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,
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.
(GEN-IDV-09-10816-D)
For Research Use Only. Not for use in Diagnostic Procedures.
Trademarks and/or registered trademarks mentioned herein, including associated logos, are the property
of AB Sciex Pte. Ltd., or their respective owners, in the United States and/or certain other countries (see
sciex.com/trademarks).
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
Contents
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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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