SCIEX 5500 Series User manual

5500 Series of Instruments
System User Guide
December 2017RUO-IDV-05-6768-A

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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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....................................................................................................................................14
Decommissioning and Disposal..................................................................................................................................15
Qualified Personnel..........................................................................................................................................................16
Laboratory Conditions......................................................................................................................................................16
Operating Conditions.................................................................................................................................................16
Performance Specifications........................................................................................................................................16
Equipment Use and Modification.....................................................................................................................................17
Contact Us.......................................................................................................................................................................17
Technical Support............................................................................................................................................................18
Documentation Symbols and Conventions.......................................................................................................................18
Related Documentation...................................................................................................................................................19
Chapter 2 Principles of Operation............................................................................................................20
System Overview..............................................................................................................................................................20
Hardware Overview...................................................................................................................................................21
Theory of Operation—Hardware ..............................................................................................................................24
Analyst®Software Overview .....................................................................................................................................26
Theory of Operation—Analyst®Software..................................................................................................................33
Chapter 3 Operating Instructions —Sample Workflows.......................................................................36
Chapter 4 Operating Instructions—Hardware........................................................................................45
Start Up the System.........................................................................................................................................................45
Reset the Mass Spectrometer...........................................................................................................................................46
Shut Down and Vent the System......................................................................................................................................46
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Adjust the Integrated Syringe Pump Position...................................................................................................................47
Plumb the Diverter Valve.................................................................................................................................................51
Plumb the Diverter Valve in Injector Mode................................................................................................................52
Plumb the Diverter Valve in Diverter Mode................................................................................................................53
Chapter 5 Operating Instructions —Hardware Profiles and Projects...................................................55
Hardware Profiles............................................................................................................................................................55
Create a Hardware Profile..........................................................................................................................................55
Add Devices to a Hardware Profile............................................................................................................................59
Troubleshoot Hardware Profile Activation.................................................................................................................61
Projects and Subprojects..................................................................................................................................................62
Create Projects and Subprojects.................................................................................................................................62
Create Subprojects.....................................................................................................................................................63
Copy Subprojects.......................................................................................................................................................63
Switch Between Projects and Subprojects..................................................................................................................64
Installed Project Folders.............................................................................................................................................64
Back Up the API Instrument Folder............................................................................................................................65
Recover the API Instrument Folder.............................................................................................................................65
Chapter 6 Tune and Calibrate..................................................................................................................66
Verify Instrument Performance........................................................................................................................................66
About the Verifying or Adjusting Performance Dialog.....................................................................................................67
Results Summary..............................................................................................................................................................67
Chapter 7 Automatic Optimization..........................................................................................................69
About Automatic Optimization........................................................................................................................................70
Types of Sample Introduction.....................................................................................................................................70
Automatically Optimize for an Analyte Using Infusion.....................................................................................................71
Confirm the Presence of Compounds.........................................................................................................................71
Perform Automatic MS and MS/MS Optimization Using Infusion with a
Known Precursor Ion and an Unknown Product Ion..................................................................................................73
Review the Optimization Results...............................................................................................................................76
Automatically Optimize for an Analyte Using FIA............................................................................................................77
Chapter 8 Operating Instructions —Acquisition Methods....................................................................84
Create an Acquisition Method Using the Acquisition Method Editor...............................................................................84
Configure the Integrated Syringe Pump.....................................................................................................................85
Add an Experiment....................................................................................................................................................85
Add a Period..............................................................................................................................................................86
Copy an Experiment into a Period..............................................................................................................................86
Copy an Experiment within a Period..........................................................................................................................86
Scan Techniques..............................................................................................................................................................87
Quadrupole-Mode Scan Types...................................................................................................................................87
LIT-Mode Scan Types.................................................................................................................................................88
About Spectral Data Acquisition......................................................................................................................................89
Chapter 9 Operating Instructions —Analyze and Process
Quantitative Data.....................................................................................................................................90
Quantitative Analysis.......................................................................................................................................................90
Quantitation Methods................................................................................................................................................90
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Contents

About Results Tables.................................................................................................................................................91
Quantitation Methods and Results Tables.................................................................................................................91
Create a Method Using the Quantitation Method Editor...........................................................................................91
Create a Results Table Using the Quantitation Wizard..............................................................................................93
Create a Standard Query (Optional)...........................................................................................................................94
Results Table Right-click Menu..................................................................................................................................97
Peak Review and Manual Integration of Peaks................................................................................................................98
Review Peaks.............................................................................................................................................................98
Manually Integrate Peaks........................................................................................................................................103
Peak Review Right-Click Menu................................................................................................................................104
Calibration Curves.........................................................................................................................................................105
View Calibration Curves...........................................................................................................................................105
Overlay Calibration Curves.......................................................................................................................................107
Calibration Curve Right-Click Menu.........................................................................................................................107
Sample Statistics............................................................................................................................................................108
View the Statistics for Standards and QCs...............................................................................................................108
Compare Results Between Batches................................................................................................................................109
Chapter 10 Operating Instructions —Analyze and Explore Data.......................................................110
Open Data Files..............................................................................................................................................................110
Navigate Between Samples in a Data File......................................................................................................................110
View Experimental Conditions.......................................................................................................................................111
Show Data in Tables......................................................................................................................................................112
Show ADC Data.............................................................................................................................................................114
Show Basic Quantitative Data........................................................................................................................................115
Chromatograms.............................................................................................................................................................116
Show TICs from a Spectrum...........................................................................................................................................117
Show a Spectrum from a TIC..........................................................................................................................................117
About Generating XICs..................................................................................................................................................118
Generate an XIC Using a Selected Range.................................................................................................................119
Generate an XIC Using the Maximum Peak.............................................................................................................119
Generate an XIC Using Base Peak Masses...............................................................................................................120
Extract Ion by Selecting Masses...............................................................................................................................120
Generate BPCs...............................................................................................................................................................121
Generate XWCs..............................................................................................................................................................123
Generate DAD Data.......................................................................................................................................................123
Generate TWCs..............................................................................................................................................................124
Adjust the Threshold......................................................................................................................................................124
Chromatogram Panes....................................................................................................................................................125
Spectra Panes................................................................................................................................................................126
Graphical Data Processing.............................................................................................................................................126
Graphs...........................................................................................................................................................................127
Manage Data...........................................................................................................................................................127
Zoom In on the Y-axis..............................................................................................................................................129
Zoom In on the X-axis..............................................................................................................................................129
Chapter 11 Reporter Software...............................................................................................................130
Analyst Reporter User Interface.....................................................................................................................................131
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Generate Reports...........................................................................................................................................................133
Chapter 12 Operating Instructions —Batches......................................................................................135
Set Queue Options.........................................................................................................................................................135
Create and Submit a Batch............................................................................................................................................136
Add Sets and Samples to a Batch............................................................................................................................136
Equilibrate the System.............................................................................................................................................139
Submit a Sample or Set of Samples..........................................................................................................................140
Change Sample Order....................................................................................................................................................140
Acquire Data..................................................................................................................................................................140
Set Sample Locations in the Batch Editor.......................................................................................................................141
Select Vial Positions Using the Locations Tab (Optional)...............................................................................................142
Set Quantitation Details in the Batch Editor (Optional)..................................................................................................143
Stop Sample Acquisition................................................................................................................................................143
Import Batch Files..........................................................................................................................................................144
Build a Batch as a Text File......................................................................................................................................144
Import a Batch from a Text File................................................................................................................................144
Batch Editor Right-click Menu........................................................................................................................................145
Queue States and Device Status....................................................................................................................................146
Queue States............................................................................................................................................................146
View Instrument and Device Status Icons................................................................................................................147
Queue Right-click Menu...........................................................................................................................................148
Chapter 13 Service and Maintenance Information...............................................................................150
Recommended Maintenance Schedule..........................................................................................................................150
Clean the Surfaces.........................................................................................................................................................152
Clean the Front-End.......................................................................................................................................................152
Symptoms of Contamination....................................................................................................................................153
Required Materials ..................................................................................................................................................153
Cleaning Best Practices............................................................................................................................................154
Prepare the Mass Spectrometer...............................................................................................................................155
Clean the Curtain Plate............................................................................................................................................156
Clean the Front of the Orifice Plate..........................................................................................................................157
Put the Mass Spectrometer Back in Service.............................................................................................................157
Inspect the Roughing Pump Oil Level............................................................................................................................158
Empty the Source Exhaust Drain Bottle..........................................................................................................................158
Storage and Handling....................................................................................................................................................160
Chapter 14 Mass Spectrometer Troubleshooting.................................................................................161
Appendix A Operating Instructions —Manual Compound Optimization..........................................164
About Manual Compound Optimization........................................................................................................................164
About Scan Types...........................................................................................................................................................165
Manually Optimize an Analyte.......................................................................................................................................165
Confirm the Presence of Compounds.......................................................................................................................165
Optimize MS-Specific Parameters............................................................................................................................167
Determine the Product Ions for Optimization...........................................................................................................168
Optimize Collision Cell Exit Potential for each Product Ion......................................................................................170
Manually Optimize the Ion Source and Gas Parameters................................................................................................171
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Prepare the Ion Source.............................................................................................................................................171
Optimize the Ion Source Parameters........................................................................................................................171
Advanced Parameters....................................................................................................................................................172
Optimize AF2...........................................................................................................................................................172
About Collision Energy Spread (CES) ......................................................................................................................173
Appendix B 5500 Series System Parameters.........................................................................................174
Appendix C Calibration Ions and Solutions..........................................................................................177
Appendix D Toolbar Icons......................................................................................................................180
Appendix E Glossary of Symbols...........................................................................................................189
Appendix F Glossary of Warnings.........................................................................................................194
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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 189 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/CSA 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 14.
•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
•RoHS Restriction of Hazardous Substances: RoHS Directive 2011/65/EU
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 14.
•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, optional bench, 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.
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Operational Precautions and Limitations

•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. SCIEX
Safety Data Sheets can be found at sciex.com/tech-regulatory.
•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 153 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%
•Buffers
•Ammonium acetate; less than 1%
•Ammonium formate; less than 1%
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Operational Precautions and Limitations

•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%
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.
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.
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Operational Precautions and Limitations

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.
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.
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Operational Precautions and Limitations

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 60% 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
WARNING! Environmental Hazard. Do not dispose of system components in municipal
waste. Follow local regulations when disposing of components.
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 160.
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.
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Operational Precautions and Limitations

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.
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.
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.
Laboratory Conditions
Operating Conditions
The system is designed to operate safely under these conditions:
•Indoors
•Altitude: Up to 2 000 m (6 400 feet) above sea level
•Ambient temperature: 5 °C (41 °F) to 40 °C (104 °F)
•Relative humidity: 80% for temperatures up to 31 °C (88 °F), decreasing lineraly to 50% at 40 °C (104 °F)
•Mains supply voltage fluctuations: ±10% of the nominal voltage
•Transient overvoltages: Up to the levels of Overvoltage Category II
•Temporary overvoltages on the mains supply
•Pollution degree: Pollution Degree 2
Performance Specifications
The system is designed to meet specifications under these conditions:
•Ambient temperature: 15 °C (59 °F) to 30 °C (86 °F)
Over time, the temperature must remain within a range of 4 °C (7.2 °F), with the rate of the change in
temperature not exceeding 2 °C (3.6 °F) per hour. Ambient temperature fluctuations exceeding the limits might
result in mass shifts in spectra.
•Relative humidity: 20% to 80%, non-condensing
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Operational Precautions and Limitations

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 mass spectrometer and ion source indoors in a laboratory that complies with the environmental conditions
recommended in the Site Planning Guide.
If the mass spectrometer and ion source 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 mass spectrometer and ion source might cause personal injury and
equipment damage, and might void the warranty. Erroneous data might be generated if the mass spectrometer
and ion source is operated either above or below the recommended environmental conditions or operated with
unauthorized modifications. Contact an FSE for information on servicing the system.
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.
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Operational Precautions and Limitations

Online Learning Center
•SCIEXUniversity
CyberSecurity
For the latest guidance on cybersecurity for SCIEX products, visit
sciex.com/Documents/brochures/win7-SecurityGuidance.pdf.
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.
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

Related Documentation
To find software product documentation, refer to the release notes or software installation guide that comes with
the software. Documentation for the hardware products can be found on the Customer Reference DVD that
comes with the system or component.
For the latest versions of the documentation, visit the SCIEX website at sciex.com.
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Operational Precautions and Limitations

The 5500 system is designed for the qualitative and quantitative analysis of chemical species.
This section includes information about the mass spectrometer and the Analyst®software. Refer to the ion source
Operator Guide for an overview of the ion source.
For information on the computer and software, refer to the Software Installation Guide for the Analyst®
software.
WARNING! Lifting Hazard. Do not move the system. Risk of personal injury
or system damage. If the system must be moved, then contact a Field Service
Employee (FSE).
System Overview
WARNING! Lifting Hazard. Make sure that at least six people are available to lift
the mass spectrometer. Follow established safe lifting procedures. Refer to the Site
Planning Guide for the weights of system components.
This system is intended for the qualitative and quantitative analysis of chemical species.
The 5500 series of instruments includes the following components:
•A SCIEX Triple QuadTM 5500 or QTRAP®5500 mass spectrometer with a roughing pump and a source of
compressed air and nitrogen
•Turbo VTM ion source that uses either the TurboIonSpray®probe or the atmospheric pressure chemical ionization
(APCI) probe. Refer to the Turbo VTM Ion Source Operator Guide.
•SCIEX-supplied computer and monitor with the Analyst®software for instrument optimization, acquisition
method development, processing, and data acquisition. For computer specifications and requirements, refer
to the Analyst®Software Installation Guide.
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Principles of Operation