Isoprime 100 User manual

ISOPRIME100 USER’S GUIDE

Isoprime User’s Guide
Version 1.02 IsoPrime100 User’s Guide Page 2 of 219
Isoprime Ltd
Isoprime House
Earl Road
Cheadle Hulme
Cheadle
SK8 6PT
Tel: [phone]
Fax: [phone]
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 [e-mail], 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 GUIDE
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 REQUIREMENTS
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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WEIGHT
The approximate weights of individual units of the instrument are shown below:
Unit
Weight
IsoPrime100
82kg
Electromagnet
45Kg
Data system
55kg
Rotary pump
25kg
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.
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
Note: Each line in the table represents an individual Mains connection and uses an individual
Mains lead.
Note: Mains supply voltage fluctuations should not exceed ±10% of the nominal voltage.

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ENVIRONMENTAL REQUIREMENTS
ROOM TEMPERATURE
The maximum operational room temperature should not exceed 25 oC (ideally 22 oC). An air-
conditioned 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 SO2or 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 0.5m
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 OPTICS
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.