Applied Biosystems CytoFluor 4000 Series User manual

Artisan Technology Group is your source for quality
new and certied-used/pre-owned equipment
• FAST SHIPPING AND
DELIVERY
• TENS OF THOUSANDS OF
IN-STOCK ITEMS
• EQUIPMENT DEMOS
• HUNDREDS OF
MANUFACTURERS
SUPPORTED
• LEASING/MONTHLY
RENTALS
• ITAR CERTIFIED
SECURE ASSET SOLUTIONS
SERVICE CENTER REPAIRS
Experienced engineers and technicians on staff
at our full-service, in-house repair center
WE BUY USED EQUIPMENT
Sell your excess, underutilized, and idle used equipment
We also offer credit for buy-backs and trade-ins
www.artisantg.com/WeBuyEquipment
REMOTE INSPECTION
Remotely inspect equipment before purchasing with
our interactive website at www.instraview.com
LOOKING FOR MORE INFORMATION?
Visit us on the web at www.artisantg.com for more
information on price quotations, drivers, technical
specications, manuals, and documentation
Contact us: (888) 88-SOURCE | [e-mail] | www.artisantg.com
SM
View
Instra

DRAFT August 30, 2001 6:30 pm
FLORFM.FM5
CytoFluor®Series 4000
Fluorescence Multi-Well Plate Reader
User Guide
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

© Copyright 1997, 2001, Applied Biosystems. All rights reserved.
For Research Use Only. Not for use in diagnostic procedures.
Information in this document is subject to change without notice. Applied Biosystems assumes no responsibility for any
errors that may appear in this document. This document is believed to be complete and accurate at the time of publication. In
no event shall Applied Biosystems be liable for incidental, special, multiple, or consequential damages in connection with or
arising from the use of this document.
ABI PRISM, Applied Biosystems, BioCAD, CytoFluor, GeneScan, INTEGRAL, POROS, Procise and Tropix are registered
trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other countries.
AB (Design), Applera, Biospectrometry, CytoCalc, Data Explorer, Expedite, FMAT, Mariner, Pioneer, Proteomics Solution
1, SPRINT, VISION, and Voyager are trademarks of Applera Corporation or its subsidiaries in the U.S. and certain other
countries.
ICAT is a trademark of the University of Washington in the U.S. and certain other countries, exclusively licensed to Applied
Biosystems Group of Applera Corporation.
MDS is a registered trademark and SCIEX is a trademark of MDS, Inc.
TaqMan is a registered trademark of Roche Molecular Systems, Inc.
Microsoft, MS, Windows, and MS-DOS are registered trademarks of Microsoft Corporation.
IBM is a registered trademark of International Business Machines Corporation.
Attophos is a trademark of JBL Scientific.
BODIPY, PicoGreen, Texas Red, SNARF, and SNAFL are registered trademarks of Molecular Probes, Inc.
AlamarBlue is a registered trademark of AccuMed International, Inc.
All other trademarks are the sole property of their respective owners.
Printed in the USA, 07/2001
PartNumber PH601380 Rev.A
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

WARNING
For continued protection against fire hazard, replace fuses with those of the same
type and rating.
AVERTISSEMENT
Remplacez les fusibles par ceux de même type et puissance pour éviter les risques
d’incendie.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

US Safety and EMC (Electromagnetic Compliance) Standards
Safety
This instrument has been tested to and complies with standard ANSI/UL 3101-1, “Electrical
Equipment for Laboratory Use; Part 1: General Requirements”, 1st Edition. It is an ETL Testing
Laboratories listed product.
EMC
This device complies with Part 15 of the FCC Rules. Operation is subject to the following two
conditions: (1) This device may not cause harmful interference, and (2) this device must accept
any interference received, including interference that may cause undesired operation.
Warning: Changes or modifications to this unit not expressly approved by the party responsible for
compliance could void the user’s authority to operate the equipment.
Note: 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 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 instruction manual, may cause harmful interference to radio communications. Operation of this
equipment in a residential area is likely to cause harmful interference in which case the user will be required
to correct the interference at his own expense.
Note: Shielded cables must be used with this unit to ensure compliance with the Class A FCC limits.
Canadian Safety and EMC (Electromagnetic Compliance) Standards
Safety
This instrument has been tested to and complies with standard C22.2 No. 1010-1-92, “Safety
Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use; Part 1:
General Requirements”. It is an ETL Testing Laboratories listed product.
Sécurité
Cet instrument a été vérifié avec la norme C22.2 No. 1010-1-92, «Spécifications de sécurité du
matériel électrique utilisé pour les mesures, les contrôles et dans les laboratoires ; Partie 1 :
Spécifications générales», et il est conforme à cette norme. C’est un produit homologué par les
ETL Testing Laboratories.
EMC
This Class A digital apparatus meets all requirements of the Canadian Interference-Causing
Equipment Regulations.
Cet appareil numérique de la classe A respecte toutes les exigences du Règlement sur le
materiel brouilleur du Canada.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

European Safety and EMC (Electromagnetic Compliance) Standards
Declaration of Conformity
Application of Council Directive(s): 73/23/EEC “Low Voltage”
89/336/EEC “Electromagnetic Compatibility”
Standard(s) to which conformity is
declared: EN61010-1 “Safety Requirements for Electrical Equipment for Mea- surement, Control and Laboratory Use”
EN55011:1991, Group 1, Class B “Radiated Emissions”
EN50082-1:1992 “Generic Immunity”
Manufacturer’s Name: Applied Biosystems
Manufacturer’s Address: 500 Old Connecticut Path
Framingham, Massachusetts 01701 USA
Type of Equipment: Laboratory Instrumentation
Model Name: CytoFluor Series 4000 Fluorescence Multi-Well Plate Reader
Model Number MIFS0C2TR
Serial Number: FX6CMQ378P and later
Year of Manufacture: 1997
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Application of Council Directive(s): 73/23/EEC “Low Voltage”
89/336/EEC “Electromagnetic Compatibility”
Standard(s) to which conformity is
declared: EN61010-1 “Safety Requirements for Electrical Equipment for Mea- surement, Control and Laboratory Use”
EN55011:1991, Group 1, Class B “Radiated Emissions”
EN50082-1:1992 “Generic Immunity”
Manufacturer’s Name: Applied Biosystems.
Manufacturer’s Address: 500 Old Connecticut Path
Framingham, Massachusetts 01701 USA
Type of Equipment: Laboratory Instrumentation
Model Name: CytoFluor Series 4000 Fluorescence Multi-Well Plate Reader with
Temperature Control
Model Number: MIFS0C2TC
Serial Number: FX6CMQ380P and later
Year of Manufacture: 1997
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Table of Contents
CytoFluorUser’sGuide vii
Table of Contents
How to Use This Guide............................................................................xi
Chapter 1 Overview of the CytoFluor System
1.1 What is the CytoFluor System? .................................................. 1-2
1.2 How Does It Work? ................................................................. 1-4
1.3 Overview of the System Process and Chapter References................ 1-5
Chapter 2 Getting Started
2.1 Parts of the CytoFluor System.................................................... 2-2
2.2 The CytoFluor Scanner ............................................................ 2-5
2.3 Computer System Requirements ................................................ 2-9
2.4 Setting Up Your System........................................................... 2-10
2.4.1 Installing the Fuses ...............................................................2-10
2.4.2 Removing the Shipping Restraints ........................................2-13
2.4.3 Connecting the Scanner to Your Computer ...........................2-15
2.4.4 Installing the Software ...........................................................2-18
2.5 Checking the System.............................................................. 2-21
2.5.1 Starting Up the CytoFluor System .........................................2-21
2.5.2 Accessing the Maintenance Screen ......................................2-23
2.5.3 Checking Scanner Settings ...................................................2-24
2.5.4 Running System Diagnostics ................................................2-24
2.5.5 Returning to the Main Setup Screen .....................................2-25
2.6 Shutting Down the System ....................................................... 2-27
Chapter 3 Scanning Operations
3.1 Creating a New File................................................................. 3-2
3.1.1 Creating a New, Original File ................................................. 3-3
3.1.2 Accessing a Previously Saved File ......................................... 3-4
3.2 Setting Scan Parameters .......................................................... 3-7
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Table of Contents
viii Applied Biosystems
3.3 Setting Up Multiple Scans in a Cycle .......................................... 3-16
3.4 Saving Scan Parameters ......................................................... 3-20
3.5 Controlling the Temperature ..................................................... 3-22
3.6 Scanning Plates .................................................................... 3-24
Chapter 4 Displaying, Printing, and Exporting Data
4.1 Overview of Post Processing ..................................................... 4-2
4.1.1 Using the Scaling Screen ....................................................... 4-2
4.1.2 Using Scaling Features .......................................................... 4-4
4.1.3 Using the Kinetics Rate Calculation Screen ..........................4-10
4.1.4 Using Kinetics Features ........................................................4-12
4.1.4.1 Setting Kinetics Parameters .................................4-12
4.1.4.2 Plotting Kinetics Data ...........................................4-14
4.2 Saving Post Processing Selections ............................................ 4-21
4.3 Printing Data......................................................................... 4-21
4.4 Exporting Files ...................................................................... 4-22
4.5 Creating an Export Format ....................................................... 4-26
4.5.1 Including Header Information ................................................4-27
4.5.2 Including Data in a Table Format ...........................................4-29
4.5.3 Including Data in a Linear Format .........................................4-30
Chapter 5 Setting the Plate Layout or Auto Scale
Parameters
5.1 Overview of the Plate Layout Screen ........................................... 5-2
5.2 Accessing the Plate Layout Screen ............................................. 5-4
5.3 Plate Layout Overview ............................................................. 5-6
5.4 Using Well Types Options ......................................................... 5-8
5.5 Entering Concentration Parameters............................................ 5-15
5.6 Defining Plates...................................................................... 5-16
5.6.1 Preparing the Scanner ..........................................................5-16
5.6.2 Defining a Plate ....................................................................5-17
5.6.3 Deleting a Plate ....................................................................5-20
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Table of Contents
CytoFluorUser’sGuide ix
5.7 Using 384 Well Plates............................................................. 5-21
5.7.1 Defining the 384 Well Plate ...................................................5-21
5.7.2 Selecting the Read Pattern Option ........................................5-22
5.8 Setting Auto Scale Parameters.................................................. 5-25
5.9 Exiting the CytoFluor System.................................................... 5-28
Chapter 6 Customizing the CytoFluor System
6.1 Replacing Optical Filters........................................................... 6-2
6.1.1 Changing the Excitation and Emission Filters ......................... 6-2
6.1.2 Changing the Filter Settings in the Maintenance Screen ........ 6-8
6.2 Testing the Scanner................................................................ 6-10
6.3 Checking or Changing the Communication Port............................. 6-12
6.4 Setting the Lamp Saver Time.................................................... 6-13
6.5 Configuring the Scanner for Top or Bottom Plate Reading................ 6-14
6.5.1 Changing the Probe Position .................................................6-14
6.5.2 Checking and Adjusting Probe Height in a Temperature-Ready
Scanner ................................................................................6-17
6.5.2.1 Checking and Adjusting Probe Height in Bottom-Read
Position (TR Models) ............................................6-17
6.5.2.2 Checking and Adjusting Probe Height in Top-Read
Position (TR Models) ............................................6-19
6.5.3 Checking and Adjusting Probe Height in a Temperature Control
Scanner ................................................................................6-21
6.5.3.1 Checking and Adjusting Probe Height in Bottom-Read
Position (TC Models) ............................................6-21
6.5.3.2 Checking and Adjusting Probe Height in Top-Read
Position (TC Models) ............................................6-23
Chapter 7 Maintaining the CytoFluor System
7.1 Cleaning the Scanner .............................................................. 7-2
7.2 Cleaning the Rails................................................................... 7-2
7.3 Replacing the Air Filter............................................................. 7-4
7.4 Replacing the Lamp................................................................. 7-5
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Table of Contents
x Applied Biosystems
Chapter 8 Accessing Technical Information
8.1 Specifications ........................................................................ 8-2
8.2 Minimum Computer Requirements (You Supply)............................. 8-3
8.3 Optical Sets for Fluorophores .................................................... 8-4
8.4 CytoFluor Standard Filter Sets ................................................... 8-6
8.5 Ordering Information................................................................ 8-7
Appendix A Introduction to Windows.........................................A-1
Appendix B Error Messages..............................................................B-1
Appendix C Warranty/Service Information................................C-1
C.1 Limited Product Warranty.......................................................... C-1
C.1 Damages, Claims, Returns........................................................ C-4
Appendix D Plate Scan Patterns .....................................................D-1
Appendix E Technical Support and Training...........................E-1
Glossary
Index
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

CytoFluor User’s Guide xi
1
How to Use This Guide
Purpose of this
guide Applied Biosystems CytoFluor Series 4000 Multi-Well
Fluorescence Reader User’s Guide describes how to set up,
use, and maintain the CytoFluor® Series 4000 Fluorescence
Multi-Well Plate Reader. This system enables you to scan
data on soluble and cell-associated fluorescence. The entire
system consists of a scanner and the CytoFluor software for
Microsoft®Windows®. The software runs on a PC that you
provide and enables you to control and maintain the scanner.
Audience This manual is written for CytoFluor system users. You should
be familiar with using a PC and Windows applications. For
your convenience, there is a glossary of terms at the back of
this document. If you need more information on Windows,
refer to the manuals provided with the Windows software.
Structure of
this guide Applied Biosystems CytoFluor Series 4000 Multi-Well
Fluorescence Reader User’s Guide is divided into chapters.
Each chapter page is marked with a tab and a header to help
you locate information within the chapter.
The table below describes the material covered in each
chapter.
Chapter 1,
Overview of the
CytoFluor System
Provides an overview of the CytoFluor
system process.
Chapter 2,Getting
Started Describes how to get started. For example, it defines the function of the
scanner parts and describes how to
set it up. It also contains steps to
install the software and check the
system.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

How to Use This Guide
xii Applied Biosystems
1Chapter 3,
Scanning
Operations
Defines how to create a new file,
access a previously saved file, and set
up the scan parameters. It also
contains details on how to scan a
plate.
Chapter 4,
Displaying,
Printing, and
Exporting Data
Contains steps to use post processing
for data display. It also describes how
to print and export data.
Chapter 5, Setting
the Plate Layout
or Auto Scale
Parameters
Provides details on how to set the
plate layout. For example, it defines
how to assign characteristics to a plate
well or group of wells. It also describes
how to set the auto scale parameters
so the system can scale the data as it
acquires it.
Chapter 6,
Customizing the
CytoFluor System
Describes how to customize the
system. It includes steps to set up and
change filter pairs, test the scanner
drives and lamp, and set the lamp
saver timer.
Chapter 7,
Maintaining the
CytoFluor System
Defines how to maintain the CytoFluor
system. For example, it describes how
to clean the scanner and change the
air filters. It also has steps to change
the lamp when needed.
Chapter 8,
Accessing
Technical
Information
Contains details on the system
specifications and catalog numbers.
Appendix A,
Introduction to
Windows
Provides basic information on how to
use Microsoft Windows and defines
basic Microsoft Windows terms.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

CytoFluor User’s Guide xiii
1
Conventions
General
Conventions The text in this manual uses these typographical conventions:
•Italic text indicates a new term in the text, usually
followed by a definition.
•Bold text indicates menu and option names in steps.
Notes, Cautions,
and Warnings Notes, Cautions, and Warnings are used for the following
reasons:
NOTE: Informs the user about important information not
critical to operating the system.
CAUTION
Warns the user about possible harm to the system or loss of
data.
Appendix B, Error
Messages Describes and defines CytoFluor system test vectors and error
messages.
Appendix C,
Warranty/Service
Information
Contains warranty, service, and return
information.
Appendix D, Plate
Scan Patterns Provides examples of the scan patterns the CytoFluor system uses
when averaging points taken in a well.
Appendix E,
Technical Support
and Training
Describes how to contact Technical
Support, obtain technical documents,
and obtain customer training
information.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

How to Use This Guide
xiv Applied Biosystems
1WARNING
Warns the user about possible bodily harm.
AVERTISSEMENT
Un avertissement fournit une information indispensable à la
sécurité de l’operateur.
Symbols used on
the system The following symbol appears on the system to alert the user
to warnings. The symbol also appears next to associated
warnings in this document.
Le symbole ci-dessous permet d’alerter l’utilisateur et precede
un avertissement.
Send us your
comments We welcome your comments and suggestions for improving
our manuals. You can send us your comments by e-mail at
T[email protected].
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

CytoFluor User’s Guide 1-1
Overview of the CytoFluor
System 1
®
This chapter includes the following sections:
1.1 What is the CytoFluor System?.............. 1-2
1.2 How Does It Work?............................. 1-4
1.3 Overview of the System Process and
Chapter References............................ 1-5
NOTE: Complete and return the provided CytoFluor ®installation qualification
report. Applied Biosystems must receive your completed installation qualification
report before you can receive technical support and product update information.
The registration number for your system software is on the program disk.
1
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Chapter 1 Overview of the CytoFluor System
1-2 Applied Biosystems
11.1 What is the CytoFluor System?
The complete CytoFluor system consists of:
• Scanner and software
• User-provided IBM®-compatible personal
computer (PC)
This system quantifies soluble and cell-associated
fluorescence. The fluorescence is measured by a
photomultiplier tube in a light-proof detection chamber. The
detected fluorescence data is displayed as arbitrary
fluorescence units (AFU).
You control the action of the scanner through the software.
The software runs on a PC operating under Microsoft
Windows software. The precision X-Y mechanism scans the
microtiter plate with a sensitive fiber-optic probe to quantify the
fluorescence in each well. The plate remains stationary during
the scanning of each row, then indexes to the next row. The
scanning system is fast; it can scan a 96-well plate in under a
minute.
You can use standard types of microtiter plates with six to
384 wells. You can select plate formats from a library of plates
or define your own plate format as described in Chapter 5,
Setting the Plate Layout or Auto Scale Parameters. For plates
with larger wells, you can choose an option to obtain an
average of multiple data points in each well. (Appendix D,
Plate Scan Patterns, defines the acquisition patterns.) In
addition, you can configure the system to read plates from the
top or bottom, depending on your application. (See Chapter 6,
Customizing the CytoFluor System, for more information.)
The scanner holds up to six excitation filters and six emission
filters to measure most common fluorophores. The
CytoFluor system ships with five excitation and five emission
filters installed. The remaining positions are filled with light
tight plugs. (See Chapter 8, Accessing Technical Information,
for a list of common fluorophores and their corresponding
filters.) In addition, the scanner requires little maintenance.
The most important routine maintenance task is changing the
air filter. (See Chapter 7, Maintaining the CytoFluor System,
for instructions.)
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

What is the CytoFluor System?
CytoFluor User’s Guide 1-3
1
There are two CytoFluor Series 4000 models:
•CytoFluor Series 4000/TC—Temperature-control
model equipped with a temperature control chamber in
which plates are scanned. Controlling the temperature
provides the ability to hold a plate at a specific
temperature or collect data from kinetic experiments.
See Section 3.5, Controlling the Temperature, for more
details.
•CytoFluor Series 4000/TR—Temperature-ready model
not equipped with a temperature control chamber. TR
models can be upgraded with a temperature control
chamber. Contact Applied Biosystems for more
information.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Chapter 1 Overview of the CytoFluor System
1-4 Applied Biosystems
11.2 How Does It Work?
The CytoFluor software uses a Microsoft Windows interface to
provide features that make the system easy to use. For
example, you select commands and options from menus and
buttons using the mouse. If you prefer, use keyboard
equivalents to access many of the functions.
The software initially displays the CytoFluor main setup
screen. This screen contains the scan set up parameters and
menu options. You can access options to assign plate
parameters to reflect your actual assay plate and experimental
setup. You can also access options to save, copy, or print your
data. (Chapter 2, Getting Started, contains more information
on the CytoFluor main setup screen.)
The scan setup parameters include identification information,
excitation and emission filter pairs, gain, number of scans and
cycles, and other run-specific information. You can edit them
at any time, before you acquire data. Once you acquire data,
you can only change the comments information in a file.
You start collecting data by selecting the Start button from the
main setup screen after you enter the scan setup information.
The software directs the scanner to move the plate into the
detection chamber. The scanner mechanism then aligns the
probe to read all selected wells, row by row. A run for a single
plate may have up to 200 cycles, with up to four different filter
pairs and sensitivities per cycle. Each group of filter pairs and
gain represents a scan.
After the system reads the final well, the plate transport
mechanism presents the plate back to the load position. The
detector is set to a low gain setting and the lamp remains on to
minimize warm-up time for successive runs. The system has a
timer that turns the lamp and detector off if no runs have been
initiated for 60 minutes. You can change this value using the
Maintenance menu as described in Chapter 6, Customizing
the CytoFluor System.
The system stores scanned information and the setup in a
CytoFluor data file. You can save and export file data from
within the application.
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com

Overview of the System Process and Chapter References
CytoFluor User’s Guide 1-5
1
1.3 Overview of the System Process
and Chapter References
This chart overviews the basic steps you follow to use
CytoFluor and refers you to the appropriate chapter for details:
Step Action Described in …
1 Set up the scanner. This involves setting the
voltage, installing fuses, and connecting it to
a PC.
Chapter 2, Getting
Started
2 Load the software, check the system
functions, and run system diagnostics. Chapter 2, Getting Started
3 Set or check the scan parameters of a file.
Or copy the parameters of an existing file
and rename it.
Chapter 3, Scanning
Operations
4 Determine the plate layout to identify
particular wells or groups of wells before
starting or completing a run (optional).
Chapter 5, Setting the
Plate Layout or Auto
Scale Parameters
5 Set the auto scale parameters so the system
can scale the data as it acquires it (optional). Chapter 5, Setting the Plate Layout or Auto
Scale Parameters
6 Customize the system before a run
(optional). Chapter 6, Customizing the
CytoFluor System
7 Insert a loaded plate and perform a run. Chapter 3, Scanning
Operations
8 Display, print, or export data. Chapter 4, Displaying,
Printing,andExporting
Data
Artisan Technology Group - Quality Instrumentation ... Guaranteed | (888) 88-SOURCE | www.artisantg.com