SCIEX X500 QTOF User manual

SCIEX X500 QTOF System
System User Guide
August 2017RUO-IDV-05-2334-E

This document is provided to customers who have purchased SCIEX equipment to use in the operation of such SCIEX
equipment. This document is copyright protected and any reproduction of this document or any part of this document is
strictly prohibited, except as SCIEX may authorize in writing.
Software that may be described in this document is furnished under a license agreement. It is against the law to copy, modify,
or distribute the software on any medium, except as specifically allowed in the license agreement. Furthermore, the license
agreement may prohibit the software from being disassembled, reverse engineered, or decompiled for any purpose. Warranties
are as stated therein.
Portions of this document may make reference to other manufacturers and/or their products, which may contain parts whose
names are registered as trademarks and/or function as trademarks of their respective owners. Any such use is intended only
to designate those manufacturers' products as supplied by SCIEX for incorporation into its equipment and does not imply
any right and/or license to use or permit others to use such manufacturers' and/or their product names as trademarks.
SCIEX warranties are limited to those express warranties provided at the time of sale or license of its products and are SCIEX’s
sole and exclusive representations, warranties, and obligations. SCIEX makes no other warranty of any kind whatsoever,
expressed or implied, including without limitation, warranties of merchantability or fitness for a particular purpose, whether
arising from a statute or otherwise in law or from a course of dealing or usage of trade, all of which are expressly disclaimed,
and assumes no responsibility or contingent liability, including indirect or consequential damages, for any use by the purchaser
or for any adverse circumstances arising therefrom.
For research use only. Not for use in diagnostic procedures.
AB Sciex is doing business as SCIEX.
The trademarks mentioned herein are the property of AB Sciex Pte. Ltd. or their respective owners.
AB SCIEX™is being used under license.
©2017 AB Sciex
AB Sciex Pte. Ltd.
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Marsiling Ind Estate Road 3
Woodlands Central Indus. Estate.
SINGAPORE 739256
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Chapter 1 Operational Precautions and Limitations................................................................................8
General Safety Information................................................................................................................................................8
Regulatory Compliance......................................................................................................................................................8
Australia and New Zealand..........................................................................................................................................8
Canada........................................................................................................................................................................9
Europe.........................................................................................................................................................................9
United States...............................................................................................................................................................9
International..............................................................................................................................................................10
Electrical Precautions.......................................................................................................................................................10
AC Mains Supply........................................................................................................................................................10
Protective Earth Conductor........................................................................................................................................11
Chemical Precautions.......................................................................................................................................................11
System Safe Fluids.....................................................................................................................................................12
Ventilation Precautions....................................................................................................................................................13
Environmental Precautions..............................................................................................................................................14
Electromagnetic Environment....................................................................................................................................15
Decommissioning and Disposal..................................................................................................................................15
Equipment Use and Modification.....................................................................................................................................16
Qualified Personnel..........................................................................................................................................................16
Contact Us.......................................................................................................................................................................17
Technical Support............................................................................................................................................................17
Documentation Symbols and Conventions.......................................................................................................................17
Chapter 2 Principles of Operation............................................................................................................19
System Overview..............................................................................................................................................................19
Hardware Overview.........................................................................................................................................................20
Panel Symbols............................................................................................................................................................24
Theory of Operation.........................................................................................................................................................24
Data Handling............................................................................................................................................................25
Theory of Operation—SCIEX OS......................................................................................................................................25
Software Overview.....................................................................................................................................................25
Scan Techniques........................................................................................................................................................25
Quantitative Analysis.................................................................................................................................................28
Integration.................................................................................................................................................................28
Results Tables............................................................................................................................................................28
Calibration Curves.....................................................................................................................................................28
Regression Equations.................................................................................................................................................29
Weighting Factors......................................................................................................................................................30
Regression Types.......................................................................................................................................................30
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Qualitative Analysis...................................................................................................................................................33
Chapter 3 Operating Instructions—Hardware........................................................................................36
Start Up the System.........................................................................................................................................................36
Shut Down and Vent the System......................................................................................................................................37
Diverter Valve..................................................................................................................................................................38
Plumb the Diverter Valve in Injector Mode................................................................................................................39
Plumb the Diverter Valve in Diverter Mode................................................................................................................40
Calibrant Delivery System................................................................................................................................................41
Replace the CDS Bottle..............................................................................................................................................41
Start the CDS.............................................................................................................................................................42
Stop the CDS..............................................................................................................................................................42
Flush the CDS.............................................................................................................................................................42
Chapter 4 Configure Devices....................................................................................................................45
Add Devices.....................................................................................................................................................................45
Edit Device Settings.........................................................................................................................................................45
Delete Devices.................................................................................................................................................................46
Deactivate Devices...........................................................................................................................................................46
Chapter 5 Configure Access to the Software..........................................................................................48
Users Overview................................................................................................................................................................48
Roles and Permissions...............................................................................................................................................48
Access to Analytics Features......................................................................................................................................50
Add Users..................................................................................................................................................................53
Deactivate a User.......................................................................................................................................................53
Remove a User...........................................................................................................................................................54
Enable Full Screen Mode..................................................................................................................................................54
Select Laboratory Information Management System (LIMS) Settings...............................................................................54
Select Queue Options.......................................................................................................................................................54
Select Regional Settings...................................................................................................................................................55
Manage the Compound Libraries.....................................................................................................................................55
Import a LibraryView Package...................................................................................................................................55
Import a Compound Database...................................................................................................................................56
Import a Cliquid Package...........................................................................................................................................57
Import an Excel File...................................................................................................................................................58
Import a Library Database Snapshot .........................................................................................................................59
Import a Library Package from a Third Party .............................................................................................................60
Install a Licensed LibraryView Package......................................................................................................................60
Compound Conflicts ..................................................................................................................................................62
Add a Compound.......................................................................................................................................................64
Add a Mass Spectrum to a Compound.......................................................................................................................64
Chapter 6 Operating Instructions—Software.........................................................................................66
About the Home Page......................................................................................................................................................66
About the Ribbon and Launcher......................................................................................................................................67
About the Status Panel....................................................................................................................................................69
Add a Project.............................................................................................................................................................71
Select a Project..........................................................................................................................................................72
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Control the Device Status...........................................................................................................................................72
Show the Status Panel...............................................................................................................................................72
Hide the Status Panel.................................................................................................................................................72
Data Acquisition Panel.....................................................................................................................................................72
User Workflows................................................................................................................................................................73
Analysts.....................................................................................................................................................................73
Method Developers....................................................................................................................................................74
Administrators...........................................................................................................................................................74
Reviewers..................................................................................................................................................................74
Batch and Queue Workspaces.........................................................................................................................................74
Manage the Batch.....................................................................................................................................................75
Import a Batch ..........................................................................................................................................................76
Import a Batch from the LIMS....................................................................................................................................77
Create a Batch Manually............................................................................................................................................78
Use the Plate Layout Feature to Create a Batch.........................................................................................................80
Create an Ion Reference Table...................................................................................................................................82
Calibrate the System Using the CDS..........................................................................................................................83
Calibrate the System Using an LC Method.................................................................................................................83
Equilibrate the System...............................................................................................................................................84
Manage the Queue....................................................................................................................................................84
Submit a Single Sample to the Queue........................................................................................................................86
Submit Multiple Samples to the Queue......................................................................................................................86
Show or Hide Columns...............................................................................................................................................87
Add a Component Component Concentration Column..............................................................................................87
Delete a Component Concentration Column..............................................................................................................87
Queue Icons...............................................................................................................................................................88
MS Method Workspace....................................................................................................................................................88
Create an MS Method................................................................................................................................................88
MS Method Experiments............................................................................................................................................90
About MS Methods....................................................................................................................................................91
MS Method Parameters.............................................................................................................................................93
Calculate the Dynamic Collision Energy for MS Methods.........................................................................................103
LC Method Workspace...................................................................................................................................................104
Create an LC Method...............................................................................................................................................104
Explorer Workspace.......................................................................................................................................................104
Verify the Presence of an Analyte............................................................................................................................104
Extract Ions..............................................................................................................................................................105
Open a Total Ion Chromatogram.............................................................................................................................108
Open a Base Peak Chromatogram...........................................................................................................................110
Show the Data and Peaks Table...............................................................................................................................112
Show Sample Information........................................................................................................................................114
Show the Graph Selection Information....................................................................................................................115
Edit Settings in Graphs.............................................................................................................................................120
Work with Data in Graphs.......................................................................................................................................122
Use the Two-Pane Operation Tools..........................................................................................................................128
Move Panes or Windows.........................................................................................................................................129
Perform a Gaussian Smooth.....................................................................................................................................131
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Threshold Data.........................................................................................................................................................132
Subset Data (to Graph Selection).............................................................................................................................134
Baseline Subtract Chromatogram............................................................................................................................135
Offset Chromatogram..............................................................................................................................................137
Centroid a Spectrum................................................................................................................................................138
Export Data as Text..................................................................................................................................................140
Export the Peak List as Text.....................................................................................................................................142
Print Data.................................................................................................................................................................142
Reset Options...........................................................................................................................................................143
Set Options..............................................................................................................................................................143
Analytics Workspace......................................................................................................................................................147
Set Project Secure Export Settings...........................................................................................................................147
Enable Project Modified Peak Warning....................................................................................................................148
Define the Project Default Settings..........................................................................................................................148
Create a Processing Method....................................................................................................................................148
About Results Tables...............................................................................................................................................150
Review Peaks...........................................................................................................................................................169
About Statistics Pane...............................................................................................................................................176
Calibration Curve: Options.......................................................................................................................................179
Analyzing Data Using Metric Plots...........................................................................................................................181
Audit Trails...............................................................................................................................................................183
Integration Algorithm Parameters..................................................................................................................................186
MQ4 Integration Algorithm Parameters...................................................................................................................186
AutoPeak Integration Algorithm Parameters...........................................................................................................188
Edit Report Templates....................................................................................................................................................189
Reporter Templates..................................................................................................................................................191
MS Tune.........................................................................................................................................................................192
Perform a Quick Status Check..................................................................................................................................192
Optimize the Detector..............................................................................................................................................193
Tune Q1...................................................................................................................................................................194
Tune TOF MS............................................................................................................................................................194
Tune Q1 High...........................................................................................................................................................195
Perform Advanced Troubleshooting.........................................................................................................................196
Restore Instrument Data..........................................................................................................................................196
Event Log Workspace.....................................................................................................................................................197
View Logs................................................................................................................................................................197
Print Logs.................................................................................................................................................................197
Archive Logs............................................................................................................................................................197
Chapter 7 Service and Maintenance Information.................................................................................199
Recommended Maintenance Schedule..........................................................................................................................199
Clean the Surfaces.........................................................................................................................................................201
Clean the Front-End.......................................................................................................................................................201
Symptoms of Contamination....................................................................................................................................202
Required Materials ..................................................................................................................................................202
Cleaning Best Practices............................................................................................................................................203
Prepare the Mass Spectrometer...............................................................................................................................205
Clean the Curtain Plate............................................................................................................................................206
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Clean the Front of the Orifice Plate..........................................................................................................................207
Put the Mass Spectrometer Back in Service.............................................................................................................207
Empty the Source Exhaust Drain Bottle..........................................................................................................................207
Replace the Check Valve and Flow Module...................................................................................................................210
Inspect the Roughing Pump Oil Level............................................................................................................................211
Storage and Handling....................................................................................................................................................212
Move the Mass Spectrometer........................................................................................................................................213
Generate a Support Package..........................................................................................................................................219
Chapter 8 Mass Spectrometer Troubleshooting...................................................................................220
Appendix A Recommended Calibration Ions........................................................................................223
APCI Calibration Ions.....................................................................................................................................................223
ESI Calibration Ions........................................................................................................................................................225
Appendix B Exact Masses and Chemical Formulas...............................................................................228
Appendix C Glossary of Symbols...........................................................................................................229
Appendix D Glossary of Warnings.........................................................................................................233
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Note: Before operating the system, carefully read all of the sections of this guide.
This section contains general safety-related information and provides regulatory compliance information. It also
describes potential hazards and associated warnings for the system and the precautions that should be taken to
minimize the hazards.
In addition to this section, refer to Glossary of Symbols on page 229 for information about the symbols and
conventions used in the laboratory environment, on the system, and in this documentation. Refer to the Site
Planning Guide for site requirements, including AC mains supply, source exhaust, ventilation, compressed air,
nitrogen, and roughing pump requirements.
General Safety Information
To prevent personal injury or system damage, read, understand, and obey all of the safety precautions and warnings
in this document, the manufacturer chemical safety data sheet (SDS), and product label information. These labels
are shown with internationally recognized symbols. Failure to heed these warnings could result in serious injury.
This safety information is intended to supplement federal, state, provincial, and local environmental health and
safety (EHS) regulations. The information provided covers system-related safety information applicable to the
operation of the system. It does not cover every safety procedure that should be practised. Ultimately, the user
and the organization are responsible for compliance with federal, state, provincial, and local EHS regulations and
for maintaining a safe laboratory environment.
Refer to the appropriate laboratory reference material and standard operating procedures.
Regulatory Compliance
This system complies with the regulations and standards listed in this section. Refer to the Declaration of Conformity
included with the system and the individual system components for dated references. Applicable labels have been
affixed to the system.
Australia and New Zealand
•Electromagnetic Compatibility (EMC): Radio Communications Act 1992 as implemented in these
standards:
•Electromagnetic Interference—AS/NZS CISPR 11/ EN 55011/ CISPR 11 (Class A) . Refer to Electromagnetic
Interference on page 15.
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1
Operational Precautions and
Limitations

•Safety: AS/NZ 61010-1 and IEC 61010-2-061
Canada
•Electromagnetic Interference (EMI): CAN/CSAA CISPR11. This ISM device complies with Canadian
ICES-001. Refer to Electromagnetic Interference on page 15.
•Safety:
•CAN/CSA C22.2 No. 61010-1
•CAN/CSA C22.2 No 61010-2-061
Europe
•Electromagnetic Compatibility (EMC): Electromagnetic Compatibility directive 2014/30/EU as
implemented in these standards:
•EN 61326-1
•EN 55011 (Class A)
Refer to Electromagnetic Compatibility on page 15.
•Safety: Low Voltage Directives 2014/35/EU as implemented in these standards:
•EN 61010-1
•EN 61010-2-061
•Waste Electrical and Electronic Equipment (WEEE): Waste Electrical and Electronic Equipment 2012/
96/EEC, as implemented in EN 40519. Refer to Waste Electrical and Electronic Equipment on page 16.
•Packaging and Packaging Waste (PPW): Packaging and Packaging Waste Directive 94/62/EC
United States
•Radio Emissions Interference Regulations: 47 CFR 15, as implemented in FCC Part 15 (Class A)
•Safety: Occupational Safety and Health Regulations, 29 CFR 1910, as implemented in these standards:
•UL 61010-1
•IEC 61010-2-061
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Operational Precautions and Limitations

International
•Electromagnetic Compatibility (EMC):
•IEC 61326-1
•IEC CISPR 11 (Class A)
•IEC 61000-3-2
•IEC 61000-3-3
Refer to Electromagnetic Compatibility on page 15.
•Safety:
•IEC 61010-1
•IEC 61010-2-061
Electrical Precautions
WARNING! Electrical Shock Hazard. Do not remove the covers. Removing the covers
might cause injury or malfunctioning of the system. The covers need not be removed
for routine maintenance, inspection, or adjustment. Contact a SCIEX Field Service
Employee (FSE) for repairs that require the covers to be removed.
•Follow required electrical safe work practices.
•Use cable management practices to control electrical cables. This will reduce the chance of a tripping hazard.
For information about system electrical specifications, refer to the Site Planning Guide.
AC Mains Supply
Connect the system to a compatible AC mains supply as instructed in this guide.
WARNING! Electrical Shock Hazard. Use only qualified personnel for the installation
of all of the electrical supplies and fixtures, and make sure that all of the installations
adhere to local regulations and safety standards.
WARNING! Electrical Shock Hazard. Make sure that the system can be disconnected
from the mains supply outlet in an emergency. Do not block the mains supply outlet.
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Operational Precautions and Limitations

WARNING! Electrical Shock Hazard. Use only the power cables supplied with the
system. Do not use power cables that are not properly rated for the operation of
this system.
An external line transformer is not needed for the mass spectrometer or roughing pump.
Protective Earth Conductor
The mains supply must include a correctly installed protective earth conductor. The protective earth conductor
must be installed or checked by a qualified electrician before the system is connected.
WARNING! Electrical Shock Hazard. Do not intentionally interrupt the protective
earth conductor. Any interruption of the protective earth conductor creates an
electrical shock hazard.
WARNING! Electrical Shock Hazard. Make sure that a protective earth conductor
(grounding cable) is connected between the sample loop and an appropriate
grounding point at the ion source. This supplementary grounding will reinforce the
safety configuration specified by SCIEX.
Chemical Precautions
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Determine
whether decontamination is required prior to cleaning or maintenance. The
customer must decontaminate the system prior to cleaning or maintenance
if radioactive materials, biological agents, or toxic chemicals have been used
with the system.
WARNING! Environmental Hazard. Do not dispose of system components in municipal
waste. Follow local regulations when disposing of components.
WARNING! Biohazard, Toxic Chemical Hazard. Connect the drain tubing to
the mass spectrometer and the source exhaust drain bottle properly, to
prevent leaks.
•Determine which chemicals have been used in the system prior to service and regular maintenance. Refer to
the Safety Data Sheets for the health and safety precautions that must be followed with chemicals.
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Operational Precautions and Limitations

•Work in a well-ventilated area or fume hood.
•Always wear assigned personal protective equipment, including powder-free neoprene or nitrile gloves, safety
glasses, and a laboratory coat.
•Avoid ignition sources when working with flammable materials, such as isopropanol, methanol, and other
flammable solvents.
•Take care in the use and disposal of any chemicals. Potential risk of personal injury if proper procedures for
handling and disposing of chemicals are not followed.
•Avoid skin contact with chemicals during cleaning and wash hands after use.
•Make sure that all exhaust hoses are connected properly and that all connections are functioning as designed.
•Collect all spent liquids and dispose of them as hazardous waste.
•Comply with all of the local regulations for the storage, handling, and disposal of biohazardous, toxic, or
radioactive materials.
•(Recommended) Use secondary containment trays beneath the roughing pump, the solvent bottles, and the
waste collection container to capture potential chemical spills.
System Safe Fluids
The following fluids can safely be used with the system. Refer to Required Materials on page 202 for information
about safe cleaning solutions.
CAUTION: Potential System Damage. Do not use any other fluid until confirmation is
received from SCIEX that it does not present a hazard. This is not an exhaustive list.
•Organic Solvents
•MS-grade acetonitrile; up to 100%
•MS-grade methanol; up to 100%
•Isopropanol; up to 100%
•HPLC-grade or higher water; up to 100%
•Tetrahydrofuran; up to 100%
•Toluene and other aromatic solvents; up to 100%
•Hexanes; up to 100%
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Operational Precautions and Limitations

•Buffers
•Ammonium acetate; less than 1%
•Ammonium formate; less than 1%
•Phosphate; less than 1%
•Acids and Bases
•Formic acid; less than 1%
•Acetic acid; less than 1%
•Trifluoroacetic acid (TFA); less than 1%
•Heptafluorobutyric acid (HFBA); less than 1%
•Ammonia/ammonium hydroxide; less than 1%
•Phosphoric acid; less than 1%
•Trimethylamine; less than 1%
•Triethylamine; less than 1%
Ventilation Precautions
The venting of fumes and disposal of waste must comply with all of the federal, state, provincial, and local health
and safety regulations. It is the responsibility of the customer to make sure that the air quality is maintained in
compliance with local health and safety regulations.
The source exhaust system and roughing pump must be vented to a dedicated laboratory fume hood or an external
exhaust system.
WARNING! Fire Hazard. Make sure that the source exhaust system is connected and
functioning to prevent flammable vapor from accumulating in the ion source.
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Take care
to vent exhaust gases to a dedicated laboratory fume hood or exhaust system
and make sure that the ventilation tubing is secured with clamps. Make sure
that the laboratory has appropriate air exchange for the work performed.
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Operational Precautions and Limitations

WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Do not
operate the mass spectrometer if the source exhaust drain and roughing
pump exhaust hoses are not properly connected to the laboratory ventilation
system. Perform a regular check of the exhaust tubing to make sure that
there are no leaks. The use of mass spectrometers without proper system
ventilation might constitute a health hazard and might result in serious injury.
WARNING! Radiation Hazard, Biohazard, or Toxic Chemical Hazard. Use the
ion source only if you have knowledge of and training in the proper use,
containment, and evacuation of toxic or injurious materials used with the
ion source.
WARNING! Puncture Hazard, Radiation Hazard, Biohazard, or Toxic Chemical
Hazard. Discontinue use of the ion source if the ion source window is cracked
or broken and then contact a SCIEX Field Service Employee (FSE). Any toxic
or injurious materials introduced into the equipment will be present in the
source exhaust output. Dispose of sharps following established laboratory
safety procedures.
Environmental Precautions
Use qualified personnel for the installation of electrical mains, heating, ventilation, and plumbing supplies and
fixtures. Make sure that all of the installations comply with local bylaws and biohazard regulations. For information
about the required environmental conditions for the system, refer to the Site Planning Guide.
Allow access space around the equipment when setting up the system.
DANGER! Explosion Hazard. Do not operate the system in an environment containing
explosive gases. The system is not designed for operation in an explosive
environment.
WARNING! Biohazard. For biohazardous material use, always comply with local
regulations for hazard assessment, control, and handling. This system or any part
is not intended to act as a biological containment.
CAUTION: Potential Mass Shift. Maintain a stable ambient temperature. If the temperature
changes by more than 2 °C per hour, then the resolution and mass calibration might be
affected.
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Operational Precautions and Limitations

Electromagnetic Environment
Electromagnetic Compatibility
Basic Electromagnetic Environment: Environment existing at locations characterized by being supplied
directly at low voltage from the public mains network.
Performance Criteria A (Criteria A): Equipment shall operate as intended with no degradation of performance
and no loss of function during or after test.
Performance Criteria B (Criteria B): Equipment may experience loss of function (one or more) during test
but shall operate as intended with some degradation of performance and functions self-recoverable after test.
Performance Criteria C (Criteria C): Equipment may experience loss of function (one or more) during test
but shall operate as intended with some degradation of performance and functions recoverable by operator after
test.
The equipment is intended for use in a basic electromagnetic environment.
The expected performance loss under the electromagnetic immunity conditions is less than 20% change in total
ion count (TIC).
Make sure that a compatible electromagnetic environment for the equipment can be maintained so that the device
will perform as intended. If the power supply line is subject to high electrical noise, then install a surge protector.
Electromagnetic Interference
Class A Equipment: Equipment which is suitable for use in all establishments other than domestic and those
directly connected to a low voltage power supply network which supplies buildings used for domestic purposes.
[Derived from CISPR 11:2009, 5.3] Class A equipment shall meet Class A limits.
This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part
15 of the FCC (Federal Communications Commission) Compliance Rules.
These limits are designed to provide reasonable protection against harmful interference when the equipment is
operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency energy
and, if not installed and used in accordance with the operator's manual, can cause harmful interference to radio
communications.
Operation of this equipment in a residential area is likely to cause harmful interference in which case you will be
required to correct the interference, at your own expense. Changes or modifications not expressly approved by
the manufacturer could void your authority to operate the equipment.
Decommissioning and Disposal
Before decommissioning, decontaminate the entire system following local regulations.
When removing the system from service, separate and recycle different materials according to national and local
environmental regulations. Refer to Storage and Handling on page 212.
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Operational Precautions and Limitations

Note: SCIEX will not accept any system returns without a completed Decontamination Form. Contact an FSE
to obtain a copy of the form.
Do not dispose of system components or subassemblies, including computer parts, as unsorted municipal waste.
Waste Electrical and Electronic Equipment
Follow local municipal waste ordinances for proper disposal provisions to reduce the environmental impact of
waste, electrical, and electronic equipment (WEEE). To safely dispose of this equipment, contact a local Customer
Service office for complimentary equipment pick-up and recycling.
Equipment Use and Modification
WARNING! Personal Injury Hazard. Contact the SCIEX representative if product
installation, adjustment, or relocation is required.
WARNING! Electrical Shock Hazard. Do not remove the covers. Removing the covers
might cause injury or malfunctioning of the system. The covers need not be removed
for routine maintenance, inspection, or adjustment. Contact a SCIEX Field Service
Employee (FSE) for repairs that require the covers to be removed.
WARNING! Personal Injury Hazard. Use SCIEX-recommended parts only. Use of parts
not recommended by SCIEX or use of parts for any purpose other than their intended
purpose can put the user at risk of harm or negatively impact system performance.
Use the system indoors in a laboratory that complies with the environmental conditions recommended in the Site
Planning Guide.
If the system is used in an environment or in a manner not prescribed by the manufacturer, then the protection
provided by the equipment might be impaired.
Unauthorized modification or operation of the system might cause personal injury and equipment damage, and
might void the warranty. Erroneous data might be generated if the system is operated either above or below the
recommended environmental conditions or operated with unauthorized modifications. Contact an FSE for information
on servicing the system.
Qualified Personnel
Only qualified SCIEX personnel shall install, inspect, and service the equipment. After installing the system, the
Field Service Employee (FSE) uses the Customer Familiarization Checklist to orient the customer on system
operation, cleaning, and basic maintenance.
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Operational Precautions and Limitations

Only personnel qualified by the manufacturer shall maintain the equipment. A laboratory designate can be
familiarized with the Qualified Maintenance Person (QMP) procedures during the installation. A QMP is a person
who is suitably aware of the electrical and chemical risks associated with servicing laboratory equipment.
Contact Us
SCIEX Support
•sciex.com/contact-us
•sciex.com/request-support
Customer Training
•In North America: [email protected]
•In Europe: [email protected]
•Outside the EU and North America, visit sciex.com/education for contact information.
Online Learning Center
•SCIEXUniversity
For the latest guidance on cybersecurity for SCIEX products, visit sciex.com/productsecurity.
Technical Support
SCIEX and its representatives maintain a staff of fully-trained service and technical specialists located throughout
the world. They can answer questions about the system or any technical issues that might arise. For more
information, visit the SCIEX website at sciex.com.
Documentation Symbols and Conventions
The following symbols and conventions are used throughout the guide.
DANGER! Danger signifies an action which leads to severe injury or death.
WARNING! Warning signifies an action that could cause personal injury if precautions
are not followed.
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Operational Precautions and Limitations

CAUTION: Caution signifies an operation that could cause damage to the system or
corruption or loss of data if precautions are not followed.
Note: Note emphasizes significant information in a procedure or description.
Tip! Tip provides useful information that helps apply the techniques and procedures in the text for a specific
need and provides shortcuts, but is not essential to the completion of a procedure.
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Operational Precautions and Limitations

The SCIEX X500 QTOF system is designed for the qualitative and quantitative analysis of chemical species.
This section includes information about the mass spectrometer and the SCIEX OS. Refer to the ion source Operator
Guide for an overview of the ion source.
System Overview
The SCIEX X500 QTOF system includes the following components:
•A SCIEX X500 QTOF mass spectrometer with a roughing pump.
•A Turbo VTM ion source that uses either the twin ESI probe or the twin atmospheric pressure chemical ionization
(APCI) probe. Refer to the Turbo VTM Ion Source Operator Guide.
•A SCIEX-supplied computer and monitor with the SCIEX OS for instrument optimization, acquisition method
development, processing, and data acquisition. For computer specifications and requirements, refer to the
Release Notes for the SCIEX OS.
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Principles of Operation

Hardware Overview
Figure 2-1 Front and Right Side View: X500R
System User GuideSCIEX X500 QTOF System
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Principles of Operation