Agilent Technologies Triple Quadrupole LC/MS User manual

Agilent Triple Quadrupole LC/MS System
User Guide

Notices
Document Identification
D0037077 Revision A.00
October 2023
Copyright
© Agilent Technologies, Inc. 2023
No part of this manual may be
reproduced in any form or by any means
(including electronic storage and retrieval
or translation into a foreign language)
without prior agreement and written
consent from Agilent Technologies, Inc.
as governed by United States and
international copyright laws.
Agilent Technologies, Inc.
5301 Stevens Creek Blvd.
Santa Clara, CA 95051
Warranty
The material contained in this document
is provided “as is,” and is subject to being
changed, without notice, in future
editions. Further, to the maximum extent
permitted by applicable law, Agilent
disclaims all warranties, either express or
implied, with regard to this manual and
any information contained herein,
including but not limited to the implied
warranties of merchantability and fitness
for a particular purpose. Agilent shall not
be liable for errors or for incidental or
consequential damages in connection
with the furnishing, use, or performance
of this document or of any information
contained herein. Should Agilent and the
user have a separate written agreement
with warranty terms covering the
material in this document that conflict
with these terms, the warranty terms in
the separate agreement shall control.
Technology Licenses
The hardware and/or software described
in this document are furnished under a
license and may be used or copied only in
accordance with the terms of such
license.
Restricted Rights Legend
U.S. Government Restricted Rights.
Software and technical data rights
granted to the federal government
include only those rights customarily
provided to end user customers. Agilent
provides this customary commercial
license in Software and technical data
pursuant to FAR 12.211 (Technical Data)
and 12.212 (Computer Software) and, for
the Department of Defense, DFARS
252.227-7015 (Technical Data -
Commercial Items) and DFARS
227.7202-3 (Rights in Commercial
Computer Software or Computer
Software Documentation).
Safety Notices
CAUTION
A CAUTION notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly
performed or adhered to, could
result in damage to the product or
loss of important data. Do not
proceed beyond a CAUTION
notice until the indicated
conditions are fully understood
and met.
WARNING
A WARNING notice denotes a
hazard. It calls attention to an
operating procedure, practice, or
the like that, if not correctly
performed or adhered to, could
result in personal injury or death.
Do not proceed beyond a
WARNING notice until the
indicated conditions are fully
understood and met.
Software Revision
This guide is valid for MassHunter 12.1,
until superseded.
Instrument Manufacturing
Manufactured by Agilent
Technologies Singapore Pte. Ltd.
No. 1 Yishun Avenue 7, Singapore
768923
Operating Temperature
Operating Temperature: 15 °C to 35 °C
Storage Temperature: -40 °C to 70 °C

Agilent Triple Quadrupole LC/MS System User Guide 3
In This Guide
This guide provides information on the Ultivo, 6475A, and 6495D LC/TQ systems
running MassHunter Data Acquisition 12.1 or higher.
Additional Resources
User Documentation
Data analysis and library management documentation can be found by scanning
the code or navigating to https://aglt.co/DALibMgmtDocs.
Instrument documentation, step by step videos, and more can be found by
scanning the code or navigating to https://aglt.co/LCMSUserDocs.
Agilent Triple Quadrupole LC/MS Supplies
Make sure that you don’t run out of essential columns and supplies. Use this quick
reference list to keep your shelves stocked by navigating to
https://aglt.co/LCTQSupplies.

4 Agilent Triple Quadrupole LC/MS System User Guide
Technical Support
To find your local sales and support contact, visit the following page:
https://www.agilent.com/en/contact-us/page
For technical support, visit the following page:
https://www.agilent.com/en/support
Agilent Community
To get answers to your questions, join over 10,000 users in the Agilent Community.
Review curated support materials organized by platform technology. Ask
questions to industry colleagues and collaborators. Get notifications on new
videos, documents, tools, and webinars relevant to your work.
https://community.agilent.com/

Agilent Triple Quadrupole LC/MS System User Guide 7
Content
Technical Support 4
1Introduction 12
Sustainability Information 13
Packaging End-of-Life 13
Product End-of-Life 13
Agilent Regulatory Compliance Statement 14
CE Compliance 14
UK Compliance 15
Electromagnetic Compatibility 16
EMC Declaration for South Korea 17
Detachable Power Cord Declaration for Japan 17
Sound Emission Certification for Federal Republic of Germany 17
Waste Electrical and Electronic Equipment (WEEE) Directive 18
2 Hardware Overview 20
Ultivo Triple Quadrupole LC/MS 21
Front view 21
Rear view 22
Calibrant Delivery System 23
6475A Triple Quadrupole LC/MS 24
Front view 24
Side view 25
Calibrant Delivery System 26
6495D Triple Quadrupole LC/MS 27
Front view 27
Side view 28
Calibrant Delivery System 29
Magnets 30

Content
Agilent Triple Quadrupole LC/MS System User Guide 8
Instrument Status Indicator Lights 33
Instrument Status Indicators in Acquisition 34
Ion Sources 35
Electrospray Ionization (ESI) source 35
Agilent Jet Stream (AJS ESI) source 36
Atmospheric Pressure Chemical Ionization (APCI) source 37
Multimode Ionization (MMI) source 38
Nanospray ESI source 39
3Tuning 40
About Tuning 41
Autotune and checktune 42
Starting the Instrument 43
Calibrating the LC/TQ (Checktune) 44
6475A and Ultivo 44
6495D 45
Configure Tune - (6495D only) 46
Calibrating the LC/TQ (Autotune) 48
6475A and Ultivo 48
6495D 49
Generating a Detailed Tune Report 50
6495D 51
Scheduling a Checktune 52
Scheduling an Autotune 54
Advanced Tune - 6495D 56
Diagnostic Tune - 6495D only 57

Content
Agilent Triple Quadrupole LC/MS System User Guide 9
4 Basic Operation 58
Overview 60
Starting Up and Shutting Down the Instrument 61
Starting in Standby mode 61
Turning off the instrument 61
Starting the Mass Hunter Data Acquisition Software 63
MassHunter Data Acquisition windows 64
Instrument Status window 65
Actuals window 65
Chromatogram Plot window 66
Spectrum window 67
Method Editor window 67
Sample Run window 68
Worklist window 68
Method Optimizer window 69
dMRM Method Split window 69
Preparing the LC Modules 70
Switch LC stream to Waste 70
Preparing the Triple Quad LC/MS 74
Performing a checktune or autotune 74
Switching LC stream to MS 74
Monitoring MS baseline and spectral displays 74
Viewing the System Activity Log for events and errors 75

Content
Agilent Triple Quadrupole LC/MS System User Guide 10
Setting Up an Acquisition Method 76
Setting Up and Running a Single Sample 80
Setting Up and Running a Worklist 81
Reviewing Results with Qualitative Analysis 85
Analyzing Data with Quantitative Analysis 86
5 Maintenance 88
Maintenance Overview 90
Routine Tasks 91
Cleaning the spray chamber - daily 91
Checking and filling the calibrant bottle - weekly 92
Cleaning the spray chamber - weekly 93
Flushing the nebulizer - weekly 96
Periodic Tasks 98
Checking the rough pump oil level 98
Draining and replacing the MS40+ pump oil and replacing the filter 99
Draining and replacing the MS120+ pump oil 101
Replacing the MS120+ pump filter 103
Replace Oil Mist/Exhaust Filter - MS120+ 104
Replacing the nitrogen gas filters 105
General Maintenance Tasks 107
Installing or removing the nebulizer 107
Inspecting the nebulizer 109
Adjusting or replacing the nebulizer needle 111
Installing the capillary 113
Removing the capillary (system with a VacShield) 115
Cleaning the capillary 116
Cleaning a clogged capillary 118
Flushing the Calibrant Delivery System 119
Replacing the electron multiplier horn (Ultivo only) 121
Replacing the MS selection valve rotor seal (Ultivo only) 122
Cleaning the corona needle 123

Content
Agilent Triple Quadrupole LC/MS System User Guide 11
Replacing the corona needle 124
Disinfection 125
Source Maintenance 126
Changing to a source that uses a different tuning mix 126
Installing and removing sources 126
Electrospray Ionization (ESI) source 128
Agilent Jet Stream (AJS ESI) source 130
Atmospheric Pressure Chemical Ionization (APCI) source 132
Multimode Ionization (MMI) source 134

Agilent Triple Quadrupole LC/MS System User Guide 12
1Introduction
Sustainability Information 13
Packaging End-of-Life 13
Product End-of-Life 13
Agilent Regulatory Compliance Statement 14
CE Compliance 14
UK Compliance 15
Electromagnetic Compatibility 16
EMC Declaration for South Korea 17
Detachable Power Cord Declaration for Japan 17
Sound Emission Certification for Federal Republic of Germany 17
Waste Electrical and Electronic Equipment (WEEE) Directive 18

1Introduction
Sustainability Information
13 Agilent Triple Quadrupole LC/MS System User Guide
Sustainability Information
Packaging End-of-Life
The Agilent Triple Quadrupole LC/MS system is packaged using cardboard,
polyethylene foam, a polyethylene bag, and a wood pallet. In the US, cardboard is
readily recyclable, and while plastic bags are recyclable, the infrastructure is not
available in the majority of the market. In the US, Agilent is enrolled in the
How2Recycle program (https://how2recycle.info/) to facilitate the
communication of material recycling instructions. In select countries, Agilent
participates in the EU/UK Green DOT Package Recycling Program to support the
take-back and responsible management of the packaging materials at their
end-of-life. In the remaining EU countries, the cardboard is readily recyclable and
the plastic bag, foam and wood pallet are recycled, landfilled, or incinerated
depending on the country and its available infrastructure.
Product End-of-Life
Agilent offers a take-back program for its Triple Quadrupole LC/MS system
customers in US, EU, and UK markets. Refer to
https://www.agilent.com/environment/product/index.shtml for more
information.

1Introduction
Agilent Regulatory Compliance Statement
Agilent Triple Quadrupole LC/MS System User Guide 14
Agilent Regulatory Compliance Statement
CE Compliance
Your Agilent instrument has been designed to comply with the requirements of
the applicable directives of the European Union, such as Electromagnetic
Compatibility (EMC) Directive, Low Voltage Directive (LVD), Machinery Directive
(MD), RoHS Directive, etc.
Agilent has confirmed that each product complies with the relevant Directives by
testing samples against the harmonized EN (European Norm) standards
published on the Official Journal of the European Union (OJEU).
Proof that a product complies with these directives is indicated by:
•the CE Marking appearing on the rear of the product, and
•the documentation package that accompanies the product containing a copy
of the Declaration of Conformity. The Declaration of Conformity is the legal
declaration by Agilent that the product complies with the relevant directives
listed above, and shows the EN standards to which the product was tested to
demonstrate compliance.

1Introduction
UK Compliance
15 Agilent Triple Quadrupole LC/MS System User Guide
UK Compliance
Your Agilent instrument has been designed to comply with the requirements of
the applicable regulations of the United Kingdom, such as The Electromagnetic
Compatibility Regulations 2016, The Electrical Equipment (Safety) Regulations
2016, The Supply of Machinery (Safety) Regulations 2008, The Restriction of the
Use of Certain Hazardous Substances in Electrical and Electronic Equipment
Regulations 2012, etc.
Agilent has confirmed that each product complies with the relevant Regulations
by testing samples against the designated standards published on GOV.UK.
Proof that a product complies with these regulations is indicated by:
•the UKCA Marking appearing on the rear of the product, and
•the documentation package that accompanies the product containing a copy
of the Declaration of Conformity. The Declaration of Conformity is the legal
declaration by Agilent that the product complies with the relevant regulations
listed above, and shows the designated standards to which the product was
tested to demonstrate compliance.

1Introduction
Electromagnetic Compatibility
Agilent Triple Quadrupole LC/MS System User Guide 16
Electromagnetic Compatibility
This product conforms to the following regulations on Electromagnetic
Compatibility (EMC) and Radio Frequency Interference (RFI):
•CISPR 11/EN 55011: Group 1, Class A
•EC/EN 61326-1
•AUS/NZ
•Canada ICES-001 (This ISM device complies with Canadian ICES-001. Cet
appareil ISM est conforme à la norme NMB-001 du Canada).
Group 1 ISM equipment Group 1 contains all Industrial, Scientific, and Medical
(ISM) equipment in which there is intentionally generated and/or used
conductively coupled radio- frequency energy which is necessary for the internal
functioning of the equipment itself.
Class A equipment This equipment 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.
This device complies with the requirements of CISPR11, Group 1, Class A as
radiation professional equipment. Therefore, there may be potential difficulties in
ensuring electromagnetic compatibility in other environments, due to conducted
as well as radiated disturbances.
If this equipment does cause harmful interference to radio or television reception,
which can be determined by turning the equipment off and on, the user is
encouraged to try one or more of the following measures:
1Relocate the radio or antenna.
2Move the device away from the radio or television.
3Plug the device into a different electrical outlet, so that the device and the
radio or television are on separate electrical circuits.
4Make sure that all peripheral devices are also certified.
5Make sure that appropriate cables are used to connect the device to
peripheral equipment.
6Consult your equipment dealer, Agilent Technologies, or an experienced
technician for assistance.
Changes or modifications not expressly approved by Agilent Technologies could
void the user’s authority to operate the equipment.

1Introduction
EMC Declaration for South Korea
17 Agilent Triple Quadrupole LC/MS System User Guide
EMC Declaration for South Korea
사용자안내문
This equipment has been evaluated for its suitability for use in a commercial
environment. When used in a domestic environment, there is a risk of radio
interference.
이 기기는 업무용 환경에서 사용할 목적으로 적합성평가를 받은 기기로
서 가정용 환
경에서 사용하는 경우 전파간섭의 우려가 있습니다 .
※ 사용자 안내문은 " 업무용 방송통신기자재 " 에만 적용한다 .
Detachable Power Cord Declaration for Japan
電源 コ ー ド セ ッ ト の取扱い に つ い て （日本国内向け）
製品に は、 同梱 さ れ た電源 コ ー ド セ ッ ト を お使い く だ さ い。 同梱 さ れ た電源
コードセット
は、 他の製品で は使用で き ま せ ん。
Notice - The power cords for Japanese market
Your product must only use the power cord that was shipped with this product.
Do not use this power cord with any other product.
Sound Emission Certification for Federal Republic of
Germany
Sound pressure
Sound pressure Lp < 70 dB(A) according to DIN EN ISO 7779.
Schalldruckpegel
Schalldruckpegel LP < 70 dB(A) nach DIN EN ISO 7779.

1Introduction
Waste Electrical and Electronic Equipment (WEEE) Directive
Agilent Triple Quadrupole LC/MS System User Guide 18
Waste Electrical and Electronic Equipment (WEEE)
Directive
This product complies with the European WEEE Directive marking requirements.
The affixed label indicates that you must not discard this electrical/electronic
product in domestic household waste.
NOTE
Do not dispose of in domestic household waste.
To return unwanted products, contact your local Agilent office or refer to
https://www.agilent.com/environment/product/index.shtml for more
information.

19 Agilent Triple Quadrupole LC/MS System User Guide
This page intentionally left blank.

Agilent Triple Quadrupole LC/MS System User Guide 20
2 Hardware Overview
Ultivo Triple Quadrupole LC/MS 21
Front view 21
Rear view 22
Calibrant Delivery System 23
6475A Triple Quadrupole LC/MS 24
Front view 24
Side view 25
Calibrant Delivery System 26
6495D Triple Quadrupole LC/MS 27
Front view 27
Side view 28
Calibrant Delivery System 29
Magnets 30
Instrument Status Indicator Lights 33
Instrument Status Indicators in Acquisition 34
Ion Sources 35
Electrospray Ionization (ESI) source 35
Agilent Jet Stream (AJS ESI) source 36
Atmospheric Pressure Chemical Ionization (APCI) source 37
Multimode Ionization (MMI) source 38
Nanospray ESI source 39

2 Hardware Overview
Ultivo Triple Quadrupole LC/MS
21 Agilent Triple Quadrupole LC/MS System User Guide
Ultivo Triple Quadrupole LC/MS
Front view
Figure 1. Front view of Ultivo
Ion Source
Status Indicator
CDS Bottle
Right Side
Cover

2 Hardware Overview
Rear view
Agilent Triple Quadrupole LC/MS System User Guide 22
Rear view
Figure 2. Rear view of Ultivo
Circuit Breakers
LAN Connection
8 amp Fuses
Serial Port
Line Voltage
Fore Line
Pump
Fan Shroud
Assembly