Agilent Technologies NovoCyte Quanteon Manual

NovoCyte Quanteon Flow Cytometer
Operator's Guide
For Research Use Only. Not for use in diagnostic procedures.

Notices
Manual Part Number
150135
Third Edition, March 2021
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© Agilent Technologies, Inc. 2021
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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
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WARNING
CAUTION

In This Guide
NovoCyte Quanteon Flow Cytometer Operator's Guide 3
In This Guide
This guide covers following module: NovoCyte Quanteon Flow Cytometer and
associated standard accessories.
1Prologue
This chapter describes the purpose and scope of this guide, symbols used in this
guide, glossary, safety and limitations, Agilent regulatory compliance statement
and technical support information.
2Introduction
This chapter provides overview of NovoCyte Quanteon flow cytometer, including
basic instrument operation principle, system requirements, and system
components.
3Installation
This chapter provides information on how to install NovoCyte Quanteon
instrument and associated standard accessories, including installation warnings,
space and environment requirements, instructions for lifting and carrying, and
installation procedures.
4Instrument Operation
This chapter provides the procedures to operate NovoCyte Quanteon flow
cytometer, including instrument startup, verify and modify instrument
configuration, instrument QC test, and instrument shutdown.
5Running Samples
This chapter describes the typical procedures of running examples on NovoCyte
Quanteon instrument using human peripheral blood lymphocyte subsets analysis
as an example.
6System Maintenance
This chapter describes the procedures to maintain NovoCyte Quanteon flow
cytometer, including scheduled and unscheduled maintenance.
7Troubleshooting

In This Guide
4 NovoCyte Quanteon Flow Cytometer Operator's Guide
This chapter describes general instrument troubleshooting and diagnostic
guidelines.
8Version History
Appendix A: NovoCyte Quanteon Laser and Detection Channel
Configuration
This chapter provides additional information on NovoCyte Quanteon laser and
detection channel configuration.
Appendix B: NovoCyte Quanteon Technical Specifications
This chapter provides technical specifications of NovoCyte Quanteon flow
cytometer and associated standard accessories.

Contents
NovoCyte Quanteon Flow Cytometer Operator's Guide 5
Contents
In This Guide 3
Contents 5
1Prologue 11
Using this Guide 11
Symbols 11
Glossary 14
Safety and Limitations 16
General Safety 17
Ergonomics 19
Electrical Safety 20
Laser Safety 20
Laser Product Classification 21
Biosafety 21
Limitations 22
Agilent Regulatory Compliance Statement 23
CE Compliance 23
Electromagnetic Compatibility 23
EMC Declaration for South Korea 25
Detachable Power Cord Declaration for Japan 25
Sound Emission Certification for Federal Republic of Germany 25
Waste Electrical and Electronic Equipment (WEEE) Directive 25
Regulatory Compliance Identification Number 26
Technical Support 26
2Introduction 29

Contents
6 NovoCyte Quanteon Flow Cytometer Operator's Guide
Overview 29
Basic Principle 29
Optics System 29
Fluidics System 37
Electronics System 41
System Requirements 43
Software 43
Workstation 43
Fluidics Station 43
Compatible Sample Tubes 44
Instrument Reagents 44
QC Particles 44
System Components 44
NovoCyte Quanteon Instrument 45
NovoCyte Workstation and Monitor 46
NovoCyte Fluidics Station II 47
NovoCyte Fluidics Cart (Optional) 49
NovoSampler Q (Optional) 49
3Installation 51
Installation Warnings 51
Space Requirements 52
Environmental Requirements 52
Instruction for Lifting and Carrying 52
Install NovoCyte Quanteon 53
Connect NovoCyte Workstation 54
Connect NovoCyte Fluidics Station II 54

Contents
NovoCyte Quanteon Flow Cytometer Operator's Guide 7
Connect NovoCyte Fluidics Cart (Optional) 55
Connect NovoSampler Q (Optional) 55
Connect Instrument to Power Supply 56
4Instrument Operation 57
Instrument Start-up 57
Pre-Inspection 57
Power on the Instrument 57
Turn on Workstation 58
Add Instrument Reagents 59
Empty Waste 60
Verify and Modify Instrument Configuration 61
View and Verify Instrument Configuration 61
Modify Instrument Configuration 61
Instrument QC Test 68
Instrument Shutdown 68
5Running Samples 71
Overview 71
Create Experiment 72
Define Sample Acquisition Parameters 74
Set Sample Acquisition Conditions 76
Stop Condition 76
Flow Rate 77
Threshold 77
Run Sample 80
Perform Fluorescence Compensation 82
Automatic Fluorescence Compensation 82

Contents
8 NovoCyte Quanteon Flow Cytometer Operator's Guide
Manual Fluorescence Compensation 92
Analyze Data 97
Append Data 101
Delete Data 102
Save Data 102
Import and Export Files 103
6System Maintenance 107
Scheduled Maintenance 107
Preventative Maintenance 108
Replacing Fluidic System Consumables 113
Replace 0.05 µm Sheath Fluid Ultrafiltration (UF) Filter (Optional) 122
Unscheduled Maintenance 125
Debubble 125
Clean the External Surface of the Instrument 126
Decontamination 126
Prime Fluidic System before Long-Term Storage 127
Prime Fluidic System after Long-Term Storage 128
Purge Fluidic System before Shipment 128
Calibrate NovoCyte Fluidics Station II 130
Clean the Optical Filters 131
Clean Fluidic System 132
7Troubleshooting 133
8Version History 137
Appendix A: NovoCyte Quanteon Laser and Detection Channel
Configuration 139
Laser Configuration 139

Contents
NovoCyte Quanteon Flow Cytometer Operator's Guide 9
Detection Channel Configuration 139
Appendix B: NovoCyte Quanteon Technical Specifications 143
NovoCyte Quanteon Technical Specifications 143
NovoCyte Workstation and Monitor Specifications 146
NovoCyte Fluidics Station II Specifications 146

Contents
NovoCyte Quanteon Flow Cytometer Operator's Guide 10
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Prologue
NovoCyte Quanteon Flow Cytometer Operator's Guide 11
1Prologue
This chapter describes the purpose and scope of this guide, symbols used in this
guide, glossary, safety and limitations, Agilent regulatory compliance statement
and technical support information.
Using this Guide
This guide describes the information and procedures to install, operate, maintain,
and troubleshoot NovoCyte Quanteon flow cytometer and associated standard
accessories.
For additional information about NovoExpress software, please refer to
NovoExpress Software Guide. For additional information about NovoSampler Q,
please refer to NovoSampler Q Operator’s Guide. For additional information about
NovoCyte Fluidics Cart, please refer to NovoCyte Fluidics Cart Operator’s Guide.
Symbols
The following table lists the symbols which may be used in this guide.
Table 1 Symbols used in this guide
Symbol
Meaning
Description
BIOHAZARD
This symbol indicates that certain precautions must be
taken when working with potentially infectious
biological specimens and materials.
LASER RADIATION
This symbol indicates that the operation could
potentially cause exposure to laser radiation.
Protective measures should be taken during the
operation.

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12 NovoCyte Quanteon Flow Cytometer Operator's Guide
Table 1 Symbols used in this guide
WARNING
This symbol indicates that improper or unsafe
operation could result in instrument damage, data loss,
and personal injury.
SHOCK HAZARD
This symbol indicates that the operation has a risk of
electric shock.
The following table lists the symbols which may appear on the instrument:
Table 2 Symbols appear on the instrument
Symbol
Meaning
Description
KC Marking
This symbol indicates compliance with Korea EMC
regulation requirements for Broadcasting and
Communication Equipment.
RCM Marking
This symbol indicates compliance with EMC regulations in
Australia and New Zealand.
CE marking
This symbol indicates conformity with the provisions of
relevant directives for CE marking.
SGS marking
This symbol indicates SGS has evaluated the safety of this
product to comply with the provisions of relevant
standards for US and Canada.
WEEE Symbol
This symbol indicates conformity with Directive
2012/19/EU on Waste Electrical and Electronic Equipment
(WEEE).
Environment Friendly
Use Period (EFUP)-
China RoHS label
This symbol indicates the product contains certain
hazardous substances and can be used safely during its
environmental protection use period (40 years) which
should enter into the recycling system after 40 years.
CAN ICES-
1/NMB-1
Canadian EMC
Regulation
This symbol indicates the product conforms to following
standards:
•CISPR 11/EN 55011: Group 1, Class A
•IEC/EN 61326-1
This ISM device complies with Canadian ICES-001
ISM 1-A
ISM Class A Group 1
Product Statement
This symbol indicates the product conforms to following
standards:

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NovoCyte Quanteon Flow Cytometer Operator's Guide 13
Table 2 Symbols appear on the instrument
•Group 1 ISM equipment: Group 1 contains all ISM
equipment in which there is internationally generated
and/or used conductively coupled radio-frequency
energy which is necessary for the internal functioning
of the equipment itself.
•Class A Equipment: equipment 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 product complies with the requirement of CISPR 11,
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.
COM
COM communication port
USB
USB communication port
NET
Network communication port
The following precaution labels appear on Agilent flow cytometer and associated
accessories to indicate a potential hazard. Please do not remove these labels. Use
appropriate precaution to avoid injury by the indicated hazard. Please refer to
Safety and Limitations in this guide for more information.
Table 3 Precaution labels appear on Agilent Flow Cytometer and Accessories
Symbol
Meaning
Description
BIOHAZARD
This symbol indicates that certain precautions
must be taken when working with potentially
infectious biological specimens and materials.
SHOCK HAZARD
This symbol indicates that the operation has a
risk of electric shock.
LASER RADIATION
This symbol indicates that the operation could
potentially cause exposure to laser radiation.
Protective measures should be taken during
the operation.
MOVING PARTS
This label indicates the moving parts in the
instrument. Be careful during the operation.

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14 NovoCyte Quanteon Flow Cytometer Operator's Guide
Table 3 Precaution labels appear on Agilent Flow Cytometer and Accessories
CLASS I LASER
PRODUCT
This symbol indicates the laser is a Class I
product (see Laser Product Classification in
this guide for more information.)
PINCH HAZARD
This symbol indicates the part may cause
potential pinch hazard. Keep hands and fingers
away from the part.
WARRANTY VOID
This symbol indicates that the user is not
allowed to remove or disassemble the parts.
Doing so will void the warranty on the product.
Glossary
The following table lists the glossary which may appear in this guide.
Table 4 Glossary used in this guide
Term
Definition
ADC
Analog-to-Digital Converter
Alexa Fluor
Alexa Fluor Dye
AmCyan
AmCyan Fluorescent Protein Dye
APC
Allophycocyanin Dye
APC-Cy7
APC and Cyanine 7 Tandem Dye
APD
Avalanche Photodiode
BP
Band Pass
BUV
Brilliant Ultraviolet
BV
Brilliant Violet
BXXX
488 nm (blue) laser excited fluorescence channels or photodetectors. For example,
B572 denotes the 572/28 channel excited by the 488 nm laser, and so on.
CSV
Comma-Separated Values

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NovoCyte Quanteon Flow Cytometer Operator's Guide 15
Table 4 Glossary used in this guide
CV
Coefficient of Variation
EYFP
Enhanced Yellow Fluorescent Protein Dye
FCS
Flow Cytometry Standard
FITC
Fluorescein Isothiocyanate Dye
FPGA
Field Programmable Gate Array
FRM
Full Reflection Mirror
FSC
Forward Scatter, Forward Scattered Light
HPCV
Half-Peak Coefficient of Variation
LP
Long Pass
MESF
Molecules of Equivalent Soluble Fluorochrome
MFI
Mean Fluorescence Intensity
Pacific Blue
Pacific Blue Dye
Pacific Orange
Pacific Orange Dye
PD
Photodiode
PE
Phycoerythrin Dye
PE-Alexa Fluor
Phycoerythrin and Alexa Fluor Tandem Dye
PE-Cy5
Phycoerythrin and Cyanine 5 Tandem Dye
PE-Cy5.5
Phycoerythrin and Cyanine 5.5 Tandem Dye
PE-Cy7
Phycoerythrin and Cyanine 7 Tandem Dye
PerCP
Peridinin Chlorophyll Protein Dye
PerCP-Cy5.5
Peridinin Chlorophyll Protein and Cyanine 5.5 Tandem Dye
PerCP-eFluor
Peridinin Chlorophyll Protein and eFluor Tandem Dye
PE-Texas Red
Phycoerythrin-Texas Red Dye
PI
Propidium Iodide Dye
PMT
Photomultiplier Tube
Qdot
Qdot Dye
RXXX
637 nm or 640 nm (red) laser excited fluorescence channels or photodetectors. For
example, R695 denotes the 695/40 channel excited by the 637 nm or 640 nm laser,
and so on.
SD
Standard Deviation
SIP
Sample Injection Probe

Prologue
16 NovoCyte Quanteon Flow Cytometer Operator's Guide
Table 4 Glossary used in this guide
SiPM
Silicon Photo Multiplier
SP
Short Pass
SSC
Side Scatter
TEC
Thermoelectric Cooling
UVXXX
349 nm (ultraviolet) laser excited fluorescence channels or photodetectors. For
example, UV615 denotes the 615/20 channel excited by the 349 nm laser, and so
on.
VXXX
405 nm (violet) laser excited fluorescence channels or photodetectors. For example,
V445 denotes the 445/45 channel excited by the 405 nm laser, and so on.
YXXX
561 nm (yellow) laser excited fluorescence channels or photodetectors. For
example, Y586 denotes the 586/20 channel excited by the 561 nm laser, and so on.
Cy is a trademark of GE Healthcare/Amersham Biosciences.
Brilliant Violet is a trademark of Sirigen Group, Ltd.
Pacific Blue and Pacific Orange are trademarks of Life Technologies Corporation.
Alexa Fluor and Texas Red are registered trademarks of Life Technologies Corporation.
Qdot is a registered trademark of Quantum Dot Corporation.
eFluor is a registered trademark of eBioscience, Inc.
BD Horizon Brilliant Ultraviolet (BUV) is a trademark of Becton, Dickinson and Company or
its affiliates.
PerCP: US patent 4,876,190
APC-Cy7: US patent 5,714,386
PE-Cy7: US patent 4,542,104
Safety and Limitations
Agilent flow cytometers and associated accessories are limited to be operated by
professionals trained by Agilent Technologies or an authorized representative.
Agilent flow cytometer incorporates safety measures to protect the operator.
Please refer to this guide to operate the instrument in strict accordance with the
instructions and in accordance with the provisions of instrument maintenance and
repair. Please ensure that the safety information can be found at any time. The

Prologue
NovoCyte Quanteon Flow Cytometer Operator's Guide 17
instrument may be damaged if it is operated under any conditions that are not
described in this guide.
General Safety
The following general safety precautions must be observed during all phases of
operation of Agilent flow cytometer and associated accessories. Failure to comply
with these precautions or with specific warnings or operation instructions in the
operator's guide violates safety standards of design, manufacture, and intended
use of the instrument. Agilent Technologies assumes no liability for the customer's
failure to comply with these requirements.
CAUTION
Do not use this product in any manner not specified by the manufacturer.
The protective features of this product may be impaired if it is used in a
manner not specified in the operation instructions.
WARNING
Before applying power, verify that all safety precautions are taken according
to the operator's guide of the individual instrument. Verify that the voltage
range and frequency of your power distribution matches to the power
specification of the individual instrument. Never use cables other than the
ones supplied by Agilent Technologies to ensure proper functionality and
compliance with safety or EMC regulations. Make all connections to the unit
before applying power. Note the instrument's external markings are
described in Table 3 of this guide.
WARNING
If your product is provided with a grounding type power plug, the instrument
chassis and cover must be connected to an electrical ground to minimize
shock hazard. The ground pin must be firmly connected to an electrical
ground (safety ground) terminal at the power outlet. Any interruption of the
protective (grounding) conductor or disconnection of the protective earth
terminal will cause a potential shock hazard that could result in personal
injury. Please refer to Electrical Safety of this guide for additional
information.

Prologue
18 NovoCyte Quanteon Flow Cytometer Operator's Guide
WARNING
Do not operate the instrument in the presence of flammable gases or fumes.
WARNING
Do not remove the instrument cover. Only Agilent authorized personnel are
allowed to remove instrument covers. Always disconnect the power cables
and any external circuits before removing the instrument cover.
WARNING
Do not modify the instrument. Do not install substitute parts or perform any
unauthorized modification to the product. Return the product to an Agilent
Sales and Service Office for service and repair to ensure that safety features
are maintained.
WARNING
Instruments that appear damaged or defective should be made inoperative
and secured against unintended operation until they can be repaired by
qualified service personnel.
WARNING
The handling of toxic and hazardous solvents and flammable liquids can
hold health risks. When working with solvents, ensure to observe appropriate
safety procedures (for example, goggles, safety gloves and protective
clothing) as described in the material safety data sheet supplied by the
solvent vendor, especially when toxic or hazardous solvents and flammable
liquids are used. Do not use solvents with an auto-ignition temperature
below 200ºC.
WARNING
When operating the instrument, keep your hands and clothing away from the
instrument. Do not touch the sample injection probe (SIP) when the
instrument is in operation. Mechanical movable parts within the instrument
can pinch or cause injury to hands or fingers.
WARNING
To avoid burns, do not touch the fan guards on the back of the instrument.
The fan guards may get hot during and after instrument operation.

Prologue
NovoCyte Quanteon Flow Cytometer Operator's Guide 19
CAUTION
The data is automatically stored on the workstation’s hard drive. But if the
workstation hard drive data are deleted or the hard drive is corrupted, the
data can be unrecoverable. Please regularly backup the data to a server or
other mobile storage devices.
WARNING
To prevent accidents and to ensure the quality of the data after Agilent
Technologies professionals install the instrument, moving the instrument is
not recommended. If you need to move the instrument, be sure to contact
Agilent Technologies professionals. Agilent Technologies professionals will
re-install the instrument in accordance with requirements and ensure the
optimal operation of the instrument.
WARNING
The sample injection probe is a mechanical movable part and may pinch or
injure your fingers. To prevent accidents, do not put your hand underneath
the sample injection probe during the sample acquisition process. Also,
when placing or removing the sample tube, do not put your hand underneath
the sample injection probe.
CAUTION
Do not place any heavy objects on top of the instrument. Doing so may
cause damage to the instrument, resulting in compromised instrument
performance and abnormal data.
WARNING
Regarding the restrictions on the use of reagents, please see the relevant
package insert and technical data sheet of the reagents.
Ergonomics
This product is large and the weight is more than 51 lb (23 kg).
WARNING
To avoid injury to personnel and potential equipment damage, use sufficient
assistance and proper lifting techniques when moving or lifting the product.

Prologue
20 NovoCyte Quanteon Flow Cytometer Operator's Guide
Electrical Safety
WARNING
To prevent electrical shock and instrument damage, please follow the
guidelines listed below.
•Unless otherwise specified, turn off the power switch and unplug the power
cord before servicing the instrument.
•Connect the instrument only to an approved power source. If damaged
electrical wires, plugs, or cables are detected, promptly contact your Agilent
Technologies representative for replacement.
•Only use the power outlets that are located at a conveniently accessible
location so that the instrument, workstation, and monitor can be easily
plugged to and unplugged from the power outlets.
•To ensure your safety, the power cord must be inserted in the three-pin socket
with a protective ground connection. Please make sure the three-pin socket
connects to the ground reliably.
•If leaks are detected, immediately turn off the power by pressing and holding
the power button on the front of the instrument for about 6-7 seconds.
Immediately contact your local Agilent Technologies representative for
support.
•If the power cord becomes frayed, broken, or damaged, please contact Agilent
Technologies. Do not replace with a lower rated cord. If the equipment is been
used in a manner which is not specified by Agilent Technologies, the
protection provide by the equipment may be impaired.
Laser Safety
Laser or laser systems emit intense, coherent electromagnetic radiation that has
the potential of causing irreparable damage to human skin and eyes. The main
hazard of laser radiation is direct or indirect exposure of the eye to thermal
radiation from the visible and near infrared region (325 - 1400 nm). Direct eye
contact with the laser will burn the cornea, retina, or both injury and may lead to
possible blindness.
There are other potentially serious hazards in other spectral regions. Excessive
ultraviolet exposure produces an intolerance to light (photophobia) accompanied
by redness, a tearing discharge from the mucous membrane lining the inner
surface of the eyelid (conjunctiva), shedding of the corneal cell layer surface
(exfoliation), and stromal haze. These symptoms are associated with