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