridge
should easily slide into place with very little force.
NOTICE The ion volume and lenses have keying features to assure the
lens spring contacts will align with the metal parts of the lenses. ▲
5. Gently pull the source holder away from the ion source cartridge.
NOTICE When the source exchange tool is inverted, the source should
stay attached. If this does not happen, the source will not insert correctly
into the instrument. ▲
6. Turn the source exchange tool around so that the ion source
cartridge is furthest away from you.
7. Firmly grasp the black handle of the ion cartridge tool in one hand
and use your other hand to pull the metal barrel out and away from
the handle so that tool is fully extended.The ion source cartridge is
now hidden inside the barrel.
8. When the barrel can go no further, twist the handle to the left to
lock it into position.
9. Insert the barrel end of the ion cartridge tool into the vacuum
interlock and twist it to the right to lock it into position. Be sure the
black handle remains in the locked position.
Evacuate
Button
NOTICE Make sure you take the correct track on the tool or the ion
volume will disassemble inside the instrument. If that happens, the tool
will get stuck and you will have to shut down, vent the instrument, and
manually remove the source cartridge through the top of the
instrument. ▲
13. Push the handle toward the instrument until the end of the handle
aligns with the engraved line at the end of the barrel. When you
reach this line, the tool is all the way in and the ion source cartridge
has been placed back onto the ion source block. You may notice
slight resistance when the handle is approximately 2 cm from the
engraved line. This is normal. Do not force the cartridge into the
instrument. To release the source from the spring contacts make
small repeated rotations of the handle to the left and right quickly.
Gently apply pressure to the back of the handle.
NOTICE Do not push down on the handle of the source exchange tool
while inserting the ion source cartridge. This could result in opening an
air leak that may cause your instrument to shut itself down to protect
the vacuum pumps. ▲
14. Twist the handle of the source exchange tool to the right and pull it
back toward you and down the right side of the barrel’s metal track
until the line at the end of the track appears.
15. Pull the vacuum interlock handle down to close the interior ball
valve.
16. Twist the end of the vacuum interlock handle and flip the swing
handle up so that it rests next to the vacuum interlock knob
location. Then twist the end again to hold it in place.
19. For optimal performance, wait at least 30 minutes for the ion source
to heat up to the same temperature as the inside of the instrument.
Otherwise, the masses or intensities may drift during operation.
You can ONLY clean the following durable components inside the
vacuum manifold:
• Repeller
• Ion volume
• Lens 1
• Lens 2
• Lens 3/RF lens
• Ion cartridge sleeve
• Heat shield for the source interface board
• Screws
NOTICE You only need to clean the repeller, ion volume and all the
lenses most frequently. Cleaning the other components are not part of
the expected maintenance. ▲
! CAUTION Material and Eye Hazard. Wear impermeable laboratory gloves and
eye protection when cleaning components.
NOTICE Clean only the metal pieces of the repeller, lens 1 and lens
3/RF lens with aluminum oxide. ▲
! WARNING Electric Current. Electric shock hazard. Exposing the Dremel tool to
standing water may cause an electrical shock.
! WARNING Fire Hazard. Using the Dremel tool near flammable vapors may cause
a fire.
Electron
Entrance Hole
NOTICE Tip Clean the CI ion volume under a microscope to verify that
you removed all debris. ▲
with fresh water, and put the beaker and contents in a ultrasonic
bath again for five minutes. Repeat until the water is clear.
5. Use forceps to immediately transfer the components to a clean
beaker of acetone.
! WARNING Fire Hazard. Acetone is flammable and volatile, so make sure the
ultrasonic bath is properly ventilated to prevent the buildup of vapors.
a. Place the beaker and its contents in an ultrasonic bath for one
minute.
b. Use forceps to transfer the components to a beaker of fresh
acetone.
c. Place the beaker and its contents in an ultrasonic bath for one
minute.
7. Wearing gloves, blow clean, dry gas on the components to remove
the acetone.
Acetone should not be allowed to dry on the part. It will leave a residue
that may affect instrument performance.
Calibrant
reservoir
Calibrant
Reservoir
Calibrant
Reservoir
Cover
4. Inject the FC 43. If you see liquid pooled on top of the white frit,
remove the excess liquid according to local environmental
regulations.
• Setting the solvent delay so that the analyzer will not turn on
while the solvent peak is eluting.
Screws
2. Open the small center panel and remove the screw at the back of the
panel using a flat-head screwdriver.
Screw
3. Carefully pull the entire central panel back to remove it. Set it aside.
Vacuum
Interlock
Panel
5. Pull the manifold door out to open. Once the alignment pins are
clear of the thumbscrews, swing the manifold door open.
6. Remove the glass manifold cover from the top of the manifold
assembly.
7. Look through the top of the instrument and use a clean T10
Torxhead screwdriver to loosen the screw holding the filament
retaining clip in place. Then rotate the clip away from the filament.
Source
Interface
Board
Filament
Filament
Screw
Retaining
Spring
8. Disconnect the filament board and wires from the source interface
board.
10. Insert the replacement filament into its slot, rotate the spring into
position, and slightly tighten the screw holding the filament
retaining clip in place.
11. Bend the filament wires so they do not touch any metal component.
You may want the old filament as a model.
13. Return the glass manifold cover to the top of the instrument.
14. Swing the manifold door so that it is parallel to the opening. Guide
the alignment pins into the thumbscrews.
NOTICE The manifold door will not swing closed. There will be a 1 cm
gap. You must push the door to close it completely. Do not apply excess
force to the thumbscrews or components may be damaged. ▲
NOTICE Once the manifold door is closed, ensure the filament wires do
not contact the metal surface of the door. ▲
15. Use a T20 Torxhead screwdriver to replace the four screws around
the manifold door. Do not overtighten the screws.
Consumables
For information on consumables such as fittings, nitrogen gas, or
cleaning agents, refer to the Consumables chapter in the Q Exactive GC
Preinstallation Requirements Guide.
The forepump oil is used for cooling, lubrication, and sealing of the
forepump. See “Maintenance of the Forepump” on page 8-8 for
information about forepump oil disposal. Also refer to the Material
Safety Data Sheet (MSDS) for the forepump oil.
Your signature on the Health and Safety Form confirms that the
returned parts have been decontaminated and are free of hazardous
materials. You can order the form from a Thermo Fisher Scientific field
service engineer.
Contents
Filament Components
Dual Filament . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120404-1940
Filament Retaining Spring Kit . . . . . . . . . . . . . . . . . . . . . . . . 1R120404-1405
Screw for Filament Retaining Spring . . . . . . . . . . . . . . . . . . . . 1R76913-0305
Valve Spring
Clip
Interior O-Ring
Tools
Bushing in the Source Exchange Tool . . . . . . . . . . . . . . . . 1R120406-2203
Seal in the Source Exchange Tool . . . . . . . . . . . . . . . . . . . 1R120406-2204
Clip in the Source Exchange Tool . . . . . . . . . . . . . . . . . . . . .1R76483-2102
Source Exchange Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120406-2000
VPI Toolkit, which includes*: . . . . . . . . . . . . . . . . . . . . . . 1R120467-0003
Source Holder. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120471-0001
Source Removal Tool (Small) . . . . . . . . . . . . . . . . . . . . . 1R120406-2250
Source Plug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120589-1000
Source Plug Holder. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120589-1050
CI Ion Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120404-4112
EI/CI Ion Volume. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R120404-4113
T10 Torxhead Key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1R3812-5T10
T20 Torxhead Key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1R3812-5T20
T30 Torxhead Key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1R3812-5T30
Forceps, 8 in. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R76360-0008
Wrench, Open-Ended, 1/4-in., 5/16-in. . . . . . . . . . . . . . . 1R76360-0109
Wrench, Open-Ended, 3/8 in., 7/16-in. . . . . . . . . . . . . . . 1R76360-0108
Wrench, Open-Ended, 1/2-in., 9/16-in. . . . . . . . . . . . . . . 1R76360-0110
Wrench, Open-Ended, 1/2 in., 7/16-in. . . . . . . . . . . . . . . 1R76360-0111
*The VPI tool kit also includes the Source Exchange Tool (P/N 1R120406-2000)
Pump Components
Turbomolecular Pump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R119268-0002
Rough Pump (RV3). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R76505-3007
Vacuum Hose (Order 10 ft). . . . . . . . . . . . . . . . . . . . . . . . . . . 1R76505-0625
Claw Clamp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R76505-0017
Centering Ring . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R76505-2001
Convectron Gauge. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A0105-00501
Oil Mist Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R76505-0036
Foreline Adapter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1R119244-0025
Vacuum Pump Oil. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A0301-15101
Other Parts
Gas Supply Parts
Teflon hose 10 m (length); 6 mm o.d. . . . . . . . . . . . . . . . . . . . . . . . .0690280
Fan Filter
Fan Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1234880
Contents
WEEE Compliance
This product is required to comply with the European Union’s Waste
Electrical & Electronic Equipment (WEEE) Directive 2002/96/EC. It is
marked with the following symbol:
C E
calibration parameters 6-5 electrodynamic squeezing, of ions 3-20
central electrode electronic components 5-9
schematics 3-19 electronics service switch
voltages 3-20, 3-32 function 3-6
central electrode pulser board 3-32 location 3-7
checking leaks, in gas lines 8-7 usage 6-7, 6-9, 6-11
circuit breakers 3-7 emergency shutdown 4-8, 5-4
cleaning emission sound pressure level 5-10
drying durable components, 8-41 entrance lens 3-12, 3-15
fan filters 8-14 entrance voltage 3-18, 3-32
instrument surface 8-6 error diagnosis 7-7–7-8
sonicating durable components, 8-40 Ethernet
supplies, 8-38 port 3-9
clothing 4-11 replaceable parts 9-5
collector switch 3-30
V
vacuum W
analyzer chamber 3-24
warning labels
compartments 3-23
forepump 8-9
control 3-11
instrument 4-3
deterioration 3-26
location 8-6
establishing 6-9
WEEE Compliance D-3
failure 6-10
gauges 3-11, 3-31 wheels, of the instrument 5-7
manifold 3-23 workbench, for instrument 5-4
quality 3-31
Vacuum / Bakeout window 6-11
vacuum control board 3-26 X
vacuum interlock handle, purpose of, 8-18 Xcalibur 3-29
Vacuum LED 3-5, 6-10
vacuum system
controls 3-24
maintenance 8-10 Z
moisture 3-26 Z-lens 3-3, 3-12, 3-24
schematics 3-23