ISOPRIME100 USER’S GUIDE
Isoprime User’s Guide
Isoprime Ltd
Isoprime House
Earl Road
Cheadle Hulme
Cheadle
SK8 6PT
Tel: +44 (0) 161 488 3660
Fax: +44 (0) 161 488 3699
http://www.Isoprime.co.uk/
This manual describes the detailed operation and maintenance of the IsoPrime100 mass
spectrometer with IonVantage v1.5
If you feel that more information is required or if you would like to suggest how the manual
could be improved, then please contact the customer service department at Isoprime Ltd. or
your local Isoprime representative.
ASSISTANCE
If you encounter difficulties with the operation of your instrument or need software support,
please contact the customer service department at service@isoprime.co.uk, alternatively log on
to http://www.isoprime.co.uk/resolve to report the problem.
Customer service will raise a call log to track the progress of your enquiry, which
ensures that the problem will not be forgotten. The call will be passed to the
appropriate technical people for answering. Calls will be handled locally where
possible and escalated to the factory if a local response is not possible. All logged
calls must be dealt with to a successful conclusion before they can be closed.
Contact details are provided on the Isoprime website at http://www.Isoprime.co.uk/
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ISOPRIME100 USER’S GUID E
WARRANTY
The information contained within this document is subject to change without notice
Isoprime Ltd. makes no warranty of any kind with regard to this material, including, but not
limited to, the implied warranties of merchantability and fitness for a particular purpose.
Isoprime Ltd. shall not be liable for errors contained herein or for incidental damages in
connection with the furnishing, performance, or use of this material.
SAFETY INFORMATION
The IsoPrime100 mass spectrometer meets the following IEC (International Electromechanical
Commission) classifications:
Safety Class 1
Transient Over Voltage Category II
Pollution Degree 2
You must comply with all local and national requirements for electrical and mechanical safety.
The instrument has been designed and tested in accordance with recognized safety standards. If
the instrument is used in a manner not specified by the manufacturer, the protection provided
by the instrument may be impaired.
Whenever the safety protection of the IsoPrime100 is compromised, disconnect the instrument
from all power sources and secure the unit against unintended operation.
Suitably qualified personnel only should perform maintenance procedures. Substituting parts or
performing any unauthorized modification to the instrument may result in a safety hazard.
Disconnect the mains supply before removing covers.
Please contact the customer service department at the above address, or your local Isoprime
representative, should you require any further information.
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SAFETY SYMBOLS
Warnings in this manual or on the instrument must be observed during all phases of service,
repair, installation and operation of the instrument. Failure to comply with these precautions
violates the safety standards of design and the intended use of the instrument.
Isoprime Ltd. assumes no liability for the customer’s failure to comply with these requirements.
The following safety symbols are used in the manual or on the instrument. Warnings are given
to highlight situations or conditions where failure to observe the instruction could result in
injury or death to persons. Cautions are given to highlight situations or conditions where failure
to observe the instruction could result in damage to the
equipment, associated equipment or process.
Warning: this is a general warning symbol, indicating that there is a
potential health or safety hazard.
Warning: this symbol indicates that hazardous voltages may be present.
Warning: this symbol indicates that hot surfaces may be present.
Warning: this symbol indicates that there is danger from corrosive
substances.
Warning: this symbol indicates that there is danger from toxic substances.
Caution: this is a general caution symbol, indicating that care must be taken
to avoid the possibility of damaging the instrument or affecting its
operation.
Warning: high magnetic fields. Pacemaker wearers should not approach any
closer than 1m.
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CONTENTS
Assistance ..................................................................................................................................................................... 2
IsoPrime100 User’s Guide .............................................................................................................................................. 3
Warranty ...................................................................................................................................................................... 3
Safety Information ........................................................................................................................................................ 3
Safety Symbols ............................................................................................................................................................. 4
Contents ....................................................................................................................................................................... 5
Site Requirements ...................................................................................................................................................... 15
Benchtop Requirements ......................................................................................................................................... 15
Dimensions ........................................................................................................................................................ 15
Weight ............................................................................................................................................................... 16
Electrical Requirements .............................................................................................................................................. 16
Environmental Requirements .................................................................................................................................. 17
Room Temperature ............................................................................................................................................ 17
Humidity ................................................................................................................................................................. 17
Dust Free Environment ........................................................................................................................................... 17
Rotary Pump Exhaust Fumes ................................................................................................................................... 17
Magnetic Fields....................................................................................................................................................... 18
Compressed Air ...................................................................................................................................................... 18
System Description ..................................................................................................................................................... 19
Introduction ........................................................................................................................................................... 19
Ion Optics ................................................................................................................................................................... 20
Overview ................................................................................................................................................................ 20
The Ion Source ........................................................................................................................................................ 21
Gas Inlet Probe ....................................................................................................................................................... 23
Analyser Magnet ..................................................................................................................................................... 24
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Electromagnet .................................................................................................................................................... 24
Analyser Housing ..................................................................................................................................................... 27
Collectors ................................................................................................................................................................ 28
Triple Collector ................................................................................................................................................... 28
ESF Collector ....................................................................................................................................................... 30
The Vacuum System .................................................................................................................................................... 33
Overview ................................................................................................................................................................. 33
Pressure Measurement ........................................................................................................................................... 35
Pirani Gauge ....................................................................................................................................................... 35
Penning Gauge .................................................................................................................................................... 35
Electronic Units ........................................................................................................................................................... 35
Locations of the Electronic Units .............................................................................................................................. 36
System Controller ........................................................................................................................................................ 37
Source High Voltage Supplies .............................................................................................................................. 38
Turbomolecular Pump Controller ............................................................................................................................. 39
Head Amplifier ........................................................................................................................................................ 39
Electromagnet Supply .............................................................................................................................................. 40
Mains Distribution ................................................................................................................................................... 40
Overview of IonVantage .............................................................................................................................................. 42
Determining Version and Change Note Information ................................................................................................. 42
Starting IonVantage ................................................................................................................................................. 43
Closing Down IonVantage ........................................................................................................................................ 44
Closing IonVantage after a Crash ............................................................................................................................. 44
Structure of IonVantage .............................................................................................................................................. 47
The Sample List ....................................................................................................................................................... 47
The Tune Page ......................................................................................................................................................... 48
The Inlet Editor ........................................................................................................................................................ 48
The Script Message Window .................................................................................................................................... 49
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File Locations .......................................................................................................................................................... 51
The IonVantage Folder ............................................................................................................................................ 51
IonVantage Projects .................................................................................................................................................... 52
Introduction ........................................................................................................................................................... 52
Creating a New Project ........................................................................................................................................... 53
Switching between Projects .................................................................................................................................... 55
Project File Structure .............................................................................................................................................. 56
Scope of Project Files .............................................................................................................................................. 57
The Sample List ........................................................................................................................................................... 58
Running Samples from the Sample List .................................................................................................................... 58
Sample List Fields .................................................................................................................................................... 60
Editing the Sample List ............................................................................................................................................ 62
Setting up the Total Number of Rows ................................................................................................................. 62
Adding Samples .................................................................................................................................................. 62
Inserting Samples ............................................................................................................................................... 63
Deleting Samples ................................................................................................................................................ 63
Fill Down ............................................................................................................................................................ 64
Fill Series ............................................................................................................................................................ 64
Editing Information in Cells ................................................................................................................................. 65
Clearing Selected Cells ........................................................................................................................................ 65
Editing the Sample List via an Autosampler Plate Layout ..................................................................................... 66
Selecting Samples .......................................................................................................................................... 67
Inserting Samples .......................................................................................................................................... 67
Adding Samples ............................................................................................................................................. 67
Replacing Samples ......................................................................................................................................... 68
Editing Columns ................................................................................................................................................. 68
Modifying the Sample List Fields ......................................................................................................................... 69
Using Sample List Format Files ................................................................................................................................ 70
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The Tune Page ............................................................................................................................................................. 72
Pumping Control ..................................................................................................................................................... 73
Pumping Down ................................................................................................................................................... 73
Venting ................................................................................................................................................................... 73
Tuning Control ............................................................................................................................................................. 74
Source Control......................................................................................................................................................... 74
Tune Files ................................................................................................................................................................ 76
Source Parameters .................................................................................................................................................. 77
Tuning the mass spectrometer .................................................................................................................................... 78
Coarse tuning the Ion Source ................................................................................................................................... 79
Fine Tuning of source parameters ............................................................................................................................ 83
Notes on Tuning.................................................................................................................................................. 83
Optimisation by scanning source parameters ...................................................................................................... 84
Instrument Linearity ........................................................................................................................................... 85
Map Files ..................................................................................................................................................................... 87
Acquisition Map ...................................................................................................................................................... 87
Display Map ............................................................................................................................................................ 87
The Map Editor ........................................................................................................................................................ 88
Edit Acquisition Map ........................................................................................................................................... 88
Edit Display Map ................................................................................................................................................. 89
Changing a Map File ............................................................................................................................................ 89
Editing Display Properties ................................................................................................................................... 90
Enable Status – Rio Property ........................................................................................................................... 93
Running a Scan ............................................................................................................................................................ 94
Setting up a Peak Centre Scan .................................................................................................................................. 95
Running a Peak Centre Scan..................................................................................................................................... 96
Peak Display ................................................................................................................................................................ 97
Auto Peak Centre .................................................................................................................................................... 98
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Head Amplifier Zeroes ................................................................................................................................................ 99
The Function of Zeroes ........................................................................................................................................... 99
Electronic Zeroes ...................................................................................................................................................100
Collector Zeroes .....................................................................................................................................................100
Beam Zeroes Dialog ...............................................................................................................................................101
Tune Page Methods ...................................................................................................................................................102
Editing a Method ...................................................................................................................................................102
Running a Method from the Tune Page ..................................................................................................................105
Events....................................................................................................................................................................106
Overview...........................................................................................................................................................106
Peak Jump .........................................................................................................................................................107
IO Command .....................................................................................................................................................110
End of Acquire ...................................................................................................................................................111
Scan ..................................................................................................................................................................112
Function ............................................................................................................................................................114
Acquire Map .....................................................................................................................................................115
Stopping an Acquisition .........................................................................................................................................116
Data Display...............................................................................................................................................................116
Viewing Scans ........................................................................................................................................................116
The Peak Display Window..................................................................................................................................116
Peak Display Options .............................................................................................................................................117
Zooming In ........................................................................................................................................................117
Options.........................................................................................................................................................118
Templates .........................................................................................................................................................119
Peak Centre Options ..........................................................................................................................................120
Viewing Acquisitions ..................................................................................................................................................121
View Data Display ..................................................................................................................................................121
Loading Data Files .............................................................................................................................................121
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Zooming in on Data ........................................................................................................................................... 123
Diagnostics and Security............................................................................................................................................. 124
IsoPrime100 Diagnostics............................................................................................................................................ 124
PC Security ................................................................................................................................................................ 127
Remote Control ..................................................................................................................................................... 127
Anti-Virus .............................................................................................................................................................. 127
Backing up ............................................................................................................................................................. 128
Warranty ............................................................................................................................................................... 128
Archiving ............................................................................................................................................................... 128
Background Information ............................................................................................................................................ 129
Basics of Mass Spectrometry ..................................................................................................................................... 129
The Mass Spectrometer Equation .......................................................................................................................... 129
Mass Spectrometers .............................................................................................................................................. 129
Analytical and Isotope Ratio Analysers ................................................................................................................... 130
Peak Shape ............................................................................................................................................................ 130
Dispersion ............................................................................................................................................................. 132
Resolution ............................................................................................................................................................. 133
Vacuum System ......................................................................................................................................................... 136
Vacuum Measurement .......................................................................................................................................... 136
Units of Pressure ................................................................................................................................................... 137
Gas Flow and Vacuums .......................................................................................................................................... 138
Viscous Flow ..................................................................................................................................................... 138
Molecular Flow ................................................................................................................................................. 138
Pumps ................................................................................................................................................................... 139
The Rotary Vane Pump..................................................................................................................................... 140
The Turbomolecular Pump ................................................................................................................................ 142
Pressure Gauges ............................................................................................................................................... 143
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The Pirani Gauge...........................................................................................................................................143
The Penning Gauge .......................................................................................................................................144
The Principle of Continuous Flow ...............................................................................................................................144
Calculations and Corrections......................................................................................................................................145
Enrichment Delta ( ..............................................................................................................................................145
Isotopic Abundance (Atom %) ................................................................................................................................145
Internal Reproducibility..........................................................................................................................................146
Standard Deviation () ......................................................................................................................................146
Standard Error ( mean) ...................................................................................................................................146
Carbon Dioxide Corrections (Craig Formulae).....................................................................................................147
Nitrogen Corrections .........................................................................................................................................147
Standard Formula for High Enrichments ........................................................................................................148
Modified Formula for Low Enrichments ........................................................................................................148
Derivation of Nitrogen Formulae ...................................................................................................................148
Other Analytical Considerations ................................................................................................................................151
General Sequence of Data Reduction .....................................................................................................................151
Sequence of Data Reduction ..............................................................................................................................152
A Simple Example for Carbon Dioxide ................................................................................................................154
Calculations Specific to Carbon Dioxide .............................................................................................................154
International Standards ................................................................................................................................156
Atom% Carbon .............................................................................................................................................156
Calculations Specific to Nitrogen .......................................................................................................................157
Atomic% Nitrogen.........................................................................................................................................157
Enriched Nitrogen Analysis ...........................................................................................................................157
Atom Percent Formulae .........................................................................................................................................158
Carbon Dioxide ..................................................................................................................................................158
Nitrogen ............................................................................................................................................................159
Oxygen ..............................................................................................................................................................159
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Sulphur Compounds .......................................................................................................................................... 160
Nitrous Oxide (N20) ........................................................................................................................................... 160
Maintenance ............................................................................................................................................................. 162
Introduction .......................................................................................................................................................... 162
Tools ..................................................................................................................................................................... 162
Emergency Fault Conditions ...................................................................................................................................... 163
Emergency Instrument Shutdown .......................................................................................................................... 163
Electrical Power Failure ......................................................................................................................................... 164
Failure of Helium Supply ........................................................................................................................................ 166
Routine Maintenance of the Mass Spectrometer ...................................................................................................... 166
Changing the Rotary Pump Oil ............................................................................................................................... 166
Changing the Molecular Sieve in the Foreline Traps ............................................................................................... 167
Changing the Oil Mist Filters .................................................................................................................................. 168
Maintenance of the Compressor (if Supplied) ........................................................................................................ 168
Drainage of the Compressed Air Water Trap (if Fitted) ........................................................................................... 168
Changing the Helium Gas Bottle............................................................................................................................. 168
Mass Spectrometer Repairs ....................................................................................................................................... 169
Overview ............................................................................................................................................................... 169
Venting the Mass Spectrometer............................................................................................................................. 170
Removing the Ion Source ....................................................................................................................................... 170
Removing the Source Flange ............................................................................................................................. 170
Removing the Ion Source .................................................................................................................................. 173
Replacing the Ion Source ....................................................................................................................................... 174
Fitting the Ion Source to the Source Flange ....................................................................................................... 174
Replacing the Source Flange .............................................................................................................................. 176
Changing the Ion Source Filament .......................................................................................................................... 178
Removing the Old Filament ............................................................................................................................... 178
Positioning the New Filament............................................................................................................................ 179
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Attaching the Filament Support Assembly to the Source ....................................................................................180
Disassembly of the Ion Source ................................................................................................................................181
Removal of the Magnet, Filament and Trap ............................................................................................................182
Disassembly of the Stack ........................................................................................................................................187
Disassembly of the Ion Box ....................................................................................................................................188
Dismantling the Trap Assembly ..............................................................................................................................190
Dismantling the Magnet Assembly .........................................................................................................................191
Assembly of the Ion Source ....................................................................................................................................191
Folding Photo-Etched Components ........................................................................................................................192
Trap ..................................................................................................................................................................192
Source Wraparound ..........................................................................................................................................192
Filament Shield..................................................................................................................................................193
Rebuilding the Ion Box Assembly ............................................................................................................................194
Rebuilding the Trap Assembly ................................................................................................................................195
Rebuilding the Magnet Assembly ...........................................................................................................................196
Reassembly of the Stack.........................................................................................................................................197
Cleaning Procedures ..................................................................................................................................................199
Rough Cleaning ......................................................................................................................................................199
Pre-Cleaning ..........................................................................................................................................................199
Final Cleaning ........................................................................................................................................................200
Cleaning the Flight Tube.........................................................................................................................................200
Cleaning the Penning Gauge ..................................................................................................................................200
Electronics Repair ......................................................................................................................................................201
Removal of System Controller ................................................................................................................................201
Refitting the System Controller ..............................................................................................................................203
Removal of the Bakeout Power Supply ...................................................................................................................205
Replacing the Bakeout Power Supply .....................................................................................................................206
Removal of the Electromagnet Power Supply .........................................................................................................206
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Replacement of the Electromagnet Power Supply .................................................................................................. 208
Removal of the Head Amplifier .............................................................................................................................. 208
Replacement of the Head Amplifier ....................................................................................................................... 209
Fuse Replacement ................................................................................................................................................. 211
Mains Inlet to IsoPrime100 ............................................................................................................................... 211
System Controller ............................................................................................................................................. 212
Bakeout Supply Unit.......................................................................................................................................... 212
Electromagnet Power Supply ............................................................................................................................ 213
Fault Finding .............................................................................................................................................................. 214
Introduction .............................................................................................................................................................. 214
Poor Operating Pressure ........................................................................................................................................... 214
On the Pirani Gauge .............................................................................................................................................. 214
On the Penning Gauge ........................................................................................................................................... 215
High Background Levels ............................................................................................................................................. 215
For Argon .............................................................................................................................................................. 215
Dirty Background Scan ........................................................................................................................................... 216
Valves cannot be Operated ....................................................................................................................................... 217
Poor Mass Spectrometer Peak Shape ........................................................................................................................ 217
Non-Linear Signal ...................................................................................................................................................... 218
Reference gas box ................................................................................................................................................. 218
Source Tuning........................................................................................................................................................ 218
Magnet Position .................................................................................................................................................... 218
Leak Checking Using Argon ........................................................................................................................................ 218
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SITE R EQUI REMENTS
The site requirements, concerning the IsoPrime100 mass spectrometer, are described in this
section. For the full site requirements concerning the mass spectrometer peripherals, the
appropriate manual must be consulted.
BENCHTOP REQUIREMENTS
DIMENSIONS
The IsoPrime100 is a bench top instrument and may be placed on normal laboratory benches.
The bench must be of a construction adequate to support the weight of the IsoPrime100 and
associated prep systems. Refer to the appropriate peripheral manual for dimension and weight
information.
The bench should also be free of any vibration or movement that may impair the performance
of the IsoPrime100.
It must be level and free from vibrations.
The IsoPrime100 (including reference gas injector box) has overall dimensions of:
Width 795mm
Depth 585mm
Height 535mm
The width without the reference gas injector box is 690mm.
There must be a 50mm diameter hole to allow the foreline to pass through or behind the bench.
The IsoPrime100 is supplied with 2m of flexible tubing to connect to the rotary pump, which is
placed on the floor beneath the instrument.
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Unit
Weight
IsoPrime100
82kg
Electromagnet
45Kg
Data system
55kg
Rotary pump
25kg
System
Circuit
Source
Max.
Current @
110V 60Hz
Max.
Current @
230V 50Hz
Max. Fuse
Rating
Approx.
Heat
Output
Transient
Sensitive
IsoPrime100
Mass
spectrometer
Mains
7.2 A
3.4 A
10 AT
600 W
Yes
IsoPrime100
Rotary pump
Mains
4.4 A
2.4 A
10 AT
300 W
No
Data system
Computer +
printer
Mains
N/A
3 A
10 AT
500 W
Yes
WEIGHT
The approximate weights of individual units of the instrument are shown below:
ELECTRICAL REQUIREMENTS
Electrical requirements for the IsoPrime100 peripherals must comply with the
specifications given in the appropriate peripheral manual.
Warning: Users should ensure that the provision of the Mains supplies
described in this document is in accordance with any local regulations.
The table below summarises the electrical characteristics for the IsoPrime100, pumping system
and data system.
Note: Each line in the table represents an individual Mains connection and uses an individual
Mains lead.
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Note: Mains supply voltage fluctuations should not exceed ±10% of the nominal voltage.
IsoPrime User’s Guide
ENVIRONMENTAL REQUIREMENTS
ROOM TEMPERATURE
The maximum operational room temperature should not exceed 25 oC (ideally 22 oC). An airconditioned room will be required if the ambient room temperature exceeds 25 oC. Large
temperature fluctuations caused by sunlight or drafts (including air conditioning units) should be
avoided during measurement, and should not exceed 1 oC/hour.
Heat dissipation into the room can be calculated by adding the approximate heat outputs given
in the electrical requirements table above. The heat outputs of any additional peripherals
should also be included.
HUMIDITY
The relative humidity should not exceed 60 oC at any temperature.
DUST FREE ENVIRONMENT
High dust levels increase the probability of computer disk drive failures. Dust particles will also
block air filters and fans on the instrument that may cause overheating if not cleaned regularly.
ROTARY PUMP EXHAUST FUMES
The exhaust ports of the rotary pumps are fitted with oil mist filters, however you may wish to
connect to an exhaust line (15 mm internal diameter) leading out of the building.
Note: All gases entering the mass spectrometer are exhausted through the rotary pump. The
safe exhausting of these fumes should be given careful consideration when working with
hazardous materials such as SO2 or CO (carbon monoxide).
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MAGNETIC FIELDS
The instrument should be positioned away from strong external magnetic fields such as those
that may be generated by power or transmission lines, transformers or other scientific
equipment.
The instrument, when fitted with an electromagnet can generate sufficient external magnetic
field to interfere with the normal operation of the computer. The data systems should be
located at least 1.2 m away from the electromagnet. Pacemaker wearers should not approach
closer than 1 m when the magnet is switched on.
For multiple instrument installations fitted with electromagnets the magnets should be placed
at least 2 m apart from each other.
COMPRESSED AIR
The IsoPrime100 requires no compressed air but its reference gas box requires a regulated
compressed air supply of 60psi. If a compressed air line is not available, a compressor must be
supplied. Other instrument peripherals will require compressed air. Check the appropriate
manual for details.
A water and oil mist filter should be fitted to the supply line and contain at least a 0.5m
particulate filter. The addition of a 0.3 m mist filter is recommended for compressor
installations to minimise the amount of oil transferred from the compressor to the instrument.
The airline connections on the reference gas box and prep systems are 6 mm (OD) push fit.
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SYSTEM DESCRIPTION
INTRODUCTION
The IsoPrime100 is the base unit of a modular isotopic analysis system. A wide range of
accessories can be added to the instrument, which allows the system to be readily expanded to
meet the evolving requirements of the user.
All of the major components of the analyser are located on the bench top, where they are easily
accessible for maintenance. Sample preparation systems may be mounted on either side of the
instrument.
The IsoPrime100
The IsoPrime100 cubicle contains the following components:
Ion optics (analyser).
Inlet isolation valve.
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Electronics unit.
Head amplifier.
High vacuum pumping system.
Electrical wiring assembly.
ION OPTIC S
OVERVIEW
The ion optics (analyser) is contained within a rectangular vacuum chamber on top of the
instrument. This arrangement provides ready access to the source, collector and isolation valve.
The source and collectors may be removed as complete assemblies on their mounting flanges
for ease of maintenance.
The ion optics has a horizontal geometry. The source is mounted on the right-hand side of the
instrument (viewed from the front), whilst the collectors are mounted on the left-hand side.
The turbomolecular pump is situated directly below the source housing. The pump is situated
within a forced airflow environment that ensures that the pump is maintained at the correct
operating temperature for long and trouble free operation. This arrangement provides good
abundance sensitivity, low backgrounds and minimum inter-sample memory.
The instrument case is formed from folded steel to provide a rigid and stable base for the ion
optics.
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THE ION SOURCE
The IsoPrime100 ion source is a type of Electron Impact (EI) source. The source is a
small chamber in which gas molecules are ionised by collisions with electrons.
Ion Source Mounted on Source Flange
The electrons are emitted by thermal excitation from an incandescent wire filament, and then
accelerated through the source by a voltage between the filament and source of 50-100 eV. The
electrons are collimated by a narrow electron entrance slit opposite the filament, and then
follow a helical path through the source under the influence of a magnetic field. The magnetic
field is produced by two small permanent magnets (the source magnets). The field raises the
ionisation efficiency by increasing the probability of collisions between gas molecules and
electrons.
The majority of electrons are not involved in ionisation, and are collected at the trap,
giving rise to a trap current. The current through the trap is used in a feedback loop to
control the emission from the filament via the filament current. This is known as a
trap-regulated system, and provides a constant flow of electrons through the source.
The ion source is based on the proven ion optics design of the Optima and Prism Instruments.
The following design changes have been made for ease of maintenance and assembly:
The part count has been reduced by 20%.
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Filament replacement has been simplified.
The defining (source) slit may now be replaced without requiring the disassembly of the
source stack.
The stack ceramics are now shielded from ion burn to give them an extended lifetime.
The design of the source wraparound and filament shield has been simplified.
The source connections are now push-fit.
The inlet probe is now self-locating for a better gas-tight fit.
The source block is a machined component that forms the base and two sides of the source box.
Machined into the side of the source block is the gas inlet aperture, through which a ceramic
inlet probe admits gas to the source.
A wraparound is added to the source block to form the source box. The wraparound is
a photo-etched sheet that forms the top, front and bottom surfaces of the source box. It
contains the electron entrance hole on the filament side of the source (top) and exit hole on the
trap side (bottom). The ion exit slit is positioned on the front face of the source box.
The ion repeller is a flat electrode at the back of the source box, opposite the ion exit
slit. The repeller is used to adjust the region of ionisation with respect to the slit.
The half plates are two electrodes that form an electrostatic lens that provides a focusing effect
on the ions as they emerge from the ion exit slit. The half plates also provide steering of the ion
beam in the y-direction, by differential offset of the voltage references.
The defining (source) slit ensures that the ion beam is well defined as it leaves the
source. This slit is held at ground potential in order to collect any scattered ions.
The Z plates are two electrodes that provide beam steering in the z-plane.
Finally, the alpha plate defines the maximum beam width prior to entry into the flight
tube.
The source voltages and currents used are variable and depend on the gas species being
analysed. The voltages and currents are supplied from the electronics units and controlled by
the computer.
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The electrical connections to the source are made via a number of feed-through connectors
located in the source-mounting flange, shown below.
GAS INLET PROBE
The gas inlet probe, shown below, is composed of three components, and is supported by the
inlet probe feed-through that is welded into the source flange.
Source Feed-through Connectors
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Gas Inlet Probe
The stainless steel inlet tube holder slides within the inlet probe feed-through and is forced
towards the source by a compression spring. The end of the inlet tube holder is tapered
internally to accept one end of the inlet tube.
The inlet tube is manufactured from ceramic and is tapered on both ends. One end fits within
the tapered end of the inlet tube holder whilst the other end is pressed by the compression
spring into the gas entry aperture of the ion box.
The tapers on both the ion box and the inlet tube holder are designed so that a line seal is
formed between the ceramic inlet tube and the other tapers. This design means that the inlet
probe is a self-aligning and also ensures that the seal is gas tight.
ANALYS ER MAGNET
ELECTROMAGNET
The electromagnet has been designed to operate with a current of 1-5 A. The jaws of the
electromagnet provide full coverage of the ion path when working with widely separated
masses, for example masses 2 and 3. The magnet also provides a wide focal plane, allowing the
use of a wide array of collectors.
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IsoPrime100 Electromagnet
The magnet power supply is mounted underneath the electromagnet and is controlled via
electronics built into the system controller. The magnet current is fully adjustable from the
computer over the range 0-5 A with 16-bit resolution. This provides the IsoPrime100 with a mass
range of 0 to ~100 AMU.
The magnet is mounted on a carriage, which is shown below:
Magnet Carriage
The carriage has a location plate with three ball bearing castors fitted through it.
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Mounted on the thread protruding behind one of the castors is a brass nut that engages in the
base of the magnet.
The magnet sits on three brass nuts and the whole carriage is free to roll about the support plate.
The magnet is clamped into position using a bolt from beneath the support plate. The bolt may be
engaged in two positions, away from the analyser housing (for magnet removal/replacement) or
towards the analyser housing (the operating position). The hole in the forward position allows the
magnet to be moved over the normal adjustment range without removal of the bolt.
When the magnet is in the correct position it should be clamped securely by tightening the bolt.
The height, pitch, and yaw of the magnet can be adjusted using the three brass nuts.
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ANALYS ER HOUSING
The analyser housing is manufactured from stainless steel. The grade of steel used ensures that
the remnant magnetic fields within the analyser are low.
The housing is rectangular in section with two end flanges sealed with Viton. The end flanges
carry the source and collectors. The flight tube is constructed from stainless steel plate, and is
integrated into a cut out in the side of the housing.
Baffles are fixed within the analyser to restrict unwanted ions from reaching the collectors. The
baffles are readily removable for cleaning during normal maintenance.
The design of the integrated flight tube in the housing provides an unobstructed focal plane that
allows a number of masses to be measured simultaneously.
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COLLECTORS
TRIPLE COLLECTOR
The IsoPrime100 universal collector system is shown below. The universal collector comprises
three Faraday cups, each with a different width of resolving slit. This system accommodates the
variations in the ion beam separations of different gases, such as CO2 and N2, without the need
for moveable collector assemblies. In the case of hydrogen an extra collector is added to the
assembly.
Universal Triple Collector
The narrowest slit accepts the ion beam from the minor 1 isotope (beam 2) and is referred to as
the axial collector. This slit provides the maximum resolving power of the system. The slit is
wider than the width of the ion beam and therefore the scanned peak is flat topped, which
limits errors in ratio measurement caused by small drifts in ion beam position.
The larger outer collectors have slits that are approximately three times wider than the slit in
front of the axial cup. These wider slits accept ion beams from the major and minor 2 isotopes
(beams 1 and 3, respectively).
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An electron suppressor plate is fitted to each collector between the resolving slit and the
Faraday cup. The suppressor is maintained at approximately -38 V and rejects any secondary
electrons generated by ion bombardments inside the Faraday cup. A BNC connector on the
flange provides the suppressor voltage.
The three collectors are attached to a mounting plate, which is in turn fixed to the
collector flange. The mounting plate extends along the focal plane of the analyser,
which is an extension of the plane that passes from the source slit through the centre of the
magnet radius. This geometry allows collectors to be mounted at any point along the plane.
The diagram below illustrates which isotope species is collected in each Faraday bucket for each
of the main gases analysed:
Diagram showing the layout of the Universal Collector and the Collection of Coincident
Isotopic Species
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The signal leads from the collectors are double screened to avoid any pickup from unwanted
ions. The leads connect to the ten-pin collector feed-through which is located inside the feedthrough shroud. The locations of the feed-throughs for the Major, Minor 1, Minor 2 and Mass 2
collectors are shown below:
To measure hydrogen in dual inlet mode, the hydrogen collector option is required. This
includes an additional Faraday cup that is positioned on the edge of the mounting plate, closest
to the magnet. This cup is used to collect the mass 2 beam, whilst the mass 3 beam is collected
in the minor 2 Faraday.
ESF COLLECTOR
In order to measure precise HD/H2 (D/H) ratios by continuous flow, the hydrogen ESF
(Electrostatic Filter) option collector is required. The mass 2 ions are collected in the cup as
shown below. The HD ions pass through a small ESF and into the repositioned minor 2 collector.
The ESF is an energy filter that reduces the low energy He+ peak tail that would normally be
superimposed on the HD+ signal during continuous flow analysis. The
peak tail represents helium ions that have lost energy during collision with gas
molecules in the flight tube. The result of the energy loss is that the flight path of the ions is
altered, and the ions arrive at the collector at a lower mass position
than would normally be the case. The ESF is set up to reject any ions that have lost any of their
original source energy.
View of Collector feed through from Inside of the Housing
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MINOR2
BUCKET
MINOR 1
BUCKET
H2 BUCKET
MAJOR BUCKET
ESF
The layout of the ESF collector is shown below:
The diagram below illustrates how helium ions that have lost energy pass through the mass 3
collector slit, but are then rejected by the ESF:
Rejection of Low Energy Helium Ions by the Electrostatic Filter
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A charcoal filter is positioned in the path of the helium mass 4 beam. This filter absorbs the ions,
so preventing unwanted scattering throughout the collector assembly.
The following photograph shows the ESF collector with the ten pin feed-through:
Plan View of the ESF Hydrogen Collector
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TH E VACUUM SYS TEM
OVERVIEW
The pumping system produces the high vacuum required for high precision stable isotope
analysis. It also provides the high pumping speeds essential for the high gas flow rates required
for continuous flow applications.
The layout of the pumping system is shown below. The pumping system incorporates an
Edwards RV3 rotary pump that provides the backing for an Edwards EXT255 or nEXT 240D
turbomolecular pump.
Schematic Diagram of the Pumping System
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The rotary pump is connected to the IsoPrime100 by a 2 m length of flexible hose, allowing the
pump to be conveniently positioned behind and below the instrument.
The backing line from the rotary pump is connected to a foreline trap filled with activated
alumina. An isolation valve allows the rotary pump to be isolated from the turbomolecular
pump, enabling the rotary pump to remain operational during the venting of the analyser. This
ensures that moisture from the air is not adsorbed onto the foreline trap, which would prolong
pump-down times.
The isolation valve and foreline trap are mounted on the rear of the IsoPrime100 for easy
access. The foreline trap is fitted with a vent valve, which enables the packing to be replaced
without needing to vent the analyser.
The rotary pump is fitted with an oil mist filter to prevent unwanted emission of pump oil
vapour into the laboratory atmosphere.
An automatic vent valve is fitted to the turbomolecular pump. This ensures that even under
conditions of power failure, the chances of rotary pump oil entering the analyser are minimised.
A filter is fitted to the vent valve to stop unwanted particles entering the vacuum system during
the venting process.
Fans fitted into the instrument housing cool the turbomolecular pump. Two
fans are mounted on the rear panel of the IsoPrime100. One of them is mounted directly
behind the analyser turbo pump and electronics case. This fan draws air into the case,
cooling the analyser turbo pump. The other fan, mounted at the other end of the electronics
case, extracts air from the case, creating a flow of air from right to left.
An EXC100L controller mounted on the left of the IsoPrime100 controls all the components of
the turbomolecular pump.
The source control electronics remain disabled until the turbo pump reaches full speed.
Please refer to the maintenance section and the manufacturer’s manual for service procedures for
all components of the pumping system.
Caution: routine pump maintenance is essential for the reliable
performance of the IsoPrime100. If the manufacturer’s recommended
service schedule is followed, the system will provide continuous troublefree operation.
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PRESSURE M EASUREMENT
PIRANI GAUGE
An AFG. S NW16 active Pirani gauge is used to measure the pressure in the analyser
pumping backing line. This gauge is located adjacent to the turbo pump roughing port
and continuously measures the vacuum whenever the electronics unit is powered.
PENNING GAUGE
A Penning or Active Inverted Magnetron AIM gauge is fitted to the ion optics housing to monitor
the pressure of the system. The gauge is mounted on a NW25 elbow beneath the collector end
of the housing. The software displays the measured pressure.
The Penning gauge is controlled and monitored from the electronics unit, which is located on
the right-hand side of the IsoPrime100 cubicle. The gauge is enabled as soon as the turbo pump
reaches ~95% speed.
The system protects the Penning gauge against over-pressure by monitoring the turbo pump
speed. If the turbo pump speed drops below 95%, the gauge is disabled.
Any condition that results in over-pressure will also cause the ion source power supply to be
switched off.
ELECTRONIC UNITS
Warning: the electronic units have the potential to cause serious injury. If
the instrument is used in a way not specified by the manufacturer, the
protection provided by the equipment may be impaired.
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Electromagnet
Amplifier
System Controller
LOCATIONS OF THE ELECTRONIC UNITS
The electronic units that are fitted in the IsoPrime100 include the following:
System Controller
Turbomolecular pump controller
Head Amplifier
Electromagnet supply
Bakeout Power supply
The minimum electronic configuration for an IsoPrime100 consists of the system controller, the
turbomolecular pump controller and the head amplifier. The other units may be present,
depending on the configuration of the instrument.
Head
TMP
Controller
Layout of Electronic Units (front view)
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Mains Inlet
Roughing Isolation Valve
Foreline Trap Vent Valve
Rating Plate
RS232 Connection
Layout of Electronic Units (rear view)
SYSTEM CONTROLLER
The system controller, which controls all the electronic systems of the instrument, is
located on the right hand side of the cubicle. The proximity of the high voltage
supplies to the source provides the greatest protection to the system against flashover.
The controller is based around a dedicated Motorola 68000 microprocessor.
The data system computer controls the instrument via a fibre optic link.
The system controller supports the following functions:
Active gauge interface for the Pirani and Penning gauges
Power supplies for instrument cooling
Valve control for continuous flow interfaces
Electromagnet control
Head amplifier power supply
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Three additional channels of data acquisition for FID (flame Ionisation Detector)
and two TCD (Thermal Conductivity Detector) signals.
TCD Power supply
GC and EA start/stop signals.
Turbomolecular pump controller logic
Bakeout control.
Control of all the source electronics and high voltage supplies
The system controller can be easily removed, allowing it to be replaced on site.
SOURCE HIGH VOLTAGE SUPPLIES
Warning: the voltages and currents generated by these units may cause
serious injury.
Three supplies located within and controlled by the system controller produce high voltage that
drives the ion source. The three supplies provide voltage for the accelerating potential, focusing
and half plate steering.
The high voltage supplies are referenced to the ground potential of the instrument. The system
controller also produces the Z steering voltage.
The source control unit is built into the system controller and generates other current and
voltage supplies required for the operation of the ion source. The whole of the
source control is floated at accelerating potential and superimposes its supplies upon this
voltage.
Source voltages and currents generated by the source control unit are:
Filament Current
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Trap Current
Electron Voltage
Ion Repeller Voltage
All the source voltages and currents are provided by cables that are connected to the top of the
system controller. The source connections and cables are protected by a cover fitted over the
end of the analyser housing.
All source potentials are monitored by the system controller and can be displayed on the data
system computer.
TURBOMOLECULAR PUMP CONTROLLER
The turbo pump controller (Edwards EXC100L) is situated on the left hand side of the
instrument. The unit is connected to the system controller for speed readout and on/off
control. For more information about the controller, refer to the manufacturer’s manual.
HEAD AMPLIFIER
The ten channel amplifier is housed in a rugged aluminium casting. Electrical connection to the
collectors is by a ten-pin gold feed-through. The connectors in the amplifier are spring-loaded to
ensure good contact.
The amplifier contains up to ten low temperature coefficient resistors. The standard configuration
used with an ESF collector contains 4 amplifiers with the following resistances:
Warning: Before removing Head Amp cover, disconnect 9-pin
power/communication cable, as removing/installing DAQ boards
whilst powered on may result in Head Amp damage.
Minor 1: 1 x 1011 ohms
Minor 2: 1 x 1011 ohms
Major: 1 x 109 ohms
Mass 2 : 1 x 109 ohms
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As the maximum output voltage of each amplifier is 100 V, the maximum current in each
channel is as shown:
Minor 1: 1E-9 A
Minor 2: 1E-9 A
Major: 1E-7 A
Mass 2: 1E-7 A
The amplifier digitises the amplified signal prior to transmission.
Caution: the amplifier contains components that are very sensitive to
static and should be handled carefully. Before removing the amplifier,
turn off the source to prevent voltage build-up on the feed-through pins.
Before fitting the amplifier back on, short the ten feed-through pins to the
collector housing. Only when the amplifier has been refitted and
connected is it safe to switch the source back on.
ELECTROMAGNET SUPPLY
The electromagnet power supply is located directly underneath the electromagnet and is
mounted within the electromagnet support. The unit is powered from the mains circuit. It
contains a raw DC supply and a programmable DC-DC converter under the control of the system
controller.
MAINS DISTRIBUTION
Caution: never touch or attempt to clean any of the components inside the
amplifier, as this will result in contamination. Such contamination may
produce small tracking currents that could have a serious affect on
performance.
The power supply for the IsoPrime100 is provided by a single IEC connector located at the rear
of the instrument on the left hand side. This power input is connected to an IEC distribution
block mounted on the rear panel. Connection leads from this block provide power to the various
electronic units fitted to the instrument.
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A double fused IEC inlet connector protects the mains circuit. Fuse ratings and type are clearly
indicated on the ratings plate of the instrument. See the Maintenance chapter for details of all
fuses in the system.
Caution: under no circumstances should electronic units other than those
fitted within the IsoPrime100 cubicle be connected to the distribution block.
Failure to observe this precaution may result in overloading of the mains
supply system.
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OVERVIEW OF IONVANTAGE
DETERMINING VERSION AND CHANGE NOTE INFORMATION
To determine which version of IonVantage is presently installed, select Help from the menu bar
of any IonVantage application, and select About xxxx...(where xxxx may be Sample list,
InletEditor, Tune page or ScriptEditor).
A dialog similar to the one shown below will be displayed:
The screen shows the current release and build date of IonVantage. Each release of IonVantage
may have several versions, as the software is modified if bugs are found after the release.
The window marked Software Change Notes, Patches, Hotfixes installed displays the
identity of any change notes that are presently installed on the system. The arrow buttons may
be used to scroll through the list of change notes installed.
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Page
Window
STARTI NG IONVA NTAGE
To start IonVantage, either double click the icon on the desktop, or choose Start,
Programs, IonVantage, IonVantage.
The IonVantage splash screen will appear and IonVantage will be loaded. The configuration will
be the same as the last one used.
Once IonVantage has been loaded, the following windows will be displayed:
IonVantage
Sample
Message
Tune
Page
Inlet
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CLOSING DOWN IONVANTAGE
To stop IonVantage, Press the button in the top right corner of the sample list, or select File,
Exit. The sample list and other windows will then be closed.
Occasionally the following dialog box will be displayed:
Whenever this dialog appears, press the No button.
Caution: Do not select Yes in the dialog box shown above unless you are
certain that you wish to change the inlet file.
CLOSING IONVANTAGE AFTER A CRASH
In some circumstances IonVantage may not close correctly, or the software may crash and
produce error messages. To ensure that IonVantage is stopped correctly, the task manager
should be used to close down IonVantage, as follows:
Start the Task Manager.
To launch the task manager, either:
Right-click on the blue part of the task bar at the bottom of the screen, ensuring that the cursor
is not positioned over one of the application buttons. Select Task Manager from the menu:
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Component
Task Name
Alternate Task Name
Sample List
IonVantageUI.exe
-
Inlet Editor
InletEditor.exe
-
Inlet Kernel
InletKernel.exe
-
Tune Page
Stables.exe
-
Script Editor
ScriptEditor.exe
Script~1.exe
Excel
Excel.exe
-
ActiveRioServer
ActiveRioServer.exe
-
DP Launcher
IsoPrimeDP.exe
-
DI Integration
QCPlus.exe
-
DP Launcher
IsoPrimeCFDP.exe
-
Or:
Press Ctrl Alt Delete. The Windows Security window will appear.
Click on the button labelled Task Manager to launch the task manager.
Click on the Processes tab, which displays the details of the currently running
IonVantage processes. The full range of IonVantage processes (components) is
shown below:
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All of the IonVantage processes (with the exception of ActiveRIOServer) must
be stopped to allow IonVantage to be restarted correctly. To stop a process, select
the process name and then press the End Process button in the bottom right
hand corner. Alternatively, right click on the process name and select End
Process from the resulting menu.
Isoprime User’s Guide
The following warning dialog will appear:
Press YES to end the task.
There may be more than one instance of Excel shown in the task manager.
Ensure that any presently running copies of Excel are closed and then stop each of the copies of
Excel that is shown in the task manager.
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Sample List Toolbar
Instrument Bar
Main Toolbar
Menu
STRUCTURE OF IONVANTAGE
IonVantage is a modular system that uses a number of different components to provide the
functionality required for the IsoPrime100. Each component handles a different aspect of the
operations required, as described below.
THE SAMPLE LIST
The sample list application is the heart of IonVantage, and is opened whenever IonVantage is
started. The sample list page is shown below:
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THE TUNE PAGE
The tune page application is used to operate the mass spectrometer and provides control over
functions such as pumping, source tuning, run scans and data acquisition.
THE INLET EDITOR
The inlet editor displays information on a number of different pages. The Status page is
displayed at start up:
IonVantage Tune page
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The status page gives an overview of the current condition of the inlet. The LEDs in the
Indicators panel indicate whether or not the inlet is presently in operation, and give the status
of the autosampler. If a GC is configured then the status page displays information relating to
the GC. The other pages of the inlet editor are accessed from the View menu or via the toolbar
buttons.
The inlet editor is described in more detail in the IonVantage User’s Guide for each preparation
system.
THE SCRIPT MESSAGE WINDOW
The script message window serves as a central location for the logging of messages in
IonVantage. The information that appears in this window describes the operations being
performed by the tune page, inlets and data processing.
The message window is shown below:
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In the example above, the messages are the result of a successful start-up of the software with
an Elemental Analyser (EA) configured.
To close the message window, press the button.
To restore the message window, follow these steps:
Right-click on the ScriptEditor button in the task bar at the bottom of the
screen.
Select Restore from the displayed menu.
The script editor will appear. To open the script message window, select View,
Messages from the script editor menu bar.
Minimise the script editor again using the minimise button.
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FILE LOCATIONS
IonVantage comprises numerous files stored in two major locations on the hard disk.
The IonVantage folder contains the program and support files, and the IonVantage
Projects folder contains the default project information for the supported inlets.
THE IONVANTAGE FOLDER
The IonVantage folder structure is shown below:
Custom. This folder contains all the custom inlets and their support scripting
files.
Default.pro. This folder contains the IonVantage default project (see below for a
detailed description of IonVantage projects).
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Plates and Racks. These folders contain definitions of the plates and beds
used by auto samplers.
RIOINI. This folder contains hardware configuration information which defines
how the instrument is controlled.
The SIRMS folder contains data processing files and the reference library
IONVANTAGE PROJEC TS
INTRODUCTION
IonVantage projects are used to organise the data acquired by the IsoPrime100. A project
contains all the information involved in the analysis of a sample. This includes the
files that control the inlet, the autosampler, the source tuning and the acquisition,
together with the sample lists, sample data and any subsequent batch analysis results.
An IonVantage project is identified by the extension .PRO appended to the end of the project
name, such as Default.PRO.
By default, all projects are stored in the C:\IonVantage Projects folder, separate from the main
IonVantage program folder. This arrangement means that archived data files are not affected by
any subsequent software re-installation or update.
The name of the current project is shown in the title bar of the sample list, after the
word IonVantage. The project name is followed by the name of the sample list file, for example:
In this example the project is called Test 1
A number of default projects are provided with IonVantage. These can be used as templates
from which the user can set up working projects. A default project is supplied with each of the
IsoPrime100 preparation systems, for example Default DI test.PRO is supplied for the testing
of the dual inlet, and Default GC.PRO is supplied for GC analysis. Each default project
includes all the files necessary for the operation of the related preparation system.
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It is not possible to acquire data into the default projects. The default projects are used as
templates to create new projects and analysis cannot be performed until the project/sample list
has been renamed.
Caution: do not store data files in the default project folders. If
IonVantage ever needs to be re-installed, the data files will be
replaced and the data will be lost.
Users may create their own template projects by setting up a new project based upon the
appropriate default project and then modifying the files as required. New projects may then be
created and based upon the new template.
CREATING A NEW PROJECT
Carry out the following steps to set up a new project:
Select Project Wizard from the Projects menu of the sample list. This will bring up
the following menu:
Enter a name for the project, a description of the project and a location for the
folder. Although projects may be set up in any location, users are advised to
save them to a local hard disk. Saving a project to a networked drive or
removable media may compromise operation because of the slower access time.
Press the Next button. The following window is displayed:
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Users may either create a completely new project that is not based on a
template, or a new project that is based on a pre-existing project.
Selecting Create using current project as template copies all the tuning
files, sample list files and method files from the current project to the new
project. However, any data present in the current project are not copied.
Selecting Create using existing project as template enables the user to choose any
existing project as the template via the browse button. Pressing the browse button results in the
display of the Select existing project dialog, which is used to select the required project
template:
When IonVantage is started for the first time, the only projects available are the default projects
listed below:
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Once a template project has been selected, press the Finish button. The new project
will be created and will then become the current project.
SWITCHING BETWEEN PROJECTS
Users may switch between projects without re-starting IonVantage, as follows:
Select Projects, Open Project from the sample list menu. This displays the following
dialog box:
Select a project from the list and press the OK button. The selected project is now the
current project.
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PROJECT FILE STRUCTURE
Project folders are all stored in IonVantage Projects, as shown below:
A project folder contains all the information for that project. The structure of a typical project is
shown below:
The Project information is divided between subfolders as follows:
Acqudb. This folder contains all the methods, scans, tune files, maps and
configuration files that define how the data are to be acquired.
BatchDB. This folder contains the batch reports that are generated in the
project.
CurveDB. This folder is not used.
Data. This folder contains the acquired sample data. Raw sample data are stored
in a number of files within a subfolder with the extension RAW. The data
processing results are also stored in this folder. In the example above, the
subfolder is called sample 1.RAW. Sample 1 is the name defined in the
File Name field of the sample list.
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MethDB. This folder contains integration parameter files which are used in the
integration of sample data.
PeakDB. This folder only contains files if the project contains DI data. The
folder stores the peak database files used by the data processing in the
calculation of the sample results.
SampleDB. This folder contains the sample list files that have been created in
the current project.
SCOPE OF PROJECT FIL ES
During operation, IonVantage uses the files in only one project. Whenever the File, Open
command is used, the dialog will automatically open in the appropriate folder within the
project. Similarly, whenever the File, Save command is used, the changes only have an effect
within the current project.
If a different project is opened, a new set of files becomes active. Any changes that were made
in the old project will no longer be visible.
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TH E SAMPLE LIST
The sample list is the main IonVantage window, and is used to set up and carry out data
acquisition and processing.
Template sample list files are provided with each inlet. The template files may be renamed and
altered as required.
RUNNING SAMPLES FROM THE SAMPLE LIST
A single sample is defined by an individual row in the sample list. To run samples from the
sample list, carry out the following steps:
Select the samples to be run. To select one sample, press the numbered button
on the left hand side of the appropriate row, which becomes highlighted. To
select more than one sample, click and drag the mouse down the column until all
of the required samples are highlighted, as shown below:
To select all of the samples in the list, click on the unlabelled cell in the top left hand corner,
directly above row number 1. The whole sample list will also run if no rows are highlighted.
Press the start run button or select Run, Start from the sample list menu.
The Start Sample List Run dialog is displayed:
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The numbers of the samples to be analysed are displayed in the From Sample and To
Sample fields. Check that the correct samples are selected.
Check Acquire Sample Data or Auto Process Samples as required. Note
that Auto Quantify samples is not currently active.
If the acquire sample data option is checked, the inlet file and the MS (method) file defined in
the sample list are both run, allowing data to be acquired.
If the auto process samples option is checked, the data are processed using the file that is
defined in the Process field of the sample list.
Both options may be selected independently. This allows data to be reprocessed after a run, for
example after changes have been made to some of the data
processing parameters.
Press the OK button to start the sample run
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SAMPLE LIS T FIELDS
Data acquisition and processing on the IsoPrime100 is controlled by the fields (columns) that are
set up in the sample list. The fields required by a particular user depend on the configuration of
the system and the present application.
The procedure used to modify the format of the sample list is described in Modifying the Sample
List Fields in Editing the Sample List, below:
All of the fields that are required or may be required are described below:
File Name. This defines the IonVantage data file, in which all the data relating to a
particular sample are stored. Raw data are sent to this file during the acquisition and
the file has the extension .raw. Each sample list entry must have a unique file name.
Caution: if a file name is re-used in the same project, the existing data
will be overwritten and lost.
MS File. This is the name of the method used to acquire the data. The MS file contains
information about the source tuning, any peak jumps required, the beams
acquired and the timing of any valve operations carried out during the analysis.
Inlet File. The inlet file is the name of the inlet method file. This file defines the operations
performed by the inlet that are used to introduce the sample into the mass spectrometer.
Bottle. The bottle field defines the location of each sample when an autosampler is being used.
When an autosampler is not present a value is still required.
Process. This field identifies the data processing file that is run once the sample
acquisition has finished. IsoPrimeDP should always be entered in this field.
Process Options. This field controls the actions performed by the data processing. Valid entries
are:
BatchStart- starts a new batch file using the file name as the name of the batch
PrintReport- prints an individual sample report at the end of data processing.
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BatchEnd- closes a batch report.
BatchEnd PrintReport- closes the batch and prints the batch report.
If the process options field is left empty, the sample data are processed but no report is printed.
The Weight, Injection Volume, Sample Type and Standard fields are only used for certain
preparation systems, and are described in the user guides for these preparation systems.
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EDITING THE SAMPLE LIST
SETTING UP THE TOTAL NUMBER OF ROWS
The number of rows in the sample list may be chosen by pressing the button. This
displays the Samples dialog box:
The number displayed in the text box is the current number of rows in the sample list.
To increase the size of the sample list, increase the number displayed in the text box
and then press OK. The new rows are added to the bottom of the list, and any
information present in the bottom row of the sample list is duplicated into all of the
new rows.
Note that if the number entered is smaller than the present number of rows, the excess
rows are deleted from the end of the list and any information present in these rows is
lost.
ADDING SAMPLES
Add new rows to the bottom of the sample list as follows:
Either press the add sample toolbar button or right-click and choose Add from
the drop down menu. The cursor may be positioned anywhere in the sample list. The
Samples dialog appears, as shown above.
Enter the number of new rows required and click OK.
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The new samples are added to the end of the sample list. Any information in the last row
of the sample list is duplicated into the new rows. The sample name and bottle number
fields are automatically incremented.
INSERTING SAMPLES
Insert new sample rows into the sample list as follows:
Move the cursor to the row directly below the position in the sample list where
the new row is required. Only one cell in the row needs to be selected.
To insert the new row, either press the insert sample toolbar button or press the
Insert keyboard key, or right-click in the sample list and choose Insert from the drop
down menu.
A new row is added above the currently selected row. Any information in the row above the
current row is duplicated and the sample name and bottle number fields are automatically
incremented. The cursor is moved to the new row.
If multiple rows are selected, selecting Insert will result in the addition of the same number of
new rows as the number of presently selected rows, and any information in the selected rows
will be duplicated.
DELETING SAMPLES
Delete single or multiple sample rows as follows:
Click on the numbered cell(s) on the left hand edge of the sample list to select
the row(s) to be deleted.
Either press the delete sample button or right-click in the sample list and choose
Delete from the drop down menu.
Note that it is not possible to delete all of the rows in the sample list. If all the rows are
highlighted and the delete sample button is then pressed, the sample rows are only cleared, not
deleted.
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FILL DOWN
The fill down operation facilitates the entry of sample information into the sample list. The
process duplicates the information in a selected cell into lower cells in the same column. Several
columns may be filled down at the same time. Any information previously present in the cells to
be filled is replaced by the new information. If the copied cell is empty, the cells being filled will
be empty, and any pre-existing information will be cleared.
To use the fill down operation:
Click on the sample cell or cells to be copied, and drag downwards to highlight
the region to be filled. At least two samples must be selected, but any number of
columns or rows may be filled.
Either press the
button or right-click in the sample list and choose Fill Down
from the drop down menu.
FILL SERIES
The fill series function is also used to speed up the entry of sample information into the sample
list. This process sequentially increments any numerical information in the selected column(s). If
there is more than one number in a cell then only the last
number is incremented. The command may only be used to format the File Name, Bottle and
Sample ID columns.
To use the fill series operation:
When there is more than one number in the cell(s) being copied, only the last number is
sequentially incremented.
Click on the sample cell or cells to be copied, and drag downwards to highlight
the region to be filled. At least two samples must be selected, but any number of
columns or rows may be filled.
Press the button or right-click in the sample list and choose Fill Series from the
drop down menu.
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EDITING INFORMATION IN CELLS
The information in any cell in the sample list may be directly modified by single clicking on the
cell and then overwriting, or double clicking and then editing the text.
In the MS File, Inlet File, Process and Process Options columns, cells may be edited by double
clicking and selecting a new file name from the drop down box.
Users may cut or copy the information in cells and then paste the information into new cells, as
follows:
Highlight the cell(s) to be copied.
Either choose Edit and select Cut or Copy, as required, or right-click in the sample list
and select Cut or Copy from the drop down menu.
Highlight the cell(s) into which the new information is to be pasted.
Either choose Edit and select Paste, or right click in the sample list and select Paste
from the drop down menu. The paste operation may be repeated as often as necessary.
Caution: note that the paste area must be the same size as the cut and copy
area.
CLEARING SELECTED CELLS
The information in any cells in the sample list may be deleted as follows:
Highlight the cells to be cleared. Complete rows may be selected by pressing the
numbered cells on the left hand side of the sample list, and complete columns may be
selected by clicking the relevant column title cells.
Either choose Edit, Delete, or press the Delete keyboard button, or right-click and
choose Delete Contents from the drop down menu.
All the information in the sample list may be cleared by selecting Edit, Select All and
then pressing the Delete keyboard button.
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EDITING THE SAMPLE LIST VIA AN AUTOSAMPLER PLATE LAYOUT
When a Gilson autosampler is configured in the system, the plate layout pane shown below may
be used to facilitate the editing of the sample list:
Display the plate layout as follows:
Position the cursor over the thick vertical bar on the right hand margin of the
IonVantage page. The cursor will change to a double-headed horizontal arrow.
Click and drag the bar to the left
Clicking on the button will show or hide the map.
The top of the pane shows the location of the plates on the autosampler bed. Plates may be
selected by clicking on them.
The lower portion of the pane shows the selected plate. The title shows the number of the plate
on the bed. Below the plate title is a plan of the plate that shows the positions and numbers of
individual samples.
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SELECTING SAMPLES
To select samples, click on the plate containing the samples of interest in the bed layout. The
plate number will change to the appropriate value.
Select the samples to be run by using one of the following methods:
Click on the individual sample locations on the plate plan. The sample positions
will turn green when selected. To de-select a sample, click on the sample
position again.
Click and drag a box around the samples of interest. All the samples contained
within the box will be selected. To de-select the samples, draw another box
around them.
Click on the select all button , or select none button .
INSERTING SAMPLES
Insert new samples (rows) into the sample list as follows:
Select the samples in the plate layout pane (see above).
The insert button will insert the samples below the highlighted area. Select the row in
the sample list above where the new samples are to be inserted.
Press the insert samples button .
The samples are inserted into the sample list above the selected row. Any information already
present in the row above the selected row is duplicated into the new rows. The names and
bottle numbers of the new samples are automatically incremented.
ADDING SAMPLES
Add new samples to the sample list as follows:
Select the samples in the plate layout pane.
Press the add samples button .
The samples are added to the end of the sample list. Any information in the bottom row of the
list is duplicated into the new rows. The names and bottle numbers of the new samples are
automatically incremented.
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REPLACING SAMPLES
Replace the bottle numbers of samples in the sample list as follows:
Select the samples that are to be added to the list by selecting them in the plate
layout pane. The number of samples selected must be the same as the number of
samples to be replaced.
In the sample list, select the rows containing the samples to be replaced.
Press the replace samples button .
Only the bottle numbers are replaced for each sample. All other information present in the
sample list remains the same.
EDITING COLUMNS
To change the width of a column, position the cursor on the line between the two column
headings, until a double-headed arrow appears. Click and drag the border until the column is the
required width.
To change a column title, or to modify the alignment of the column text, proceed as follows:
Highlight the column.
Either press the format toolbar button , or Right mouse click on the column and
select properties.
Both Commands display the Field Properties dialog box:
Make the necessary adjustments and press the OK button.
The alignment of column text may also be adjusted as follows:
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Highlight the column(s).
Either press the toolbar buttons to left-align, centre-align or right-
align the text, respectively, or select Samples, Field, Align and choose Left, Centre
or Right.
Note that column title text is always centre aligned.
MODIFYING THE SAMPLE LIST FIELDS
The range of columns displayed in the sample list may be modified using the
Customise Field Display dialog box. This dialog may be used to change both the type of the
columns that are present and the order in which they appear.
Either press the
toolbar button , or right-click and choose Customise Display.
These commands all result in the display of the following dialog box:
To include or exclude a column in the sample list, check or un-check the box on
the left hand side.
To change the order of the columns, highlight the field to be moved, and press the move
up or move down button until the field is in the required position.
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Checked fields that appear higher up the list are positioned further to the left in the sample list
than fields lower down. Fields in the list that are not checked do not appear in the sample list
and can be ignored.
To delete a column in the sample list:
Highlight the column, either by pressing on the title cell of the column or by
selecting all the cells in the column.
Either press the
button, or choose Samples, Field, Remove Column, or right
click on the highlighted column and select Remove Column from the drop down
menu.
USING SAMPLE LIST FORMAT FILES
The sample list format file defines the range of columns that is displayed in the sample list. After
modifying a sample list using the customise field display dialog, the format may be saved and
used again at a later time. To save a particular format, click and enter a name for the file.
Four default format files are included with IonVantage. The IsoPrime100 sample list
format contains the following columns:
The EA sample list format contains additional columns for the entry of the sample weight
and the definition of blanks and standards for batch calculations.
The GC sample list format contains a column for the entry of the sample volume to be
injected by the autosampler.
To change the format of a sample list, proceed as follows:
Press the Load Format Button . The following dialog is displayed.
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Select the required format from the list available and then press OK.
Sample list format files have the extension *.fmt and are stored in IonVantage, separately from
the sample list files. As a result, opening a new sample list file has no affect on the currently
loaded format. The appropriate sample list format should be loaded independently of the sample
list.
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Title Bar
Menu Bar
Display Map
TH E TU NE P AGE
The tune page is the application that provides control over the mass spectrometer.
The main screen of the tune page is shown below:
Tool Bar
Acquisition Map
Status Bar
The upper part of the tune page window displays ion beam parameters associated with the
acquisition, and the lower part of the window displays parameters associated with the status of
the instrument. The two halves of the window are labelled with the name of the currently
loaded acquisition map or display map.
The display of the tune page dialogs may be given priority over other dialogs by
choosing View, Stay On Top. If this parameter is set, the tune page dialogs will
always be visible, even if the user selects a different and overlapping window.
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PUMPING CONTROL
PUMPING DOWN
The pumping is controlled via the Instrument menu. A tick next to Pumping indicates that
the pumps are on:
To pump down the IsoPrime100, choose Instrument, Pumping. The vent valve will close and
the turbo pump will be started. As soon as the turbo pump is started, the Speedivalve on the
backing line should be opened (located on the rear of the instrument). The speed of the turbo
may be monitored in the turbo speed bar graph in the Display panel.
VENTING
Vent the IsoPrime100 as follows:
Close the Speedivalve at the back of the instrument to isolate the backing line.
Choose Instrument and de-select (un-check) Pumping. The following
warning message is displayed:
Press the OK button. The turbo pump is switched off.
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If a dual inlet is fitted, the dual inlet must be vented independently. See Dual Inlet manual for
instruction.
It is recommended that the source be switched off before venting. If the pump is turned off
while the source is on, the source will automatically be turned off but the filament may be
damaged.
The turbo will slow down until the pump speed is 50%. At this point the vent valve will be
automatically opened and the turbo will slow rapidly as the pressure in the analyser rises.
The Penning gauge pressure is displayed in the IP High Vac panel when the pumping
is switched on and the turbo is at full speed. At other times, the message Gauge Off
is displayed.
The Pirani gauge pressure is displayed in the IP Low Vac panel. This is
the pressure of the backing line between the Speedivalve and the turbo pump.
Edwards active gauges produce error codes in the event of a failure. Consult the manufacturer’s
manual for more information.
TU NING CONTROL
SOURCE CONTROL
The source is controlled via the Instrument menu. Check Source On to turn on the source.
When the source is switched off, the Source Status bar in the Display panel of the tune page is
coloured red, and the source off message is displayed. When the source is switched on, the bar
turns green and the source status changes to operational
.
In the image above, the source is clearly on (green bar) and the source status is Operational.
When turning the source on, it may take a short period of time for the source to become
operational. This is due to a slow rise in the filament emission to protect the filament. If the
source is not operational after a number of minutes there may be a problem.
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Source
Status
Condition
Further Information
0
Operational
Normal Operation
1
High Trap Voltage
Trap voltage > 23 V. Trap circuit malfunction.
2
Low Trap Voltage
Trap voltage 1-17 V. Excessive trap current or leakage, particularly in
combination with low filament current. Also trap circuit malfunction
3
No Trap Voltage
Trap voltage < 1 V. Trap to source short circuit or trap/filament circuit
malfunction
4
Emission Limit
Electron voltage> 6 V below requested value with > 5 mA of emission
current. Filament alignment or excessive trap current request
5
ADC Fault
Internal ADC voltage monitor test failure. Suspect voltage readings
of repeller, trap, electron voltages and power supplies, and current
readings of filament, trap, source and emission
6
Low Repeller
Repeller > 6 V below requested value. Repeller to source leakage or repeller
circuit malfunction.
7
High Repeller
Repeller > 6 V higher than requested value. Repeller to source leakage or
repeller circuit malfunction.
8
High Electron Voltage
Electron voltage > 6 V higher than the requested value. Electron energy
circuit malfunction.
Hovering the mouse pointer over the source status box will bring up a message describing the
current source status in more detail.
In the above example, the source message states that the source is operating normally.
The possible source states that may occur are explained in more detail below. This is also found
in the help file of the IsoPrime100 tune page.
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9
Electron Voltage Short Circuit
Electron energy voltage < 10 V with > 5mA of emission. Filament to source
leakage or short circuit (only occurs when the filament is hot).
10
No Electron Voltage
Electron voltage < 10 V with < 5mA of emission. Electron voltage circuit
malfunction.
11
Electron Voltage Low
Electron voltage > 6 V below requested value. Electron voltage circuit
malfunction
12
Trap Leakage
Trap voltage < 17 V with trap current of at least
50µA in apparent regulation. Trap to source leakage current. Confirm by
requesting zero trap current and
monitor trap current.
13
High Trap Current
Trap current > 100 µA higher than requested value. Trap to source leakage
current. Confirm by requesting zero trap current and monitor trap current.
14
Filament Open Circuit
Low trap current with 0.12-0.45 A filament current reading. Open circuit
filament.
15
No Filament Current
Incorrect trap current with < 0.12 A filament current. Filament circuit
malfunction.
16
Low Filament Current
Low trap current with filament not in limit. Excessive resistance in filament
leads, poor filament or filament circuit malfunction.
17
Zero Trap Current
No trap current requested. Filament switches off.
18
Filament Limit
Low trap current with maximum filament current.
Poor or misaligned filament, open circuit trap lead,
electron voltage setting too low.
19
Low 22V
Supply voltage < 19 V. Power supply or circuit malfunction causing filament
circuit to switch off
20
High 22V
Supply voltage > 25 V. Circuit malfunction causing filament circuit to switch
off
255
Source Off
Source turned off
TUNE FILES
The current tune settings, source parameters and acquisition map may be saved in a tune file.
The name of the current file is displayed in the title bar. If changes have been made to the
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currently loaded file, an asterisk (*) follows the file name. The asterisk will disappear when the
changes are saved.
Tune files control the following:
The source settings to be used.
Collector information, such as the identity of the beams to be acquired.
The width of the centre scan, and the identity of the beam to be used as the
centre (axial) mass.
To load a tune file, either select File, Load Tuning or press the toolbar button. The file menu lists
the four most recently used tune files, which allows them to be easily loaded.
When the magnet current specified in the new tune file is different to the old setting, the
magnet is cycled. The new map file (if applicable) and the saved collector amp zeroes will also be
loaded.
Tune files have the prefix DI or CF, depending on whether they are dual inlet or continuous flow
tune files. The exceptions are argon and bakeout tune files that are present in every project.
Caution: do not move tuning files between projects because the wrong
acquisition map information will be carried across, which may result in
the acquisition of data that cannot be processed.
Tuning files have the extension .itf and are stored in the acqudb folder within each project. Each
file contains the following information:
Acquisition map.
Centre scan file.
Source tuning (slider settings).
Collector zeroes with time stamp.
SOURCE PARAMETERS
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To view the source tuning parameters dialog box, either press the source parameters toolbar
button or select View, Docking Windows, Source Parameters.
Note that no read-backs from the source electronics are displayed on the source parameters
page. If required, this information may be viewed in the diagnostics pages.
To change a source parameter, either drag the slider with the mouse or enter a new
value in the text box. Values may also be changed by pressing the PgUp and PgDn
keyboard keys (large step size), or pressing the cursor keys (smaller step size).
The magnet may be cycled at any time by pressing the Cycle Magnet button. This can be used to
remove hysteresis if the magnet current has been altered.
A magnet cycle involves the following steps:
The acceleration voltage is set to zero, to ensure that large beams do not affect
the collector stability.
The magnet current is set to maximum.
The magnet current is set to minimum.
The magnet current returns to the original setting.
The acceleration voltage is restored.
The magnetic field is allowed to settle between each of these steps.
To save the tuning parameters, either press the save button or choose File, Save Tuning.
If a tuning file has been modified but not saved, an asterisk (*) will be displayed in the title bar
next to the file name.
It is advised to save any modified source parameters before running samples. Most methods will
run using the current tuning parameters; however EA analysis using more than one gas species
will require saved tune files when changing between gases.
If the user attempts to open a new tune file before saving the changes to an existing file, a
message appears prompting the user to save the existing file.
TU NING THE MASS SPECTROMETER
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Source
Parameter
CO2 N2 CO
SO2 N2O
H
2
Accelerating
Voltage (V)
3500
3700
3700
2800
3500
4800
Extraction
Voltage
75 %
75 %
75 %
75 %
75 %
75 %
Half Plate
Differential (V)
Tuned for maximum sensitivity
Z Plate Voltage
(V)
Tuned for maximum sensitivity
Electron Volts
(eV)
70 to 100
95 to
100
95 to 100
95 to 100
95 to 100
95 to 100
Ion repeller
Voltage (V)
-2 to -10
-2 to -10
-2 to -10
-2 to -10
-2 to -10
+45
Trap Current*
(μA)
200-800
200-400
200-600
400-600
400
400-800
In this section, it is assumed throughout that the magnet position has been previously optimised
for best peak shape and beam coincidence.
COARSE TUNING THE ION SO URCE
Default source tunings similar to as shown below can be found in all instrument template
projects.
If for any reason a required tuning file for a specific gas is not available, the table below gives
recommended source tuning parameters for the various gas species:
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Magnet Current
(mA)
4000
3000
3000
4900
3500
900
* Trap Current settings are dependent on system requirements, for example dual inlet systems
often run with a higher trap current setting than continuous flow systems.
Starting from the values shown above, and using the gas species CO2 as an example, the
procedure for tuning the three ion beams for this gas, is described below:
Check that CO
there is a flow through the vent.
gas supply is connected to the Reference Gas module and a
2
Check that valve RG is open.
Check that the isolation valve is open.
Check that the ion source is ON.
From the IonVantage User Interface, select the Tune Page window.
Load the Tune Page file for CO2.
Open the Source parameters window, single click on the corresponding icon.
Open Source Tune Parameters
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Open the CO2 valve and setup an accelerating voltage scan as shown below:
Set the scan to run approximately 500V either side of the current tune file. Displaying the Major
and Minor1 ion, the scan should look as shown below:
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Using the Major channel as a guide the mass 44 beam is clearly visible at around 3900V. The 45
beam, being coincident with the mass 44 can be identified underneath the 44. Drag and drop
the Current slider bar somewhere over the centre of the 45 peak as shown above.
Run a peak centre (Acquire, Run Peak Centre):
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At the end of the scan, the Peak Centre Results window opens automatically. Accept the Peak
Centre, by clicking on the Accept Peak Centre button.
Save the new value for the Accelerating Voltage by clicking on the Save option of the Edit menu
from the Tune Page window.
By this stage, each of the three ion beams from the three isotopes of CO2 is focussed into each
of the three collectors. There remains to perform a fine tuning for the other parameters.
It is important to note three features from the Scan window, shown above:
(i) The Peak shape for mass 45 in the central collector is symmetrical, with
steeply rising sides.
(ii) It has a flat top with at least 10 Volts of flat.
(iii) The flat tops for the three ion beams coincide over a range of several Volts.
The focus result on the peak centre is a good indication of acceptable peak shape. A value above
0.550 would be considered to be acceptable. If this cannot be achieved it is an indication that
the ion beams are not focussing correctly into the collectors and the mass spectrometer
requires attention. It is an indication that the source may be badly tuned, dirty, or that the
magnet is not in the correct position.
FINE TUNING OF SOURCE PARAMETERS
NOTES ON TUNING
Instrument linearity and peak shape are directly affected by instrument tuning. Increasing the
source sensitivity may cause the instrument peak shape to degrade; there may also be an
adverse effect on instrument linearity. In this respect a compromise is normally reached where
peak shape, linearity and sensitivity are all acceptable.
As all instruments behave slightly differently it is worth becoming familiar with the source scans
of each individual instrument. A significant change in a source scan may be an early indication of
a problem with the instrument. Fine tuning of the source parameters is necessary in order to
obtain a linear source response with the maximum sensitivity.
The recommended source parameters given in the table in the section entitled Coarse tuning
the Ion Source gives ranges for parameters where it is most likely to obtain linearity; the
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Half
Plates
Ion
Repeller
Electron
Volts
Z Plates
Extraction
Voltage
undefined parameters and those assigned with a value of 0 are then tuned for maximum
sensitivity.
OPTIMISATION BY SCANNING SOURCE PARAMETERS
It is advisable to set the trap current (TR) to a required value (depending on required sensitivity)
before modifying other source parameters.
Run an Extraction Voltage scan (Acquire, Run Scan, EX Scan). Using the display window, drag the
current bar to optimise. Ensure that the EX% is not higher than the maximum. Never run with
the EX% over the top of the peak.
Run a scan for the half plates (HP Scan). Optimize this setting.
Optimise the ion beams for the Ion Repeller (IR), but stay within the recommended range.
Optimise the ion beams for the Electron Volts (EV), but stay within the recommended range.
Optimise the ion beams for the Z Plates (ZV).
Repeat the sequence above until the ion beam currents change only by small amounts.
Save the optimised Source parameters.
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It is now advisable to recheck the instrument peak shape and, if acceptable, check instrument
stability and linearity.
INSTRUMENT LINEARITY
Instrument linearity is most affected by the relationship of the Extraction % (EX) and the Ion
Repeller (IR). If instrument linearity cannot be achieved it can be useful to change one of these
parameters to a new “fixed” setting and retune the instrument source around this.
For example:
IR “fixed” at -7 V
EX set at 75%
Run Linearity.
Linearity is outside specification.
Retune, reduce EX to 74%.
Optimise HP, EV, ZV
Run Linearity.
Linearity is better but still out of specification.
Retune, reduce EX to 72%.
Optimise HP, EV, ZV
Run Linearity
Linearity is now acceptable.
If, having reduced the EX to outside suggested levels, linearity cannot be achieved. The above
can be repeated after changing the IR to a different “fixed” setting and ensuring all other
parameters are maximised.
If tuning for maximum sensitivity it is advisable to start tuning from tuning parameters already
proven to be linear; change one source parameter at a time and recheck linearity. With this
approach it is easy to identify which source parameter is causing the instrument to be non
linear.
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Note that no optimisation was attempted using the Trap Current. Increasing the trap current
request can significantly improve source sensitivity. If the instrument trap current is to be
changed the instrument will require retuning as described above.
If instrument linearity cannot be achieved easily with the source parameters inside of the
acceptable limits other factors outside of instrument tuning must be considered. These other
factors include:
Leaks
Poor quality gas
Contamination in the ion source
Filament distance from the ion box (Bad filament position)
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MA P FI LES
ACQUISITION MAP
The acquisition map is used to display the information that is being acquired in both
graphical and numerical format. The user can change which of the acquired channels
are displayed using the map editor (see below). Not all of the information that is
acquired is displayed (for example, ratios and the status of valves are not usually
displayed).
During the installation of IonVantage, a set of map files is included for each gas. The
files include the necessary beams, ratios and any auxiliary detector that is present.
DISPLAY MAP
The display map displays instrument readbacks that indicate the status of the instrument. The
displayed information is independent of the gas being analysed and the preparation system
being used, and the information is not stored in the tuning file.
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The user may change or add to the readbacks that are displayed using the map editor (see
below). The information displayed in the default display map includes the following:
High vacuum pressure reading from the Penning gauge.
Low vacuum pressure reading from the Pirani gauge.
Speed and power of the analyser turbo.
Source status.
THE MAP EDITOR
EDIT ACQUISITION MAP
The information displayed by the tune page may be changed using the map editor.
To open the acquisition map editor, either press the button or choose Map,
Edit Acquisition Map. This results in the display of the Define Acquisition Map window,
which displays the contents of the current acquisition map and is used to edit the map. An
acquisition map for EA CO2 analysis is shown in the following example:
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The map filename is shown in the title bar. If any changes are made to the map, an
asterisk is displayed next to the file name. The asterisk will remain there until the file is saved.
EDIT DISPLAY MAP
To edit a display map, either press the button or choose Map, Edit Display Map. This
allows the user to determine how the instrument readbacks will be displayed. The operation of
the display map editor is the same as the acquisition map editor.
To open a different map, choose File, Open and select a different map file. All the maps listed
are those that are present in the current project. Both acquisition map files and display map files
have the extension .map.
The names of the four most recently used map files are displayed in the File menu.
CHANGING A MAP FILE
To add new entries to a map file, choose Edit, Add Entry. To modify an entry, either highlight
the entry and then select Edit, Edit Entry, or double click on the entry. In both cases, the
following Select Entry dialog is displayed:
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Set up the following parameters as required:
Channel Type. This defines the type of information shown. The channel chosen affects
the range of active fields that is available in the dialog, as described below.
Label. Enter the text to be displayed beside the entry.
Mass. If beam is selected as the channel type, choose the mass of the beam to
be displayed or acquired.
Beam. If either beam or ratio is selected as the channel type, choose the
appropriate beam number.
Centre Beam. If beam is selected as the channel type, check this box to display
or acquire the beam to be used for peak centering.
Target Beam. If beam is selected as the channel type, check this box to display
or acquire the target beam. The target beam is used to optimise the inlet system.
Divisor Beam. If ratio is selected as the channel type, choose the beam number
to be used for the denominator.
EDITING DISPLAY PROPERTIES
To set up how information is displayed for each channel, press the
Edit Display Properties button. The button is present on both the Select Entry dialog and
the Select Rio Property dialog. Pressing this button displays the
following dialog:
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The dialog is used to set up the following parameters:
Channel Description Panel. The Label is the text that is displayed beside
the readback. The long and short Mnemonics define the username and label in
the inlet page, and the Operation defines the function in the inlet editor. The
In Lists setting is used to choose whether or not to display the information in
the RIO property lists.
Caution: do not change the settings in the channel description panel.
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Data Display Panel. The Bar Scaling may be set to either logarithmic or
linear.
The Numeric Format may be set to standard or scientific.
The Significant Figures box is used to set the number of significant figures to be
displayed.
Colours box. This defines the colour scheme for the selected beam
Data Scaling Panel. The Unit String is the label displayed next to the data
value, for example mBar (milliBar). The displayed value is equal to the Gain
multiplied by the actual value plus the Offset. For example, beams may be
converted to nano-Amp scale by entering a gain of 10-9. The maximum and
minimum values may also be set.
Data Conversion Panel. To use an external table for data conversion, choose
Table and select the required file. To use a script to do the conversion, select
Script and choose the file and script expression.
Changes made to the display properties of the acquisition map are not implemented until the
map has been re-loaded, either by loading a different tune file and then re-loading the original
file, or by loading a different display map and then re-loading the original display map.
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ENABLE STATUS – RIO PROPERTY
RIO Property. If readback, gauge or status are selected, this parameter defines
the RIO property to be displayed or acquired. RIO properties are parameters
that specify hardware events to be performed by the firmware during an
acquisition. The RIO property may be selected by pressing the Select button
that opens the Select Rio Property dialog shown below:
Show in Acquire Display. If this check box is clear, the channel will be
acquired but not displayed on the tune page.
Use for DI Integration. If readback, gauge or status are selected and this
command is checked, the channel is used by the data processing software for the
integration of dual inlet data.
Auxiliary Detector. If readback, gauge or status are selected and this command is
checked, the TCD signal is moved to the auxiliary channel. This allows the TCD to be
integrated for elemental compositions.
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To delete a map entry, highlight the unwanted entry and choose Edit, Delete Entry.
RUNNING A SCAN
A range of different scans may be carried out to assess the state of the instrument. To run a
scan, proceed as follows:
Choose Acquire, Edit Scan, which displays the Scan Setup dialog:
Choose File, Open and select the required scan file. Scan files have the file
extension .isf.
Make any changes to the scan parameters. The following parameters may be
adjusted:
Scanned Quantity. This defines the instrument parameter to be scanned. If
Time is selected, no parameter is scanned and data are collected for the time
specified in the Stop box. Parameters that may be scanned include the
accelerating voltage, magnet current, and various source parameters such as
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electron volts, the voltage on the half plates, Z-plates, extraction and ion
repeller, and the current on the ion trap. Other instrument settings may be scanned by selecting
Other Setting and pressing the Select button.
Scan Type. Choose Start/Stop for a normal scan, Centered for a peak centre scan, which is
centered on the current control setting.
Range. Enter the start and stop values for a start-stop scan, and the width for a centered scan.
Step. This defines the size of the time interval between steps, and the change in the scanned
parameter for each step.
Acquire Map. This specifies the channels to be acquired, if the scan is initiated from this dialog.
Display Template. The user can select a defined template for a scan. Any source parameter or
readback can be monitored during the scan.
Press the Acquire button. Data is not saved to a data file, but the beams displayed in the
defined acquire map will be shown in the peak display window.
The ten most recently run scans may be repeated by selecting them from the acquire menu.
To abort a scan, either press the Stop Acquire toolbar button or select Acquire,
Stop Acquisition.
SETTING UP A PEAK CE NTRE SCAN
A peak centre scan is associated with each tuning file. The default scan has a width of
70 V (180 V for hydrogen). To change the scan width, carry out the following steps:
Choose Acquire, Edit Scan, which opens the Scan Setup window.
Select File, Select Peak Centre Scan. Choose one of the peak centre scan
files and press Open.
Change the width. To save the changes to a new file, press File, Save As.
Press the Close button in the scan setup window. Save any changes that were
made to the current file. The selected scan file will now be used for peak centering.
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Save the tuning file, if required.
RUNNING A PEAK CENTRE SCAN
To run the peak centre scan from the tune page, either press Alt-C on the keyboard or
select Acquire, Run Peak Centre. The scan is displayed in the peak display
window. Once the peak centre scan has finished, the following dialog box appears:
This dialog displays the following information:
Centre. The calculated accelerating voltage for the centre of the peak in the centre
beam.
Change. The difference in voltage between the newly calculated setting and the
previous setting.
Beam. The size of the beam, in amps.
Focus. This provides a quantitative measure of the peak shape. The focus is the
ratio of the 90% peak width to the 10% width. The closer this value is to unity,
the more vertical are the peak sides.
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Resolution. The instrument resolution (M/M) at the peak centre of the centre
Abundance Sensitivity. This is the contribution to the background by the tail
This information is all stored in the current scan file. The software calculates the accelerating
voltage for the middle of the peak and displays the change in voltage that is necessary to update
the present value. To use the calculated value, click the Accept Peak Centre button.
The peak centre results window may be displayed at any time by choosing View, Peak Centre.
PEAK DISPLAY
The peak display window is used to view the results of the peak centre or other source scans.
IsoPrime User’s Guide
beam.
of the target beam peak at the peak centre of the centre beam.
To open the peak display page, either press the peak display toolbar button , or select View,
Peak Display. The peak display page is shown below:
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Further details are given in the Data Display chapter.
AUTO PEAK CENTRE
It is possible to include an auto peak centre in between samples during analysis. A method (MS
File) must be created and this can then be run in the sample list. An example MS file is shown
below:
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This new method can now be incorporated into any sample list. An example sample list is as
shown below:
After Sample 4 the peak centre analysis will start. Once complete the tune file will be updated
and saved to the new peak centre result. The sample list will then continue with further analysis.
HEAD A MPLI FIER ZER OES
THE FUNCTION OF ZEROES
The amp zeroes have two major functions:
To adjust the displayed beams and ratios for the electronic and collector offsets.
To correct dual inlet data for the offsets.
If the electronic offset is removed from a displayed beam, then the beam is representative of
the ion beam that is being measured. If there is no sample in the source, or if the reference gas
is turned off, the beam that is displayed is the ion background. If the reference gas is then
turned on, the observed beam is the ion background plus the beam from the reference gas.
If the collector zero is removed, both the electronic offset and the ion background are removed.
As a result, a zero beam is observed. If the reference gas is then added, the observed beam
reflects the reference gas only.
Note that both types of zeroes are only subtracted from the displayed values. The data that are
stored in the data file are the raw data from the head amplifier and do not have either type of
zero subtracted.
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In order to calculate accurate delta values for samples, it is necessary to remove the background
contribution from the measured signal. In continuous flow mode, the background value is
defined as the baseline just before the sample peak, and the background value may thus be
subtracted from the sample.
When the dual inlet is used, a constant signal is measured at all times and as a result there are
no estimates available of the zero values. The electronic and collector zeros must be measured
before the sample. The zero values are passed to the data processing for incorporation into the
results calculations.
The collector zeros comprise both the electronic offset and the ion background zeros. The
electronic offset must be measured to allow the ion background zeros to be calculated.
If the collector values are used to correct for the background, some species will be overcorrected. For example, for species such as hydrogen, a correction is required for the formation
of H3+ in the source, which is proportional to the amount of hydrogen present in the source. If
hydrogen is corrected using the collector zeroes, the results will be inaccurate, as only some of
the measured collector zero is due to the hydrogen background. Some of the background signal
is due to electronic offset, which is not affected by H3+ production.
ELECTRONIC ZEROES
Electronic zeroes are measured with the source acceleration voltage and extraction voltage set
to zero. As a result, only the intrinsic offset from the amplifier is measured and the zeroes are
equally valid for all gases. The source tuning values are restored at the end of the acquisition.
To run an electronic zero, select Instrument, Zeroes, Run Electronic Zeroes.
The new electronic zeroes form part of the tune page configuration and are saved whenever the
tune page is closed. Electronic zeroes are stored in the IonVantage folder and as a result they
are global to all projects. The same set of electronic zeros is used for all projects.
COLLECTOR ZEROES
Collector zeroes are a measure of the standing ion currents in the mass spectrometer, and
include the electrical offset of the amplifier. They reflect the backgrounds that are present under
the present tuning conditions.
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