SCIEX X500 QTOF User manual

SCIEX X500 QTOF System
System User Guide
RUO-IDV-05-9349-B January 2022

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 the sole and exclusive representations, warranties, and obligations of SCIEX. SCIEX
makes no other warranty of any kind whatsoever, expressed or implied, including without limitation,
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(GEN-IDV-09-10816-D)
For Research Use Only. Not for use in Diagnostic Procedures.
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AB Sciex™ is being used under license.
© 2022 DH Tech. Dev. Pte. Ltd.
AB Sciex Pte. Ltd.
Blk33, #04-06 Marsiling Industrial Estate Road 3
Woodlands Central Industrial Estate, Singapore 739256
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Contents
1 Operational Precautions and Limitations...............................................................................6
General Safety Information....................................................................................................... 6
Documentation Symbols and Conventions............................................................................... 6
Regulatory Compliance.............................................................................................................7
Australia and New Zealand.................................................................................................. 7
Canada.................................................................................................................................7
Europe..................................................................................................................................7
United States........................................................................................................................8
International......................................................................................................................... 8
Electrical Precautions................................................................................................................9
Mains Supply........................................................................................................................9
Protective Earth Conductor.................................................................................................. 9
Chemical Precautions............................................................................................................. 10
System Safe Fluids............................................................................................................ 11
Ventilation Precautions............................................................................................................12
Physical Precautions ..............................................................................................................13
Environmental Precautions..................................................................................................... 13
Electromagnetic Environment............................................................................................ 14
Decommissioning and Disposal......................................................................................... 15
Qualified Personnel.................................................................................................................15
Laboratory Conditions.............................................................................................................16
Safe Environmental Conditions..........................................................................................16
Performance Specifications............................................................................................... 16
Equipment Use and Modification............................................................................................ 17
2 Principles of Operation.......................................................................................................... 18
System Overview.................................................................................................................... 18
Hardware Overview............................................................................................................19
Theory of Operation........................................................................................................... 22
3 Operating Instructions — Hardware..................................................................................... 23
Start Up the System................................................................................................................23
Shut Down and Vent the System............................................................................................ 24
Diverter Valve..........................................................................................................................25
Plumb the Diverter Valve in Injector Mode......................................................................... 26
Plumb the Diverter Valve in Diverter Mode........................................................................ 27
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Calibrant Delivery System.......................................................................................................29
Replace the CDS Bottle..................................................................................................... 29
Start the CDS..................................................................................................................... 29
Stop the CDS..................................................................................................................... 30
Flush the CDS....................................................................................................................30
4 Operating Instructions — User Workflows ..........................................................................34
5 Operating Instructions—Device Configuration....................................................................36
Add Devices............................................................................................................................36
Deactivate Devices................................................................................................................. 37
6 Service and Maintenance Information ................................................................................. 38
Recommended Maintenance Schedule.................................................................................. 38
Clean the Surfaces..................................................................................................................40
Clean the Front-End................................................................................................................41
Symptoms of Contamination.............................................................................................. 41
Required Materials............................................................................................................. 41
Cleaning Best Practices..................................................................................................... 42
Prepare the Mass Spectrometer........................................................................................ 44
Clean the Curtain Plate...................................................................................................... 45
Clean the Front of the Orifice Plate....................................................................................46
Put the Mass Spectrometer Back in Service......................................................................46
Empty the Source Exhaust Drain Bottle..................................................................................47
Replace the Check Valve and Flow Module............................................................................49
Replace the CDS Bottle Intake Filters.....................................................................................50
Inspect the Roughing Pump Oil Level.....................................................................................51
Storage and Handling............................................................................................................. 52
Move the Mass Spectrometer................................................................................................. 53
Open the Dress Panel........................................................................................................60
7 Mass Spectrometer Troubleshooting...................................................................................61
A Recommended Calibration Ions........................................................................................... 67
APCI Calibration Ions..............................................................................................................67
ESI Calibration Ions................................................................................................................ 69
B Exact Masses and Chemical Formulas................................................................................ 71
C Glossary of Symbols..............................................................................................................73
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D Glossary of Warnings............................................................................................................ 79
Contact Us.................................................................................................................................. 81
Customer Training...................................................................................................................81
Online Learning Center...........................................................................................................81
SCIEX Support........................................................................................................................81
CyberSecurity..........................................................................................................................81
Documentation........................................................................................................................81
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Operational Precautions and
Limitations 1
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, for information about the symbols and conventions used in the
laboratory environment, on the system, and in this documentation, refer to the section:
Glossary of Symbols. For site requirements, including mains supply, source exhaust, ventilation,
compressed air, nitrogen, and roughing pump requirements, refer to the document: Site Planning
Guide.
General Safety Information
To prevent personal injury or system damage, read, understand, and obey all safety precautions
and warnings in this document, the manufacturer chemical safety data sheets (SDSs), and
product label information. 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 practiced. Ultimately, the user and the organization are
responsible for compliance with federal, state, provincial, and local EHS regulations and
maintaining a safe laboratory environment.
Refer to the appropriate laboratory reference material and standard operating procedures.
Documentation Symbols and Conventions
The following symbols and conventions are used throughout the guide.
DANGER! Danger signifies an action that leads to severe injury or death.
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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.
Regulatory Compliance
This system complies with the regulations and standards listed in this section. For dated
references, refer to the Declaration of Conformity included with the system and the individual
system components. 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 the section: Electromagnetic Interference.
•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 the section: Electromagnetic Interference.
•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:
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• EN 61326-1
• EN 55011 (Class A)
Refer to the section: Electromagnetic Compatibility.
•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 Directive 2012/96/EEC, as implemented in EN 40519. Refer to the section: Waste
Electrical and Electronic Equipment.
•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
International
•Electromagnetic Compatibility (EMC):
• IEC 61326-1
• IEC CISPR 11 (Class A)
• IEC 61000-3-2
• IEC 61000-3-3
Refer to the section: Electromagnetic Compatibility.
•Safety:
• IEC 61010-1
• IEC 61010-2-061
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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 decrease the chance of
a tripping hazard.
For information about system electrical specifications, refer to the document: Site Planning
Guide.
Mains Supply
Connect the system to a compatible 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.
WARNING! Electrical Shock Hazard. Use only the mains supply cables
supplied with the system. Do not use mains supply 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 examined by a qualified electrician before the system is
connected.
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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 reinforces the safety configuration specified by SCIEX.
Chemical Precautions
WARNING! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical
Hazard. Determine whether decontamination is required before cleaning
or maintenance. If radioactive materials, biological agents, or toxic
chemicals have been used with the system, then the customer must
decontaminate the system before cleaning or maintenance.
WARNING! Environmental Hazard. Do not dispose of system components in
municipal waste. Follow local regulations when disposing of components.
WARNING! Biohazard or 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. For the health and safety precautions that must be followed for a chemical,
refer to the document: Safety Data Sheet. For storage information, refer to the document:
Certificate of Analysis. To find a SCIEX Safety Data Sheet or Certificate of Analysis, go to
sciex.com/tech-regulatory.
• Always wear assigned personal protective equipment, including powder-free gloves, safety
glasses, and a laboratory coat.
Note: Nitrile or neoprene gloves are recommended.
• Work in a well-ventilated area or fume hood.
• 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. There is a potential risk of personal injury
if proper procedures for handling and disposal of chemicals are not followed.
• Avoid skin contact with chemicals during cleaning, and wash hands after use.
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• 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, and radioactive materials.
• (Recommended) Use secondary containment trays beneath the roughing pump, the solvent
bottles, and the waste container to capture potential chemical spills.
System Safe Fluids
The following fluids can safely be used with the system.For information about safe cleaning
solutions, refer to the section: Required Materials.
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.
Note: Use only new, freshly prepared LC-MS-grade or better solvents for the LC mobile phases.
•Organic Solvents
• LC-MS-grade acetonitrile; up to 100%
• LC-MS-grade methanol; up to 100%
• LC-MS-grade isopropanol; up to 100%
• LC-MS-grade or higher water; up to 100%
• Tetrahydrofuran; up to 100%
• Toluene and other aromatic solvents; up to 100%
• Hexanes; up to 100%
•Buffers
• Ammonium acetate; less than 100 mM
• Ammonium formate; less than 100 mM
• Phosphate; less than 1%
•Acids and Bases
• Formic acid; less than 1%
• Acetic acid; less than 1%
• Trifluoroacetic acid (TFA); less than 1%
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• 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! Ionizing 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! Ionizing 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. Examine the exhaust tubing regularly 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! Ionizing Radiation Hazard, Biohazard, or Toxic Chemical
Hazard. Do not use the ion source without 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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WARNING! Puncture Hazard, Ionizing 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 in
the equipment will be present in the source exhaust output. Exhaust from
equipment should be vented from the room. Dispose of sharps following
established laboratory safety procedures.
Physical Precautions
WARNING! Lifting Hazard. Use a mechanical lifting device to lift and move the
mass spectrometer. If the mass spectrometer must be moved manually, then at
least nine people are required to move the X500R system safely. Ten people
are required to move the X500B system safely. Follow established safe lifting
procedures. We recommend the use of a professional moving service. For the
weights of system components, refer to the document: Site Planning Guide.
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 document: 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.
WARNING! Environmental Hazard. Follow established procedures for disposal
of biohazardous, toxic, radioactive, and electronic waste. The customer
is responsible for disposal of hazardous substances, including chemicals,
waste oils, and electrical components, in accordance with local laws and
regulations.
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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 the test.
Performance Criteria B (Criteria B): Equipment may experience loss of function (one or
more) during the test but shall operate as intended with some degradation of performance and
functions self-recoverable after the test.
Performance Criteria C (Criteria C): Equipment may experience loss of function (one or
more) during the test but shall operate as intended with some degradation of performance and
functions recoverable by an operator after the 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 operate as intended. If the power supply line is subject to high electrical
noise, then install a surge protector.
Electromagnetic Interference
Group 1 Equipment: This equipment is classified as industrial, scientific, and medical (ISM)
equipment that might use RF energy for internal operation.
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.
CAUTION: Potential Radio Interference. This equipment is not intended for use in
residential environments and may not provide adequate protection to radio reception in
such environments.
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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. Follow established procedures for disposal
of biohazardous, toxic, radioactive, and electronic waste. The customer
is responsible for disposal of hazardous substances, including chemicals,
waste oils, and electrical components, in accordance with local laws and
regulations.
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 the section: Storage and Handling.
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.
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. SCIEX might not
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cover the damage to a system under warranty if it is serviced by personnel not authorized by
SCIEX.
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
Safe Environmental Conditions
The system is designed to operate safely under these conditions:
• Indoors
• Altitude: Up to 2,000 m (6,560 ft) above sea level
• Ambient temperature: 5 °C (41 °F) to 40 °C (104 °F)
• Relative humidity: 20% to 80%, non-condensing
• 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 2
Performance Specifications
The system is designed to meet specifications under these conditions:
• An ambient temperature of 15 °C to 26 °C (59 °F to 78.8 °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 from 20% to 80%, non-condensing
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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.
WARNING! Lifting Hazard. Use a mechanical lifting device to lift and move the
mass spectrometer. If the mass spectrometer must be moved manually, then at
least nine people are required to move the X500R system safely. Ten people
are required to move the X500B system safely. Follow established safe lifting
procedures. We recommend the use of a professional moving service. For the
weights of system components, refer to the document: Site Planning Guide.
WARNING! Crushing Hazard. Wear protective footwear when moving heavy
objects.
Use the system indoors in a laboratory that complies with the environmental conditions
recommended in the mass spectrometer document: Site Planning Guide.
If the system is used in an environment or in a manner not prescribed by the manufacturer, then
the performance and 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 outside the recommended environmental conditions or with unauthorized
modifications. Contact an FSE for information on servicing the system.
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Principles of Operation 2
The system is designed for the qualitative and quantitative analysis of chemical species.
This section includes information about the mass spectrometer. For an overview of the ion
source, refer to the document: Turbo V Ion Source Operator Guide.
System Overview
WARNING! Lifting Hazard. Use a mechanical lifting device to lift and move the
mass spectrometer. If the mass spectrometer must be moved manually, then at
least nine people are required to move the X500R system safely. Ten people
are required to move the X500B system safely. Follow established safe lifting
procedures. We recommend the use of a professional moving service. For the
weights of system components, refer to the document: Site Planning Guide.
The X500 QTOF system includes the following components:
• A X500 QTOF mass spectrometer with a roughing pump.
• A Turbo V ion source that uses either the twin electrospray ionization (ESI) probe or the twin
atmospheric pressure chemical ionization (APCI) probe. Refer to the document: Turbo V Ion
Source Operator Guide.
• A SCIEX-supplied computer and monitor with the control software for instrument
optimization, acquisition method development, data acquisition, and processing. For
computer specifications and requirements, refer to the software documentation.
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Hardware Overview
Figure 2-1 Front and Right Side View (X500B)
Item Description
1 Diverter valve in standard location. Refer to Diverter Valve
2 Alternate (left) location for diverter valve. For more information, contact an
FSE.
3 Ion source. Refer to the ion source Operator Guide.
4 Calibrant bottles. Refer to Replace the CDS Bottle.
5 Panel symbols. Refer to Panel Symbols.
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Figure 2-2 Back and Left Side View (X500B)
Item Description
1 Left bulkhead. Contains the gas, vacuum, and communication connections.
2 Vent button. Refer to Shut Down and Vent the System.
3 Sources connection. Some ion sources connect to this port.
4 AUX IO connection. Not used.
5 Ethernet connection. Used for communication with the acquisition computer.
6 Zero air gas supply
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