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TRACE MS
[Including Voyager and MD Series]
Revision A
FM101890
Xcalibur™ and TRACE™ are trademarks of ThermoQuest Corporation. Microsoft® and Windows NT® are registered trademarks
of Microsoft Corporation. Tygon® is a registered trademark of Norton Industrial Plastics.
Technical information contained in this publication is for reference purposes only and is subject to change
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Reference to System Configurations and Specifications supersede all previous information and are subject
to change without notice.
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_________________________________________________________________________ Contents
Contents
Abbreviations..........................................................................................................................................v
Typographical Conventions...................................................................................................................ix
Data Input ............................................................................................................................ix
Notes, Cautions, and Warnings.............................................................................................x
Topic Headings ....................................................................................................................xi
1. Introduction........................................................................................................................................2
Probe Source Voltage Requirements ....................................................................................2
9. Probe Control and Data Acquisition using the Solids or DCI Probe ...............................................22
Solids Probe Control ...........................................................................................................22
DCI Probe Control ..............................................................................................................24
Note. The information contained within this manual can also be applied to
the Voyager and MD Series of mass spectrometers. However, the reader
should be aware that all text, examples and Figures refer only to the
Finnigan TRACE MS for the purpose of simplification.
WARNING. Both probes can quickly reach red heat, even when out of the
vacuum lock. Exercise extreme caution at all times whilst using the system.
Abbreviations
The following abbreviations are used in this and other TRACE MS manuals
and in the online Help.
A ampere
ac alternating current
ADC analog-to-digital converter
amu atomic mass unit
AP acquisition processor
APCI atmospheric pressure chemical ionization
API atmospheric pressure ionization
ASCII American Standard Code for Information Interchange
b bit
B byte (8 b)
baud rate data transmission speed in events per second
°C degrees Celsius
cfm cubic feet per minute
CD compact disc
CD-ROM compact disc read-only memory
CI chemical ionization
CIF Carriage, Insurance and Freight Paid to
CIP Carriage and Insurance Paid to
cm centimeter
cm3 cubic centimeter
CPU central processing unit (of a computer)
CRM consecutive reaction monitoring
CSE customer support engineer
<Ctrl> control key on the terminal keyboard
d depth
Da dalton
DAC digital-to-analog converter
dc direct current
DCI desorption chemical ionization
DDS direct digital synthesizer
DS data system
kg kilogram
l length
L liter
LAN local area network
lb pound
LC liquid chromatograph
LC/MS liquid chromatograph / mass spectrometer
LED light-emitting diode
m meter
m milli (10-3)
M mega (106)
M+ molecular ion
µ micro (10-6)
min minute
mL milliliter
mm millimeter
MS scan power: MS1
MS/MS scan power: MS2
MSn scan power: MSn, n = 1 through 10
m/z mass-to-charge ratio
n nano (10-9)
NCBI National Center for Biotechnology Information (USA)
NIST National Institute of Standards and Technology
Ω ohm
p pico (10-12)
Pa pascal
PC personal computer
PCB printed circuit board
PID Photo Ionization Detector
PMD Photo Multiplier Detector
PMT Photo Multiplier Tube
P/N part number
P/P peak-to-peak voltage
ppm parts per million
viii __________________ Finnigan TRACE MS Solids & DCI Probe Manual ________________
Read This First
___________________________________________________________Typographical Conventions
Typographical Conventions
Typographical conventions have been established for ThermoQuest manuals
for the following:
• Data input
• Notes, Cautions, and WARNINGS
• Topic headings
Data Input
Throughout this manual, the following conventions indicate data input and
output via the computer:
• Prompts and messages displayed on the screen are represented in this
manual by capitalizing the initial letter of each word and italicizing each
word.
• Input that is to be entered by keyboard or buttons that are to be clicked
on by the mouse is represented in bold face letters. (Titles of topics,
chapters, and manuals also appear in bold face letters.)
• For brevity, expressions such as “choose File | Directories” are used
rather than “pull down the File menu and choose Directories.”
• Any command enclosed in angle brackets < > represents a single
keystroke. For example, “press <F1>” means press the key labeled F1.
• Any command that requires pressing two or more keys simultaneously
is shown with a hyphen connecting the keys. For example, “press
<Shift>-<F1>” means depress and hold the <Shift> key and then press
the <F1> key.
Note. Boxes such as this are used to display Notes, Cautions, and
WARNINGS.
A Note contains information that can affect the quality of your data. In
addition, notes often contain information that you may need if you are
having trouble.
A Caution contains information necessary to protect your instrument from
damage.
A WARNING describes hazards to human beings.
Topic Headings
The following headings are used to show the organization of topics within a
chapter:
Chapter 1
Chapter Name
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ThermoQuest what he or she does and doesn’t like about the manual.
Secondly, when the user returns the card, he or she is registered and placed
on the ThermoQuest mailing list. Once registered, the user will receive
ThermoQuest's newsletter Analytical News and will be notified of events of
interest, such as user meetings.
xii __________________ Finnigan TRACE MS Solids & DCI Probe Manual ________________
1. Installing and Using Probes
1. Introduction
The TRACE MS can be supplied with two different probes: Solids and DCI.
A probe consists of four elements:
• Control Unit
• Vacuum Lock
• Probe Source
• Probe
The sections that follow in this manual describe each of the above.
A Power lead is connected to the control unit. Before plugging it in, carry
out the following:
• Select the correct voltage for your power supply. The voltage selector is
on the rear of the control unit.
• Ensure that the correct fuse is fitted to the control unit. The fuse is
located on the rear of the unit, marked as PUMP FUSE (see Figure 1 on
page 4). Two packs of fuses are supplied with the control unit. The table
below shows fuse types and part numbers.
• Ensure that the equipment is earthed.
Caution. Ensure that the rotary pump fitted is of the correct voltage rating.
5. Locate the probe control unit’s communication cable. Connect one end
to the port marked Control Input on the rear of the control unit.
Connect the other end to the port marked Analog I/O on the rear of the
TRACE MS.
6. Connect the Tygon® tube that exits the rear of the control unit to the
exhaust outlet on the rotary pump.
7. Ensure that the pump has any transit covers removed (especially the
outlet connection) and that it contains the correct amount of oil (refer to
the manufacturer’s handbook or your Hardware Manual).
8. Connect the vacuum pump power cable to the IEC connector on the rear
of the control unit.
9. Select the mains voltage supply rating at the switch on the rear of the
control unit.
Caution. Ensure the correct voltage is selected on the rear of the control
unit or severe damage may be done to the instrument.
To CONTROL
CONTROL VOLTAGE MAINS
SELECTOR SOLIDS ON/OFF
PROBE
PART No 3 AMP
240V
SERIAL No
ADDRESS
DCI
PUMP
FUSE PROBE
3 AMP
Pump inlet
To ANALOG I/O on
the mass detector
Rotary pump Water
to/from
supply
Mains
Probe
Controller
WATER
quick release
valves
vacuum pumping
connection rotary pump connection
to probe lock
probe lock
(underside view)
Caution. Moving the probe through the vacuum lock with a high probe
temperature or current setting will damage seals in the lock and may also
lead to system contamination. Always allow the probes to cool before
inserting or removing.
The size of the hole alters the pressure inside the source block. A low
pressure favors EI ionization whereas a relatively high pressure favors CI+
ionization. If flexibility is required to acquire samples using different
ionization modes without having to vent the instrument, then the
combination exit plate should be fitted. This will give reasonable sensitivity
in all ionization modes. However, if only EI or CI+ acquisitions are required
then the relevant dedicated exit plate should be fitted. This will increase the
sensitivity in the chosen ionization mode. Similarly, when acquiring in CI-
only, fit the combination exit plate that has already been optimized for CI-
acquisition.
After removing the source block, remove the lenses and magnets in order to
gain access to the exit plate. Carry out this procedure as follows:
1. Hold the source by the mounting plate with the four nuts visible as
shown in Figure 4.
2. Remove the four nuts.
3. Lift the ion lock and exit plate away from the lenses and magnets.
Caution. Hold the exit plate at the edges and avoid touching the flat faces.
Caution. When fitting the four nuts illustrated in Figure 4, only tighten
them until they are finger-tight. Over-tightening may cause the source
ceramic spacers to crack.
Source block
Source Installation
To install the source and vacuum lock:
1. Remove any source already in the TRACE MS, remembering to retract
the GC Interface.
2. Ensure that the wires connecting the source will not interfere with the
passage of the probe during operation. Also, ensure that when the source
is moved on its springs, the wires do not move to block the path of the
probe.
3. The probe source has no hole for a GC Interface to enter the source,
therefore withdraw the GC interface a suitable distance back into the
GC.
4. Withdraw the column about 6 cm into the GC interface and tighten the
interfaces-locking nut. It is not necessary to remove the column but
reduce the column head pressure to 20 kPa to conserve helium.
5. Fit the probe source and vacuum lock into the TRACE MS system,
taking care not to trap any wires in the flange seal, and secure with the
two black finger nuts.
6. Move the lock fully to the left to close the lock. Do not insert the probe
at this stage.
7. Connect the Tygon tube from the front of the control box to the 6 mm
stainless steel tube on the lower part of the probe lock. This connects the
lock to the inlet of the rotary pump via the control unit.
Note. There is a different cable for the DCI and Solids probes.
3. Connect the water lines from the probe to the outlets on the box and
ensure that the water supply is ON. Check the system for water leaks
now.
In the TRACE MS Tune window (Xcalibur), make sure the Solids probe
temperature is set to 20 °C, which is the default value. Refer to the section
on the Tune window (Solids Probe control) for more information on this
(page 22).
WARNING. Beware of hot parts! The probe can heat up very quickly
(800 °C/min).
Probe
Controller
WATER
Control unit
(front view)
Water cooling
Probe IN/OUT
sample cup
Power connection
3. Connect the DCI probe to the control box with the appropriate cable,
(P/N TPRC002).
Caution. Do not switch on while the probe is removed from the mass
detector because the filament will deteriorate in atmosphere.
In the TRACE MS Tune window (Xcalibur), make sure the DCI current is
set to zero (0 mA), which is the default value. Refer to the section on the
Tune window (DCI Probe control) for more information on this (page 24).
Probe
Controller
WATER
Control unit
(front view)
Platinum filament
Power connection
8. Using Probes
The following pages describe how you use the TRACE MS Solids and DCI
probes.
Sample Loading
The procedure for loading a sample depends upon the type of probe you are
using, as described below.
Solids Probe
Two types of sample cup are available for use with the Solids probe (see
Figure 10).
For non-volatile samples, the shallow cup is recommended. With this type
of cup the sample is close to the heated ion source, aiding evaporation of the
sample.
Use a deep cup for more volatile samples. With this type of cup the sample
is deposited at the bottom, so that it is remote from the heating affect of the
ion source. The sample is then evaporated into the ion source, in a controlled
fashion, using the probe heater.
Load solid samples into the cups using a thin piece of wire, or a drawn-out
length of glass rod. Make sure that the sample is deposited at the bottom of
the cup and not around the neck. Liquid samples in solution are best loaded
using a microsyringe taking care not to leave any air pockets. Allow the
solvent to evaporate from the cup before inserting the probe into the
instrument by standing the holder in a warm place, for example on top of the
GC oven. Take care not to heat the holder too quickly, so as to avoid
blowing the sample out of the cup with solvent vapor.
A common mistake is to overload the probe. A few micrograms are
sufficient. If the sample is easily visible, there is probably too much present.
If you have a number of samples to run sequentially, load all the cups and
stand them in the holder provided.
Hold the sample cups firmly in place using a strip of tungsten foil and push
them firmly into the holder at the end of the probe so as to give good
thermal contact with the heater element.
Coil the foil round and insert it into the end of the probe. Fully insert the
probe cup so that the foil forms a spring between the cup and probe tip. The
foil should allow the cups to be inserted easily but held firmly in the probe
tip once they are in place.
Always insert the probe cups fully, so that less than 2 mm of glass protrudes
(see Figure 11).
Caution. Always use the tungsten foil in the Solids probe to hold the
sample in place, and always fully insert the probe cups so that less than
2mm of glass protrudes Failure to do this will risk the probe cups becoming
entangled in the probe lock rotary valve, causing irreparable damage.
tungsten foil
Probe tip
Figure 11. End view of probe tip showing the foil in place
DCI Probe
Load samples onto the platinum filament as a liquid or in solution using a
microsyringe; any solvent is then evaporated prior to probe insertion. As
with the Solids probe, care must be taken not to overload the probe; a few
microliters are sufficient. To achieve reproducible spectra the sample must
be deposited as an even film.
Note. There is a different cable for the DCI and Solids probes. The Solids
probe cable part number is TPRC001 and the DCI probe cable part number
is TPRC002.
2. Ensure that the probe is set to its lowest setting: 20 °C for Solids and
0 mA for DCI. Refer to the relevant section on the Tune window for
more information on this (Solids probe, see page 22; DCI Probe, see
page 24).
3. When the probe has been prepared for use, insert it into the introduction
lock until the interlock fingers reach the guide on the lock handle (see
Figure 13 and Figure 14). You will feel resistance for the last few
millimeters of travel as the probe makes contact with the first seal.
Figure 13. Inserting the probe into the introduction lock (1)
Figure 14. Inserting the probe into the introduction lock (2)
4. Pump out the introduction lock by pressing the green VACUUM button
on the front of the control unit. The light will begin flashing and then
stop.
5. When the vacuum light stops flashing, rotate the probe lock valve 90° to
the right (see Figure 15).
6. Carefully push the probe fully into place (see Figure 16).
The probe lock allows either the DCI or the Solids probes to be inserted
while the mass detector remains under vacuum. The lock is equipped with a
series of seals, as well as a rotary valve and a vacuum connection. This
combination allows the probe to be inserted and removed without subjecting
the vacuum system to any pressure fluctuations.
WARNING. This light is for indication only. Exercise caution and check
the actual temperature before handling the probe.
2. Slightly withdraw the probe back from the source, as the source will
keep the probe hot.
3. Withdraw the probe carefully from the system until the fingers on the
interlock meet the valve handle.
4. Rotate the valve fully to the left (90°) using a gentle action, feeling for
any unusual resistance.
Caution. If resistance is felt, the probe cup may have slipped out from the
end of the probe and be fouling the lock. To prevent damage to the cup,
probe or the lock, vent the instrument and withdraw the probe from the
vented system without closing the lock (by springing the fingers of the
interlock system out of the way). Locate and remedy the cause of the
resistance, and pump down after closing the lock securely.
5. Press the VACUUM button on the front of the control unit to stop
pumping of the valve area and then fully withdraw the probe from the
lock.
WARNING. The probe may still be very hot at the tip, from heat
transferred by the hot source.
Tune Window
When the TRACE MS is configured for Solids probe support, the TRACE
MS Controls area of the Tune window displays a Solids probe temperature
text box and readback in its top left corner (see Figure 17). You can use this
text box to set a value for the temperature of the Solids probe (between 20
and 750 °C) in real time. The adjacent readback shows the actual measured
temperature.
When Solids probe support is enabled for the TRACE MS, you can use the
Probe Control page in the Instrument Setup window to set temperature
ramping parameters for the Solids probe. To access the Probe Control page,
do the following:
1. Start Xcalibur by double-clicking on the Xcalibur shortcut icon on the
Windows desktop. Alternatively, click on the Start button in the
Windows Taskbar and choose Programs I Xcalibur I Xcalibur.
2. To open the Instrument Setup window, click on the Instrument Setup
button on the Xcalibur Home page, or choose GoTo I Instrument
Setup.
3. To display the Probe Control page, click on the TRACE MS button in
the Viewbar of the Instrument Setup window, then click on the Probe
Control tab (see Figure 18).
Note. The Probe Control page only displays for the TRACE MS method
editor within Instrument Setup when Xcalibur is configured for probe
support.
When the Solids probe is configured, the Probe Control page displays the
Set Solids Probe control group box (Figure 18). This group box contains a
ramp table for setting the temperature ramping parameters and also displays
a graphical representation of the ramp settings. You can enter values in the
ramp table to set up a ramp that defines the Temperature (°C) of the probe
against Time (min). This allows you to control the temperature of the Solids
probe during an acquisition.
The ramp table allows you to set up to five ramps. For each ramp you can
define a start Temperature (°C), a Time (min) during which the probe will
be held at that temperature, and a Rate (°C/min) at which the probe will be
heated to reach the start Temperature of the next defined ramp.
The ramp display graphically depicts the temperature ramp settings. The
number that appears on the right-hand side of the graph’s Time axis (x-axis)
is equivalent to the overall run time.
You can use the File I Save command to save any set ramping parameters
as part of your method.
When you have set ramping parameters for an acquisition, refer to TRACE
MS Getting Started for further information relating to setting up and
running your experiment.
Tune Window
When the TRACE MS is configured for DCI probe support, the TRACE MS
Controls area of the Tune window displays a DCI probe current text box and
readback in its top left corner (see Figure 19). You can use this text box to
set a value for the current of the DCI probe (between 0 and 1500 mA) in real
time. The adjacent readback shows the actual measured temperature.
When DCI probe support is enabled for the TRACE MS, you can use the
Probe Control page in the Instrument Setup window to set current ramping
parameters for the DCI probe. To access the Probe Control page, do the
following:
1. Start Xcalibur by double-clicking on the Xcalibur shortcut icon on the
Windows desktop. Alternatively, click on the Start button in the
Windows Taskbar and choose Programs I Xcalibur I Xcalibur.
2. To open the Instrument Setup window, click on the Instrument Setup
button on the Xcalibur Home page, or choose GoTo I Instrument
Setup.
3. To display the Probe Control page, click on the TRACE MS button in
the Viewbar of the Instrument Setup window, then click on the Probe
Control tab (see Figure 20).
Note. The Probe Control page only displays for the TRACE MS method
editor within Instrument Setup when Xcalibur is configured for probe
support.
When the DCI probe is configured, the Probe Control page displays the Set
DCI Control Ramp group box (Figure 20). This group box contains a ramp
table for setting the current ramping parameters and also displays a
graphical representation of the current ramp settings. You can enter values
in the ramp table to set up a ramp that defines the Current (mA) at the probe
filament against Time (min). This allows you to control the current on the
DCI probe filament during an acquisition.
The ramp table allows you to set up to five ramps. For each ramp you can
define a start Current (mA), a Time (min) during which the probe filament
will be held at that current, and a Rate (mA/min) at which current will be
passed through the probe to reach the start Current of the next defined ramp.
The ramp display graphically depicts the current ramp settings. The number
that appears on the right-hand side of the graph’s Time axis (x-axis) is
equivalent to the overall run time.
You can use the File I Save command to save any set ramping parameters
as part of your method.
When you have set ramping parameters for an acquisition, refer to TRACE
MS Getting Started for further information relating to setting up and
running your experiment.
10. Troubleshooting
TRACE MS vents during You are not correctly following See the section Inserting the
insertion of probe. the insertion procedure. Probe on page 18 for details.
Note. All troubleshooting tips for standard EI and CI sources also apply to
probes. See your Hardware Manual for details.
M3 x 16LG CH HD ST STL
part no. 5314018
Note. Parts M401006A, 5711035, 5711018, 5711013 and C851A are all
part of the Insertion lock spares kit which has a part number of C890A.