Thermo Varioskan User manual

Varioskan
User Manual
Rev. 2.0
Analyze • Detect • Measure • Control™
TM

Varioskan™
User Manual
Rev. 2.0

Copyright ©2005 Thermo Electron Corporation. All rights reserved. First edition printed in 2004. Printed in
Finland. Reproduction of the accompanying user documentation in whole or in part is prohibited.
The Varioskan has a national and an international patent pending.
“Varioskan” is a trademark of Thermo Electron.
“Microtiter” and “SkanIt” are registered trademarks of Thermo Electron.
All other trademarks and registered trademarks are the property of their respective holders.
Thermo Electron reserves the right to change its products and services at any time to incorporate technological
developments. This manual is subject to change without prior notice as part of a continuous product
development. Although this manual has been prepared with every precaution to ensure accuracy, Thermo
Electron assumes no liability for any errors or omissions, nor for any damages resulting from the application or
use of this information. This manual supersedes all previous editions.
Thermo Electron shall not be liable for any damages whatsoever arising out of the use or inability to use this
product.
Thermo Electron Microplate Instrumentation Business products are fully guaranteed against defective parts
and materials, including defects caused by poor workmanship, for a period of one year from the date of
delivery. Thermo will repair or replace defective parts or materials during the term of warranty at no extra
charge for materials and labor provided that the products were used and maintained in accordance with
Thermo’s instructions. The warranty is invalid if products have been misused or abused. For the warranty to
be effective, the product must have been purchased either directly from Thermo or from an authorized
Thermo distributor. The guarantee is not transferable to a third party without prior written approval from
Thermo. This guarantee is subject to the following exclusions:
●Any defects caused by normal wear and tear.
●Defects caused by fire, lightning, flood, earthquake, explosion, sabotage, war, riot, or any other occurrence
of the type listed above.
●Refurbished products that are subject to different warranty conditions.
THIS WARRANTY IS IN LIEU OF ALL OTHER EXPRESSED OR IMPLIED WARRANTIES,
INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE. The seller is not liable for any loss or damage arising out of or
in connection with the use of the product or other indirect damages. These warranty terms and conditions can
be obtained from your local Thermo dealer.
Consumables are not included in the warranty.

Thermo Electron Corporation Varioskan™User Manual 3
About This User Manual
This User Manual has been written for the actual user (e.g., laboratory
technician) and provides information on the Varioskan, including the
installation and operating instructions.
Read the manual in its entirety before operating the instrument.
This User Manual has been designed to give you the information you
need to:
●Review safety precautions
●Install the Varioskan
●Use the Varioskan in daily use and research
●Perform basic cleaning and maintenance procedures
●Troubleshoot the instrument performance
This User Manual also describes all the features and specifications of the
Varioskan instrument. Refer to Chapter 6: “Technical Specifications”.
In Chapter 8: “Troubleshooting Guide” you will find explanations of
all error and warning messages and a problem-solving guide. The user
should be familiar with the contents of Chapter 5: “Maintenance”.
For ordering information, refer to Chapter 9: “Ordering Information”.
For software-related issues, refer to the SkanIt Software for Varioskan
User Manual (Cat. no. N02723). Both the user and software manuals
can be found in PDF format on the SkanIt Software installation CD.
For the latest information on products and services, visit our worldwide
websites on the Internet at:
http://www.thermo.com
In an effort to produce useful and appropriate documentation, we
appreciate your comments on this User Manual to your local Thermo
representative.
W
ho uses this
user manual
How to use this
user manual
For more
information

About This User Manual
Safety symbols and markings
4Varioskan™User Manual Thermo Electron Corporation
These symbols are intended to draw your attention to particularly
important information and alert you to the presence of hazards as
indicated.
The following symbols and markings appear on the type label and the
instrument itself.
Power ON ▲
Power OFF ▲
Serial number ▲
Catalog number ▲
Date of manufacture ▲
Consult instructions for use ▲
Risk of radiation injury ▲
A black label with the following text (Figure 2–3):
CAUTION: WARNING: DISCONNECT SUPPLY BEFORE
SERVICING and AVERTISSEMENT: COUPER
L'ALIMENTATION AVANT L'ENTRETIEN ET LE
DEPANNAGE. ▲
Safety symbols
and markings
Safety symbols and
markings used on
the Varioskan

About This User Manual
Safety symbols and markings
Thermo Electron Corporation Varioskan™User Manual 5
The following symbols and markings appear in this User Manual.
Warning Risk of electric shock. ▲
Warning Biohazard risk. ▲
Warning Hot surface, risk of burns. ▲
Warning Risk of injury to the user(s). ▲
Warning Risk of ultraviolet radiation injury. ▲
Caution Risk of damage to the instrument, other equipment or loss of
performance or function in a specific application. ▲
Note Marks a hint, important information that is useful in the
optimum operation of the system, or an item of interest. ▲
W
arning and other
markings used in
the documentation

About This User Manual
Instrument safety and guidelines for use
6Varioskan™User Manual Thermo Electron Corporation
1. Always follow basic safety precautions when using the Varioskan to
reduce the risk of injury, biohazardous contamination, fire, or
electrical shock.
2. Read this User Manual in its entirety prior to operating the
instrument. Failure to read, understand, and follow the instructions
in the manual may result in damage to the instrument, injury to
laboratory and operating personnel or poor instrument
performance.
3. Observe all “Warning”, “Caution”, and “Note” statements as well as
safety symbols and markings on the instrument and in the
documentation.
4. Never open any other covers of the Varioskan than the dispenser
sliding cover (Figure 2–2) or measurement chamber door
(Figure 2–2) while the instrument is plugged into a power source.
5. Never open the measurement chamber door while the instrument is
busy (when the LED indicator is orange).
6. You can push in the tray manually only when the instrument is
switched off.
7. Never force a microplate into the instrument.
8. The Varioskan is intended for laboratory research use only. Observe
proper laboratory safety precautions, such as wearing protective
clothing and following approved laboratory safety procedures.
9. Preventative maintenance instructions should be followed closely to
keep the instrument in the best condition for maximum reliability.
A poorly maintained instrument will not give the best results.
Instrument safety
and guidelines
for use

Thermo Electron Corporation Varioskan™User Manual 7
Contents
Who uses this user manual ................................................................3
How to use this user manual ............................................................. 3
For more information .......................................................................3
Safety symbols and markings.............................................................4
Safety symbols and markings used on the Varioskan ...................... 4
Warning and other markings used in the documentation ............... 5
Instrument safety and guidelines for use............................................6
Introduction to the Varioskan.................................................................... 15
Introduction.................................................................................... 15
Intended use.................................................................................... 15
Advantages of using Varioskan ........................................................ 16
Functional Description ............................................................................... 17
Instrument layout............................................................................ 17
Front view....................................................................................17
Back view.....................................................................................17
Internal view ................................................................................18
Measurement techniques................................................................. 19
Fluorescence intensity ..................................................................19
Time-resolved fluorescence........................................................... 19
Photometry ..................................................................................20
Optical system................................................................................. 21
Principle of the optical system......................................................21
Excitation optics........................................................................ 22
Measurement optics ..................................................................23
Emission reading module .......................................................... 24
Photometric measurement module............................................ 24
Dispenser option.............................................................................25
Incubator ........................................................................................27
Control switches ............................................................................. 27
Track mechanism............................................................................ 28
Tray options.................................................................................... 29
Tray composition.........................................................................30
Universal tray with adapters .........................................................31
Robotic tray ................................................................................. 33
How to change the location of the holder for the tip priming
vessel ......................................................................................... 34
How to remove or replace the robotic tray adapter....................35
Installation .................................................................................................... 37
Installation checklist........................................................................37
What to do upon delivery ...............................................................38
Chapter 1
Chapter 2
Chapter 3

Contents
8Varioskan™User Manual Thermo Electron Corporation
How to unpack ............................................................................ 38
Checking delivery for completeness.............................................. 38
Checking for damage during transport ......................................... 38
Environmental requirements ........................................................ 39
Things to avoid ............................................................................39
Technical prerequisites.................................................................39
Setups before you put the instrument into operation....................... 40
How to release the transport lock .................................................40
How to install the tray ................................................................. 43
How to setup the optional dispenser ............................................45
Installation of SkanIt Software .....................................................47
How to ensure startup.................................................................. 47
Operational check ........................................................................... 48
Automatic runtime calibration .....................................................49
Routine Operation ........................................................................................51
Do’s and Don’ts of the Varioskan ...................................................51
Do ...............................................................................................51
Don’t ...........................................................................................52
Switching on ................................................................................... 53
Loading the microplate ................................................................ 54
Fluorometric measurement.............................................................. 55
Fluorometric spectrum scanning .....................................................57
Photometric measurement...............................................................58
Photometric spectrum scanning ...................................................... 58
Other functions............................................................................... 59
Orbital shaking ............................................................................59
Incubating.................................................................................... 60
Dispensing ...................................................................................61
Priming.....................................................................................61
Tip priming ..............................................................................62
Dispenser washing..................................................................... 62
Dispensing and measurement....................................................62
Helpful hints.............................................................................63
Chemical resistance of the dispenser..........................................63
Shutdown ....................................................................................... 66
Emergency situations ......................................................................67
Maintenance .................................................................................................69
Maintenance checklist ..................................................................... 69
Regular and preventive maintenance ............................................... 70
How to clean the measurement chamber......................................71
How to clean the tray................................................................... 72
How to clean the reagent basin and dispensing area .....................73
Routine maintenance of the optional dispenser ............................ 73
Daily maintenance .......................................................................73
Weekly maintenance ....................................................................74
Weak detergent or 10% bleach.................................................. 74
Weak base and acid in sequence ................................................... 74
Chapter 4
Chapter 5

Contents
Thermo Electron Corporation Varioskan™User Manual 9
Periodic maintenance ...................................................................... 75
Replacing the aspirate tube assembly or the complete dispensing
tube assembly...............................................................................75
Replacing a dispensing tip ............................................................ 76
Replacing a dispenser syringe .......................................................77
Replacing the 3-port valve............................................................... 78
Disposal of materials .......................................................................79
Decontamination procedure............................................................ 79
How to refit the transport lock.....................................................81
Maintaining a system log.................................................................83
How to pack for service...................................................................83
Service contracts..............................................................................84
Disposal of the instrument .............................................................. 84
Technical Specifications ........................................................................... 85
General specifications......................................................................85
Performance specifications ..............................................................86
Safety specifications......................................................................88
In conformity with the requirements............................................... 89
Frequently Asked Questions...................................................................... 91
Troubleshooting Guide ............................................................................... 95
Error and warning codes .................................................................95
Service request protocol................................................................... 99
Certificate of Decontamination....................................................... 99
Ordering Information................................................................................. 101
List of spare parts and accessories .................................................. 101
Upgrade kits..................................................................................102
References .................................................................................................. 103
Useful web links............................................................................ 103
Literature ......................................................................................105
Fluorescence intensity ................................................................105
Time-resolved fluorescence......................................................... 105
Photometry ................................................................................106
System Log .................................................................................................. 107
Varioskan Brief User’s Guide.................................................................. 109
Certificate of Decontamination............................................................... 111
Varioskan Feedback Form........................................................................ 113
Chapter 6
Chapter 7
Chapter 8
Chapter 9
Chapter 10
Appendix A
Appendix B
Appendix C
Appendix D

Contents
10 Varioskan™User Manual Thermo Electron Corporation
Glossary........................................................................................................115
Index .............................................................................................................117
Notes.............................................................................................................121

Figures
Thermo Electron Corporation Varioskan™User Manual 11
Figures
Figure 1–1. Varioskan spectral scanning multimode reader ........................ 15
Figure 2–2. Varioskan front view .................................................................. 17
Figure 2–3. Varioskan back view................................................................... 17
Figure 2–4. Close-up of the computer and mains supply connectors .......... 18
Figure 2–5. Varioskan internal view.............................................................. 18
Figure 2–6. Varioskan optics ......................................................................... 21
Figure 2–7. Excitation optics ......................................................................... 22
Figure 2–8. Principle of the double monochromator..................................... 23
Figure 2–9. Measurement optics .................................................................. 23
Figure 2–10. Emission optics......................................................................... 24
Figure 2–11. Photometric measurement module .......................................... 25
Figure 2–12. Varioskan dispensing system................................................... 26
Figure 2–13. Dispensing tip options: 0.40 mm, and 0.25 mm ...................... 26
Figure 2–14. Varioskan incubator cross-section ........................................... 27
Figure 2–15. Control switches....................................................................... 28
Figure 2–16. Part of the Varioskan track mechanism ................................... 29
Figure 2–17. Assembly picture of the universal tray .................................... 30
Figure 2–18. Robotic tray fitted with adapter for plate w/o lid, #126 ......... 33
Figure 2–19. Changing the location of the tip priming vessel holder .......... 34
Figure 2–20. Removing or replacing the adapter for plate w/o lid, #126 .... 35
Figure 3–21. Transport lock and transport lock tag present......................... 40
Figure 3–22. Dispenser sliding cover and measurement chamber door
opened ............................................................................................................. 41
Figure 3–23. Front cover removed................................................................. 41
Figure 3–24. Transport lock fastened (screws 1 – 4 shown)........................ 42
Figure 3–25. Releasing the transport lock (screws 1 – 4 shown)................. 42
Figure 3–26. Transport lock in its horizontal storage position (screws 3 and
4 shown) .......................................................................................................... 43
Figure 3–27. Tray holder................................................................................ 44
Figure 3–28. Fastening the tray frame to the tray holder............................. 45
Figure 3–29. Close-up of the positioning lever when the tray is out ........... 45
Figure 3–30. Varioskan with the dispenser sliding cover open.................... 46
Figure 3–31. Protective cap removed from the dispensing tip 5 – 1000 µl
(0.40 mm) ......................................................................................................... 47
Figure 3–32. Dispenser assembly ................................................................. 47
Figure 3–33. Connecting the mains supply cable ......................................... 48
Figure 4–34. Microplate loaded .................................................................... 54
Figure 4–35. Dynamic range selection.......................................................... 55
Figure 4–36. Structure of the TRF measurement cycle................................. 57

Figures
12 Varioskan™User Manual Thermo Electron Corporation
Figure 4–37. ON-OFF period time and total shaking time.............................59
Figure 4–38. Speed & diameter combinations for different plate formats ..60
Figure 5–39. Front cover removed .................................................................71
Figure 5–40. Internal view of the measurement chamber ............................ 72
Figure 5–41. Replacing the dispensing tip (A)...............................................76
Figure 5–42. Replacing the dispensing tip (B)...............................................76
Figure 5–43. Dispenser assembly..................................................................77
Figure 5–44. Replacing the dispenser syringe ..............................................78
Figure 5–45. 3-port valve replacement.......................................................... 79
Figure 5–46. Transport lock released (A) and fastened (B) (screws 1 – 4
shown)..............................................................................................................82

Tables
Thermo Electron Corporation Varioskan™User Manual 13
Tables
Table 2–1. Compatibility of the universal tray and plate-specific adapters 32
Table 2–2. Compatibility of the robotic tray and plate-specific adapter...... 33
Table 3–3. Installation checklist.................................................................... 37
Table 4–4. LED indicator................................................................................ 53
Table 4–5. Compatibility chart of solvents suitable with the plastic
materials used in the dispenser...................................................................... 64
Table 5–6. Maintenance checklist ................................................................ 69
Table 5–7. Example of a system log.............................................................. 83
Table 6–8. Technical specifications .............................................................. 85
Table 6–9. Fluorometry .................................................................................. 86
Table 6–10. Photometry................................................................................. 87
Table 6–11. Incubator .................................................................................... 87
Table 6–12. Shaker ........................................................................................ 88
Table 6–13. Dispenser ................................................................................... 88
Table 7–14. Tray vs. plate-specific adapter .................................................. 92
Table 8–15. Error codes reported .................................................................. 95
Table 8–16. Warning codes reported............................................................ 98
Table 9–17. Instrument catalog numbers.................................................... 101
Table 9–18. Codes for spare parts and accessories ................................... 101
Table 9–19. Codes for upgrade kits............................................................. 102

Tables
14 Varioskan™User Manual Thermo Electron Corporation

Thermo Electron Corporation Varioskan™User Manual 15
Chapter 1
Introduction to the Varioskan
The Thermo Electron Varioskan (Figure 1–1) is an advanced spectral
scanning multimode reader. The Varioskan is used to measure
fluorescence intensity, time-resolved fluorescence (TRF) and absorbance
in end point, kinetic and spectral measurements in the UV/Vis range
from appropriate microplate formats. In fluorometric measurements
appropriate 6- to 1536-well plates can be used, and correspondingly
appropriate 6- to 384-well plates in photometric measurements.
Incubation can be carried out in a controlled incubation temperature.
The instrument also allows shaking and reagent dispensing. The
instrument is run on SkanIt Software 2.2 (or greater), which controls all
the instrument functions and provides data processing as well as
reporting functions.
Figure 1–1. Varioskan spectral scanning multimode reader
The Varioskan spectral scanning multimode reader is intended for
professional laboratory research use by trained personnel, who
understand the nature of fluorometry and photometry. The Varioskan
is used to measure fluorescence intensity and time-resolved fluorescence
(TRF) from appropriate 6- to 1536-well plate formats or absorbance
from appropriate 6- to 384-well plate formats mentioned in the
manual. It also has incubation, shaking and reagent dispensing
capabilities.
Use for self-testing is excluded.
For validation of the entire system, it is recommended that Good
Laboratory Practices (GLP) are followed to guarantee reliable analyses.
Refer to Chapter 6: “Technical Specifications”.
Introduction
Intended use

Introduction to the Varioskan
Advantages of using Varioskan
16 Varioskan™User Manual Thermo Electron Corporation
The Varioskan provides several advantages relating mainly to the
principle of operation in that it:
●Supports applications requiring measurement in the UV/Vis/NIR
wavelength range
●Allows optimization of the measurement wavelengths according to
the application needs
●Allows use of freely selectable wavelengths and spectral scanning
●Enables measurement of multiple labels from the same well
●Allows optimization of the assays to different plate formats
depending on the throughput requirements
●Enables precise incubation of temperature-critical assays due to the
unique design of the universal tray
●Enables fast kinetic measurements due to simultaneous
measurement and dispensing
●Enables automation due to robot compatibility
●Is controlled by SkanIt Software that provides features required to
make comprehensive calculations and reports
●Ensures high-quality performance due to automatic runtime
calibration and operational checks, including safety features
Advantages of
using Varioskan

Thermo Electron Corporation Varioskan™User Manual 17
Chapter 2
Functional Description
This section shows the front, internal and back views of the Varioskan
instrument.
Figure 2–2. Varioskan front view
Figure 2–3. Varioskan back view
Instrument
layout
Front view
Back view
ON
/
OFF switch
Power, busy and
error LED indicator
Dispenser sliding cover
Measurement chamber door
Front cover
Cooling-fan outlet
Serial connector
Warning marking
USB connector
ON/OFF switch
Mains power supply connector
Type label
Indentation for lifting Varioskan
Indentation for lifting Varioskan

Functional Description
Instrument layout
18 Varioskan™User Manual Thermo Electron Corporation
Figure 2–4. Close-up of the computer and mains supply connectors
Figure 2–5. Varioskan internal view
Internal view
Dispensing head positioner (dispensing
head in positioner while dispensing; blind
plug present when no dispensing)
USB connector
Ethernet connector (not in use)
Serial connector
Mains power supply connector
Dispenser sliding cover
Plate In/Out switch
Dispensing head holder
Dispensing head positioner
(dispensing head in positioner
while dispensing; blind plug
present when no dispensing)
Prime/Empty switch
(opt., with dispenser)
Dispensing head (opt.)
Dispenser (opt.)
Reagent bottle holder
Reagent basin
Measurement
chamber door
Blind plug
Dispensing head holder
Reagent bottle holder
Dispensing head (opt.)
Blind plug