Qiagen QIAcube HT User manual

July 2013
Sample & Assay Technologies
QIAcube®HT User Manual
For QIAcube HT and QIAxtractor®

Trademarks
QIAGEN®, Rotor-Gene®, QIAcube®, QIAgility®, QIAxcel®, QIAxtractor®, (QIAGEN Group); Adobe®, Acrobat®(Adobe Systems Inc.); Carbon-Cap™,
Polycap™ (GE Healthcare); DECON-QUAT®(Veltek Associates Inc.); DNA-Exitus Plus™ (AppliChem GmbH); Excel®, Microsoft®, Windows®(Microsoft
Corporation); Gigasept®, Mikrozid®, Lysetol®(Schülke & Mayr GmbH); MagNA Pure®, Roche®(Hoffman-La Roche, Inc.); Teflon®(E.I. du Pont de
Nemours and Company).
© 2009–2013 QIAGEN, all rights reserved.

Contents
QIAcube HT User Manual 07/2013 Contents-1
Contents
1Safety Information 1-1
1.1 Proper use 1-1
1.2 Electrical safety 1-3
1.3 Biological safety 1-4
1.3.1 Samples 1-4
1.4 Chemicals 1-5
1.4.1 Toxic fumes 1-6
1.5 Waste disposal 1-6
1.6 Mechanical hazards 1-6
1.7 Maintenance safety 1-7
1.8 Symbols on the QIAcube HT 1-9
2Introduction 2-1
2.1 About this manual 2-1
2.2 General information 2-2
2.2.1 Technical assistance 2-2
2.2.2 Policy statement 2-2
2.3 Intended use of the QIAcube HT 2-2
2.3.1 Requirements for QIAcube HT users 2-3
2.3.2 Requirements for using dedicated QIAcube HT kits
on the QIAcube HT 2-4
2.3.3 Requirements for using dedicated QIAcube HT kits
on the QIAxtractor 2-4
2.3.4 QIAcube HT Software 2-4
3General Description 3-1
3.1 The QIAcube HT 3-2
3.1.1 Instrument lid 3-3
3.1.2 UV lamp 3-3
3.1.3 Pipetting head and robotic arm 3-4

Contents
Contents-2 QIAcube HT User Manual 07/2013
3.1.4 Tip chute 3-5
3.1.5 HEPA filter 3-5
3.1.6 Accessory panel 3-6
3.1.7 Feet 3-6
3.1.8 Worktable 3-6
3.2 Principles of operation 3-7
3.2.1 Vacuum chamber and components for use with
QIAcube HT kits on QIAcube HT or QIAxtractor
instruments 3-7
3.2.2 Vacuum chamber and components for use with
Capture Plate VX or Capture Plate DX on the
QIAxtractor instrument 3-10
3.2.3 Vacuum control station and waste bottle 3-13
3.2.4 Pinch valve 3-14
3.2.5 Reagent trough adapters and reagent troughs 3-16
3.2.6 Tip disposal box 3-17
3.2.7 QIAcube HT laptop, QIAcube HT Software CD,
and user manual 3-18
4Installation Procedures 4-1
4.1 Instrument delivery and installation 4-1
4.2 Requirements 4-1
4.3 AC power connection 4-2
4.4 Hardware installation 4-3
4.4.1 UV lamp 4-3
4.4.2 HEPA filter system 4-4
4.4.3 Vacuum control station 4-4
4.4.4 Pinch valve 4-5
4.4.5 Vacuum waste hose 4-5
4.5 Software installation 4-7
4.5.1 Installing the QIAcube HT Software 4-7
4.6 Connecting the instrument to the laptop 4-15
4.6.1 Connecting the computer to the QIAcube HT 4-15
4.7 Hardware Wizard 4-16

Contents
QIAcube HT User Manual 07/2013 Contents-3
4.8 Configuring the COM port 4-18
4.9 Important notes before first use 4-19
5QIAcube HT Software 5-1
5.1 Mode 5-2
5.1.1 “Normal” mode 5-2
5.1.2 “Virtual” mode 5-2
5.2 Starting the QIAcube HT Software 5-3
5.3 The software workspace 5-6
5.3.1 “Virtual” mode indicator 5-8
5.3.2 Menu bar 5-8
5.3.3 Toolbar 5-9
5.3.4 Workspace items 5-9
5.3.5 Right-hand pane 5-10
5.3.6 Status bar 5-10
5.4 Menus 5-11
5.4.1 “File” menu 5-11
5.4.2 “Control” menu 5-12
5.4.3 “Wizards” menu 5-13
5.4.4 “Options” menu 5-13
5.4.5 “Help” menu 5-15
5.5 Toolbar 5-17
5.6 Right-hand pane 5-22
5.7 Workspace items 5-23
5.8 Plates 5-24
5.8.1 Plate properties 5-24
5.8.2 Choosing the plate type 5-26
5.8.3 Defining favorite plate types 5-27
5.8.4 Changing plate function 5-28
5.9 Tips 5-29
5.9.1 Tip properties 5-30
5.9.2 Tip availability 5-31

Contents
Contents-4 QIAcube HT User Manual 07/2013
5.10 Reagents 5-34
5.10.1 Reagent properties 5-34
5.10.2 Configuring reagents 5-36
5.10.3 Required reagent volume 5-37
5.11 Samples and reactions 5-38
5.11.1 Sample properties 5-39
5.11.2 Reaction properties 5-41
5.11.3 Common properties and operations 5-45
5.11.4 Entering sample bar codes 5-47
5.11.5 Data transfer formats 5-48
5.11.6 Importing sample and reaction data 5-50
5.11.7 Exporting sample and reaction data 5-55
5.12 User management 5-61
5.12.1 User identification 5-61
5.12.2 User classes 5-62
5.12.3 Enabling access control 5-64
5.12.4 Managing user groups 5-64
5.12.5 Change current user 5-66
5.12.6 Revert to first user 5-67
5.13 Calibration 5-67
5.13.1 Calibrating plate positions 5-69
5.13.2 Calibrating plate heights 5-72
5.13.3 Calibrating volumes 5-80
5.13.4 Calibration management 5-84
5.13.5 Saving calibration data 5-84
5.13.6 Reinstating calibration data 5-86
5.13.7 Deleting calibration data 5-88
5.14 Run files 5-89
5.15 Working with run files 5-90
5.15.1 Template protocol run files 5-90
5.15.2 Obtaining run files 5-91
5.15.3 Opening new or existing run files 5-91
5.15.4 Saving run files 5-93

Contents
QIAcube HT User Manual 07/2013 Contents-5
5.16 Creating a run file with the “Vacuum extraction” wizard 5-94
5.16.1 Starting the “Vacuum extraction” wizard 5-95
5.16.2 “Vacuum extractor configuration wizard” step 5-95
5.16.3 “Table setup” step: Configuring the layout 5-98
5.16.4 “Configuration [1]” step 5-100
5.16.5 “Configuration [2]” step 5-101
5.16.6 “Load Pre-Capture Reagent 1” step 5-103
5.16.7 “Load capture plate” step 5-105
5.16.8 “Wash step 1 to wash step n” step 5-106
5.16.9 “Dry sample” step 5-108
5.16.10 “Elution steps” step 5-109
5.16.11 Wizard summary 5-111
5.16.12 Specifying vacuum processing 5-112
5.17 Setting run parameters 5-114
5.17.1 Configuring tip air intake 5-114
5.17.2 Configuring pipet speed 5-115
5.17.3 Using liquid-level tracking 5-116
5.17.4 Configuring error reporting 5-117
5.17.5 Setting tip use options 5-118
5.17.6 Setting the default file location 5-119
5.17.7 Resetting to default values 5-120
5.17.8 Saving current settings as new defaults 5-121
5.17.9 Setting system color configuration 5-122
5.17.10 Setting shutdown beep 5-125
5.17.11 Setting the screen saver operation 5-125
5.17.12 Generating filenames for reaction data export 5-126
5.18 Controlling communication and accessories 5-126
5.18.1 Selecting a COM port 5-126
5.18.2 Using the service register 5-127
5.18.3 Using the UV lamp 5-130
5.18.4 Using the HEPA filter 5-131

Contents
Contents-6 QIAcube HT User Manual 07/2013
6Operating Procedures 6-1
6.1 Switching on the QIAcube HT 6-1
6.2 Assembling the vacuum chamber 6-2
6.2.1 For plates from QIAcube HT kits 6-2
6.2.2 For Capture Plate VX or Capture Plate DX 6-4
6.3 QIAcube HT protocols 6-8
6.3.1 Performing a protocol 6-9
6.3.2 Pre-run report 6-11
6.3.3 Pre-run check errors and warnings 6-14
6.3.4 In-run open system/open circuit test 6-15
6.3.5 In-run plate detection test 6-15
6.3.6 In-run interactive vacuum steps 6-16
6.3.7 Modifying a protocol reaction list 6-19
6.4 Canceling a protocol 6-20
6.5 Post-run report 6-21
7Maintenance Procedures 7-1
7.1 Regular maintenance procedures 7-2
7.1.1 Emptying the waste bottle of the vacuum station 7-2
7.1.2 Cleaning the QIAcube HT 7-3
7.1.3 Cleaning the instrument after completing a run 7-6
7.1.4 Cleaning the instrument after shutting down 7-7
7.1.5 Cleaning instrument worktable accessories 7-8
7.2 Weekly maintenance procedure 7-11
7.3 Pipetting head service kit 7-13
7.4 Replacing HEPA filters 7-13
7.5 Replacing filters on the vacuum station 7-14
7.6 Shutting down the QIAcube HT 7-15
8Troubleshooting 8-1
8.1 Run setup errors 8-1
8.2 Important error messages 8-1

Contents
QIAcube HT User Manual 07/2013 Contents-7
8.2.1 Software errors 8-2
8.2.2 Instrument errors 8-2
8.2.3 Error codes 8-3
Appendix A A-1
Technical data A-1
Environmental conditions A-1
Mechanical data and hardware features A-2
Hardware and software features A-4
Waste Electrical and Electronic Equipment (WEEE) A-6
FCC declaration A-7
Declaration of conformity A-8
Appendix B B-1
Liability clause B-1
Appendix C C-1
Safety Information (French, FR) C-1
1Informations de sécurité C-1
1.1 Utilisation appropriée C-2
1.2 Sécurité électrique C-4
1.3 Sécurité biologique C-5
1.3.1 Échantillons C-5
1.4 Produits chimiques C-7
1.4.1 Vapeurs toxiques C-8
1.5 Elimination des déchets C-8
1.6 Dangers mécaniques C-8
1.7 Sécurité relative à la maintenance C-9
1.8 Symboles sur le QIAcube HT C-11

Contents
Contents-8 QIAcube HT User Manual 07/2013
Appendix D D-1
Safety Information (German, DE) D-1
1Sicherheitshinweise D-1
1.1 Sachgemäße Handhabung D-2
1.2 Schutz vor Stromschlag D-3
1.3 Biologische Sicherheit D-5
1.3.1 Proben D-5
1.4 Chemikalien D-7
1.4.1 Giftige Dämpfe D-7
1.5 Entsorgen von Abfällen D-7
1.6 Gefahren durch mechanische Teile D-8
1.7 Sicherheitshinweise – Wartungsarbeiten D-9
1.8 Symbole auf dem QIAcube HT D-11
Appendix E E-1
QIAcube HT and QIAxtractor accessories E-1
Appendix F F-1
Advanced settings F-1
Appendix G G-1
Sample and reaction functions for non-wizard protocols G-1
Appendix H H-1
Description of the Generic XML Format H-1
Index Index-1

Safety Information
QIAcube HT User Manual 07/2013 1-1
1Safety Information
Before using the QIAcube®HT, it is essential that you read
this user manual carefully and pay particular attention to the
safety information. The instructions and safety information in
the user manual must be followed to ensure safe operation
of the instrument and to maintain the instrument in a safe
condition.
Note: Translations of the Safety Information are available in
French in Appendix C and German in Appendix D.
The following types of safety information appear throughout
this manual.
WARNING
The term WARNING is used to inform you about situations
that could result in personal injury to you or other
persons.
Details about these circumstances are given in a box like
this one.
CAUTION
The term CAUTION is used to inform you about situations
that could result in damage to the instrument or other
equipment.
Details about these circumstances are given in a box like
this one.
The advice given in this manual is intended to supplement,
not supersede, the normal safety requirements prevailing in
the user’s country.
1.1 Proper use
WARNING/
CAUTION
Risk of personal injury and material damage
[W1]
Improper use of the QIAcube HT may cause personal
injuries or damage to the instrument.
The QIAcube HT must only be operated by qualified
personnel who have been appropriately trained.
Servicing of the QIAcube HT must only be performed by
QIAGEN Field Service Specialists.

Safety Information
1-2 QIAcube HT User Manual 07/2013
WARNING/
CAUTION
Risk of overheating
[W2]
To ensure proper ventilation, maintain a minimum
clearance of 10 cm at the sides and rear of the
QIAcube HT. Slits and openings that ensure the ventilation
of the QIAcube HT must not be covered.
WARNING/
CAUTION
Risk of personal injury and material damage
[W3]
The QIAcube HT is too heavy to be lifted by one person.
To avoid personal injury or damage to the instrument, do
not lift the instrument alone.
WARNING/
CAUTION
Risk of personal injury and material damage
[W4]
Do not attempt to move the QIAcube HT during operation.
WARNING
Explosive atmosphere
[W5]
The QIAcube HT is not designed for use in an explosive
atmosphere.
WARNING
Risk of explosion
[W6]
The QIAcube HT is intended for use with reagents and
substances supplied with QIAGEN kits. Use of other
reagents and substances may lead to fire or explosion.
CAUTION
Damage to the instrument
[C1]
Direct sunlight may bleach parts of the instrument and
cause damage to plastic parts.
The QIAcube HT must be located out of direct sunlight.
CAUTION
Damage to the instrument
[C2]
Avoid spilling water or chemicals onto the QIAcube HT.
Damage caused by water or chemical spillage will void
your warranty.

Safety Information
QIAcube HT User Manual 07/2013 1-3
WARNING
Risk of personal injury
[W7]
The robotic arm moves during position calibration while
the instrument lid is raised. Never click any buttons while
parts of your body are within the instrument workspace.
In case of emergency, switch off the QIAcube HT at the
power switch at the rear of the instrument and unplug the
power cord from the power outlet.
1.2 Electrical safety
Disconnect the line power cord from the power outlet before
servicing.
WARNING
Electrical hazard
[W8]
Any interruption of the protective conductor (earth/ground
lead) inside or outside the instrument or disconnection of
the protective conductor terminal is likely to make the
instrument dangerous.
Intentional interruption is prohibited.
Lethal voltages inside the instrument.
When the instrument is connected to line power, terminals
may be live. Opening covers or removing parts is likely to
expose live parts.
WARNING
UV irradiation hazard
[W9]
An electronic lid sensor ensures that the instrument lid
must be closed for operation of the UV lamp. Under no
circumstances should this lid sensor be disabled during the
decontamination.

Safety Information
1-4 QIAcube HT User Manual 07/2013
To ensure satisfactory and safe operation of the QIAcube HT,
follow the guidelines below:
The line power cord must be connected to a line power
outlet that has a protective conductor (earth/ground).
Do not adjust or replace internal parts of the instrument.
Do not operate the instrument with any covers or parts
removed.
If liquid has spilled inside the instrument, switch off the
instrument, disconnect it from the power outlet, and
contact QIAGEN Technical Services.
If the instrument becomes electrically unsafe, prevent
other personnel from operating it, and contact QIAGEN
Technical Services; the instrument may be electrically
unsafe when:
The line power cord appears to be damaged.
It has been stored for a prolonged period of time in
conditions outside of those outlined in Appendix A.
It has been subjected to severe transport stresses.
1.3 Biological safety
Specimens and reagents containing materials from humans
should be treated as potentially infectious. Use safe
laboratory procedures as outlined in publications such as
Biosafety in Microbiological and Biomedical Laboratories
(HHS Publication) (www.cdc.gov/biosafety/publications).
1.3.1 Samples
Samples may contain infectious agents. You should be aware
of the health hazard presented by such agents and should
use, store, and dispose of such samples according to the
required safety regulations.

Safety Information
QIAcube HT User Manual 07/2013 1-5
WARNING
Samples containing infectious agents
[W10]
Some samples used with this instrument may contain
infectious agents. Handle such samples with the greatest
of care and in accordance with the required safety
regulations.
Always wear safety glasses, 2 pairs of gloves, and a lab
coat.
The responsible body (e.g., laboratory manager) must
take the necessary precautions to ensure that the
surrounding workplace is safe and that the instrument
operators are not exposed to hazardous levels of
infectious agents as defined in the applicable Safety Data
Sheets (SDSs) or OSHA,* ACGIH,†or COSHH‡documents.
Venting for fumes and disposal of wastes must be in
accordance with all national, state, and local health and
safety regulations and laws.
1.4 Chemicals
WARNING
Hazardous chemicals
[W11]
Some chemicals used with this instrument may be
hazardous or may become hazardous after completion of
the protocol run.
Always wear safety glasses, gloves, and a lab coat.
The responsible body (e.g., laboratory manager) must
take the necessary precautions to ensure that the
surrounding workplace is safe and that the instrument
operators are not exposed to hazardous levels of toxic
substances (chemical or biological) as defined in the
applicable Safety Data Sheets (SDSs) or OSHA,* ACGIH,†
or COSHH‡documents.
Venting for fumes and disposal of wastes must be in
accordance with all national, state, and local health and
safety regulations and laws.
* OSHA: Occupational Safety and Health Administration (United States of America).
†ACGIH: American Conference of Government Industrial Hygienists (United States of America).
‡COSHH: Control of Substances Hazardous to Health (United Kingdom).

Safety Information
1-6 QIAcube HT User Manual 07/2013
1.4.1 Toxic fumes
If working with volatile solvents or toxic substances, you must
provide an efficient laboratory ventilation system to remove
vapors that may be produced.
1.5 Waste disposal
Used plasticware and containers may contain hazardous
chemicals, or contagious/biohazardous materials. Such
wastes must be collected and disposed of properly according
to local safety regulations.
For information on use and disposal of the tip disposal box,
please see Section 3.2.6, page 3-17.
For information about how to dispose of the QIAcube HT,
see Appendix A.
1.6 Mechanical hazards
WARNING
Moving parts
[W12]
Avoid contact with moving parts during operation of the
QIAcube HT. Under no circumstances should you place
your hands under the robotic arm when it is lowering. Do
not attempt to move any plates or tubes while the robotic
arm is operating.
CAUTION
Damage to the instrument
[C3]
Do not apply any manual force to the Y-arm (i.e. the
pipetting head).
We strongly recommend restarting the system if the Y-arm
was accidentally manually moved.

Safety Information
QIAcube HT User Manual 07/2013 1-7
To ensure satisfactory and safe operation of the QIAcube HT,
follow the guidelines below:
Use only recommended tips and tip racks.
Keep the instrument lid closed whenever possible.
Do not override the lid sensor under any circumstances.
When calibrating plates with the lid open, always stand
clear of the instrument when making adjustments. In
calibration mode, the lid sensor is disabled. Therefore,
do not click with the mouse or press any of the keys on
the keyboard when looking closely at plate calibrations.
Wait until the robotic arm has completed its movements
before moving any plates or tubes.
Do not place any items on the robotic arm.
Select “Pause”, located in the toolbar of the QIAcube HT
Software, to pause the instrument before removing plates
or tubes from the worktable. Wait until the robotic arm
has completed the current movement — this may take up
to 10 seconds.
1.7 Maintenance safety
Perform the maintenance as described in Section 7. QIAGEN
charges for repairs that are required due to incorrect
maintenance.
WARNING/
CAUTION
Risk of personal injury and material damage
[W13]
Only perform maintenance that is specifically described in
this user manual.
WARNING/
CAUTION
Risk of electric shock
[W14]
Do not open any panels on the QIAcube HT.
Risk of personal injury and material damage.
Only perform maintenance that is specifically described in
this user manual.

Safety Information
1-8 QIAcube HT User Manual 07/2013
CAUTION
Damage to the instrument
[C4]
Do not use solvents, or reagents containing acids, alkalis,
or abrasives to clean the QIAcube HT.
CAUTION
Damage to the QIAcube HT lid
[C5]
Do not use alcohol, solvents, reagents containing acids,
alkalis, or abrasives to clean the instrument lid. Alcohol
will damage the lid. To clean the lid, use distilled water
only.
CAUTION
Damage to the QIAcube HT side panels
[C6]
Never clean the instrument side panels with alcohol or
alcohol-based solutions.
CAUTION
Damage to transfer carriage
[C7]
Under no circumstances should the transfer carriage for
use with Capture Plate VX or Capture Plate DX be
autoclaved.

Safety Information
QIAcube HT User Manual 07/2013 1-9
1.8 Symbols on the QIAcube HT
Symbol
Location
Description
Worktable and near the
type plate
Warning symbol
Worktable and near the
tip chute outlet
Biohazard symbol
Worktable
Squeezing warning symbol
Type plate on the back
of the instrument CE mark for European Conformity
Type plate on the back
of the instrument CSA listing mark for Canada and
the USA
Type plate on the back
of the instrument Legal manufacturer
Type plate on the back
of the instrument WEEE mark for Europe
Type plate on the back
of the instrument FCC mark of the United States
Federal Communications
Commission
Type plate on the back
of the instrument C-Tick mark for Australia (supplier
identification N17965)

Safety Information
1-10 QIAcube HT User Manual 07/2013
Symbol
Location
Description
Type plate on the back
of the instrument RoHS mark for China (the restriction
of the use of certain hazardous
substances in electrical and
electronic equipment)
Worktable
Consult instructions for use