Endress+Hauser analytikjena qTOWER3auto Series User manual

Rev. A Service Manual of the
qTOWER3 auto series
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 1 to 116
Service Manual of the
qTOWER3auto
series
Revision: 2021-01

Rev. A Service Manual of the
qTOWER3 auto series
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 2 to 116
Manufacture Analytik Jena GmbH
Konrad-Zuse-Str.1
07745 Jena Germany
Phone + 49 3641 77 70
Fax + 49 3641 77 92 79
Email [e-mail]
Production Biometra GmbH
Rudolf-Wissell-Str. 30
37079 Göttingen Germany
Phone + 49 0551 50 686-10, 14 or 16
Fax + 49 0551 50 686 66
Email [e-mail]
© Copyright 2021-01, Analytik Jena GmbH
http://www.analytik-jena.com
06.05.2021
The devices at Analytik Jena’s website:
https://www.analytik-jena.com/life-science/produkte/prod/cat/real-time-pcr/prod/qtower3.html

Rev. A Service Manual of the
qTOWER3 auto series
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 3 to 116
Overview of the revisions
Version Date Modification
RV-01-2021 06.05.2021 none (new)

Rev. A Service Manual of the
qTOWER3 auto series
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 4 to 116
Contents
1General Description of qTOWER auto devices .........................7
1.1 Intended Use..............................................................................................7
2Safety instruction .......................................................................8
2.1 Symbols and signal words .........................................................................8
2.2 Safety symbols on the qTOWER³ auto.......................................................9
2.3 Technical condition of qTOWER³ auto.......................................................9
2.4 Requirements for the service personnel..................................................10
2.5 Safety instructions - electrical equipment...............................................11
2.6 Safety instructions – service and repair ..................................................11
3Technical data.......................................................................... 12
3.1 qTOWER³ auto and qTOWER³ 84 auto ....................................................12
4Technical description of instrument...................................... 13
4.1 qTOWER³ auto - Instrument overview .......................................................... 13
4.2 Basic Module 1 and 2...................................................................................... 14
4.2.1 Front and rear panel.................................................................................... 14
4.2.2 Basic housing- Front and rear panel .......................................................... 15
4.2.3 Basic housing- locking screws..................................................................... 16
4.2.4 Basic housing- mounting............................................................................. 16
4.2.5 Basic housing- Rear panel overview........................................................... 17
4.2.6 Basic housing- Base mounting.................................................................... 18
4.3 qTOWER³ auto optical head ........................................................................... 21
4.3.1 qTOWER³ auto 96 well – Optical unit - construction................................21
4.3.2 qTOWER³ auto 96 well – Optical unit – assembled component............... 22
4.3.3 qTOWER³ auto 96 well- Optical unit - construction .................................. 23
4.3.4 qTOWER³ 84 auto - 384 well unit - assembled component .....................24
4.4 Scanner and lift construction.......................................................................... 25
4.4.4 Glass plate unit .........................................................................................29
4.4.5 Cable for heated lid and lift ......................................................................29
4.4.6 Real-Time LP board Spindel motor and coller plugs ................................30
4.4.8 Ray division and flexible fibers ................................................................ 32
4.4.9 Ray division mounted with flexible fibers.................................................. 33
4.5 Module 3 - Power Module ...........................................................................35
4.5.1.2 Rear view .................................................................................................... 36
4.5.1.3 Fuses and voltage selector switch ............................................................. 36
4.5.1.4 The power module housing.....................................................................37
4.5.1.5 Internal cable connections of the power modul (black housing)............39
4.5.1.6 Internal power supply and processor board............................................40
4.6 Module 4 – MicrotiterPlateLoader (MPL) ...............................................44
4.6.1 MPL overview.............................................................................................. 44
4.6.2 MPL drawer on ground plate ...................................................................... 45
4.6.5 MPL drawer ground plate............................................................................ 46
4.6.6 MPL drawer adjustment.............................................................................. 46
4.6.7 MPL drawer wirring diagram ...................................................................... 47

Rev. A Service Manual of the
qTOWER3 auto series
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 5 to 116
5 Firmware updates........................................................................... 48
5.1.0 Firmware update of device .......................................................................48
5.2.0 Documentation of the Firmware-UniversalUpdate QTOWER³ .................48
5.3.0 Update the firmware of the Power unit via RS232...................................49
5.4.0 Update the firmware of the Control unit via RS232 .................................52
5.5.0 Update the firmware of the Control unit via RS232 .................................53
5.6.0 Update the firmware of the Optics unit via RS232...................................55
5.7.0 Update Motor unit via USB .......................................................................57
6 Technical tests ................................................................................ 59
6.1.0 Externded-Selftests for trouble shooting .................................................59
6.2.0 Installing and saving colour modules using the software ........................63
7 Maintenance ................................................................................... 65
8 Troubleshooting ............................................................................. 66
8.1.0 Detection head..........................................................................................66
8.1.1 Position of the detection head.................................................................66
8.2.3 Single fiber exchange ...............................................................................68
8.3.0 Illumination fiber bundle exchange .........................................................69
8.3.1 Detector fiber bundle exchange ...............................................................71
8.4.0 Scanner repair...........................................................................................72
8.4.1 Free movement of the scanner around neutral position..........................72
8.4.2 Setting the scanner Init-position..............................................................72
8.4.3 Alignment of the scanner motor...............................................................73
8.5.0 Lift repair ..................................................................................................74
8.5.1 Setting up the lift......................................................................................74
8.5.2 Check the lift mechanism by qPCRsoft auto in service-mode...................74
8.5.3 Adjustment of lift mechanism ..................................................................75
8.5.4 Repair the misaligned lift .........................................................................75
8.6.0 Multi Plate Loader MPL............................................................................... 77
8.7.1.0 Service Mode Starting qPCRsoft auto....................................................79
8.7.2 Checking functionality by using qPCRsoft auto ........................................79
8.7.3 Initialization ................................................................................................. 80
8.7.4 Check detector head’s firmware ................................................................. 80
8.7.5 Check smooth running of the rotary table ................................................. 80
8.7.6 Free movement of the lift ........................................................................... 80
8.7.7 Parallel adjustment of lift drive .................................................................. 80
8.7.8 Scanner’s neutral position........................................................................... 80
8.8.8 Setting default values...............................................................................80
8.9.1 Selecting test plate ...................................................................................81
8.9.2 Determing trim............................................................................................. 82
8.9.3 Determing the offset ................................................................................... 83
8.9.4 Determining sensitivity ............................................................................... 85
8.9.5 Check the fiber’s fluorescence background ................................................ 85
8.9.6 Determing of homogeneity factors............................................................. 87
8.9.7 Writing EEprom............................................................................................ 87
8.9.8 Check the thermal block for cleanness ....................................................... 89
9 Service Equipment and test tools.............................................. 90

Rev. A Service Manual of the
qTOWER3 auto series
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 6 to 116
9.1.0 TP Measuring ............................................................................................... 90
9.1.2 Test procedure and description .................................................................. 91
9.2.0 Working with single commands using the Thermal tool TUSB................. 93
9.3 Error messages of the software qPCR auto soft............................................ 96
9.3.1 Error codes.................................................................................................... 96
9.3.4 Errorcodes of QTower3 automated ........................................................101
9.3.5 Errorcodes of QTower3 84 automated ...................................................101
9.3.6 General error .............................................................................................. 102
9.3.7 Error in qPCR soft....................................................................................... 104
9.3.8 Optical unit error........................................................................................ 105
9.3.9 Error codes of the Thermal cycler ............................................................. 105
9.3.10 Power-Control-Unit ................................................................................. 109
9.4 Equipment for checking optics of 96 or 384 wells Block instruments...110
9.4.1 Measurements with special test plate...................................................... 110
9.4.2 Fluorescence test plates overview............................................................ 110
9.4.3 Preparation for the initial test .................................................................. 110
9.4.4 Fiber Sequence Test Plate 10-310P-160-14 of qT384 auto...................111
9.4.5 Checking the right sequence of fibers ...................................................... 111
9.5 Equipment for workshop.........................................................................112
9.5.1 ESD and workshop equipment................................................................112
10 Disposal ...................................................................................... 113
11 Replacement .............................................................................. 114

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 7 to 116
1General Description of qTOWER auto devices
1.1 Intended Use
The qTOWER3auto and ³84 auto are thermal cyclers for amplifying DNA by way of the poly-
merase chain reaction (PCR) licensed for real-time PCR experiments.
The integrated detector enables the measurement of the sample fluorescence in up to six
spectral channels during the PCR, with the filters used in the color or FRET modules being ex-
actly matched to the properties of the most frequently used fluorescence dyes, thereby per-
mitting a sensitive and selective detection of fluorescent PCR products.
Analytik Jena offers some number of color or FRET modules of which up to six can be installed
simultaneously in the device. Replacement and retrofit of color or FRET modules can be easily
accomplished.
qTOWER3auto is an open platform for real-time PCR and supports both intercalating dyes as
well as individual samples and kits of various manufacturers. qTOWER3auto can be used in
different applications, such as expression analyses, genotyping and the detection of patho-
gens. The qTOWER3auto is fully controlled from the PC using the program qPCRsoft auto
which provides the following functions:
Device control and monitoring
User Management
Context-sensitive help functions
Design of real-time PCR experiments and their evaluation
Storage of methods (templates) and measuring results (projects)
Planning and evaluation of
- Absolute quantifications
- Relative quantifications
- ΔΔCt analyses
- DNA melting curves
- Genotyping
Results printout
Results export to MS EXCEL or as CSV file
Results export to extended programs for the analysis of real-time PCR data (e.g. qBASE
etc.) in preparation
A detailed description of qPCRsoft auto is available in the software manual.
The qTOWER3auto combines a PCR thermal cycler with a patented fluorescence photometer.

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 8 to 116
2Safety instruction
2.1 Symbols and signal words

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 9 to 116
2.2 Safety symbols on the qTOWER³ auto
The qTOWER³ auto is fitted with safety symbols, the content of which must always be observed. Dam-
aged or missing safety symbols can cause incorrect actions leading to personal injury or material dam-
age! The safety symbols must not be removed! Dam-aged safety symbols must be replaced without de-
lay!
The following safety symbols are attached to the qTOWER³ auto and accessories:
Warning symbol
Mandatory action signs
(on heatable lid)
(on equipment backplate)
Warning against a
hazard location
Warning against hot
surface
Before opening the device always
Disconnect the mains plug
The following notice sign is attached to the rear of the qTOWER³ auto:
2.3 Technical condition of qTOWER³ auto
The qTOWER³ auto corresponds in its design and construction to the current state of the art technol-
ogy. Unauthorized modifications or changes, especially such that affect the safety of the staff and the
environment, are generally not allowed.
Observe the following:
•Any manipulation of the safety equipment is prohibited! In case of an
accident manipulations of the safety equipment will be interpreted as deliberate!
•The operator must only operate the device in a sound and operationally safe condition.
The technical condition must always comply with the legal requirements and regulations.
•Any changes in the device affecting its safety must be reported by the operating personnel
to the operator without delay.

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 10 to 116
2.4 Requirements for the service personnel
The operating and service personnel must have access to the manual at all times!
The qTOWER³ auto may only be repaired by qualified personnel who have been instructed in the
handling of the unit. The instruction also includes the communication of the contents of these oper-
ating instructions. In addition to the work safety instructions in this manual, the generally applicable
safety and accident prevention regulations of the respective country in which the unit is operated
must be
must be observed and complied with.
The operator must inform himself about the current status of these regulations.
Observe the following:
•The device must only be commissioned, operated and serviced by trained personnel instructed
in technical safety.
•The operation or servicing of the device by minors or individuals under the influence of alco-
hol, drugs or medication is not permitted.
•It must be ensured that only authorized personnel work at the device. The operating person-
nel must be familiar with the dangers arising from samples and excipients. Suitable personal
protection equipment must be worn.
•Prior to pauses or at the end of the work appropriate skin cleaning and protection measures
must be carried out.
•Eating, drinking and smoking at the installation location of the device is prohibited!
•The device must be handled with the appropriate care and kept clean in accordance with labor-
atory standards to prevent contamination of the device (e.g. on the heat-able lid). Observance
of these laboratory rules reduces the risk of being contaminated with potentially infectious ma-
terial and the risk of cross-contamination of the samples. Wear protective gloves and/or take
other safety measures if there is a chance that your skin may come to contact with infectious
material when handling the device.

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 11 to 116
2.5 Safety instructions - electrical equipment
Work on electrical components of the qTOWER³ auto may only be carried out by a qualified electri-
cian in accordance with the applicable electrical engineering rules. Life-threatening electrical volt-
ages may occur in the interior of the qTOWER³ auto!
Observe the following:
•Any work on the interior of the device may only be carried out by the customer service of Ana-
lytik Jena GmbH and specially authorized technicians.
•The electrical components must be checked regularly by a qualified electrician. Any defects,
such as loose connections, faulty or damaged cables, must be repaired without delay.
•Do not replace the removable mains cable of the device by a mains cable that does not meet
the specifications (without protective ground conductor).
•Before opening the device, it must be switched off from the power switch and the mains con-
nector must be disconnected from the mains outlet!
•The qTOWER³ auto must be switched off immediately using the power switch and the power
supply disconnected from the mains if there is any interference with the electric components.
•The qTOWER³ auto fulfills the corresponding requirements for interference emission and re-
sistance from the IEC 61326 series. Assess the electromagnetic environment of the device be-
fore operation.
•Do not operate the device near sources of strong electromagnetic radiation (e.g. unshielded,
deliberately operated high frequency source) as these may affect proper operation of the de-
vice.
2.6 Safety instructions – service and repair
•On principle, maintenance of the qTOWER³ auto is performed by the service department of
Analytik Jena GmbH or its authorized and trained specialist personnel. Unauthorized mainte-
nance can damage the device.
The following has to be observed:
•The exterior of the device may only be cleaned with a damp, not dripping, cloth
after the device has been switched off.
•Do not use alcohol (e.g. methanol or ethanol), organic solvents or abrasives to clean the de-
vice.
•Any maintenance on the device may usually only be carried out in the switched-off condition
(unless stated otherwise).

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 12 to 116
3Technical data
3.1 qTOWER³ auto and qTOWER³ 84 auto
This data can be found in the manual of the device.

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 13 to 116
4Technical description of instrument
4.1 qTOWER³ auto - Instrument overview

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 14 to 116
4.2Basic Module 1 and 2
4.2.1 Front and rear panel
Fig. 2 Front view Fig. 3 Rear view

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Valid from: 06.05.2021
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4.2.2 Basic housing- Front and rear panel
To be able to check or repair components in a basic module, the housing must first be dismantled.
The qTOWER³ auto front plates are fixed by six Magnetics on the metal housing. To do this, the
front panel can be pulled off the housing,
That’s why one images of this device are shown here, only.
The magnets inside the Front are extremely strong. Pay attention when working with metal
tools nearby. Otherwise the lacquering could be damaged.
Front panel:
Fig. 4Fig. 5Fig. 6
Different special front plates are available as qTOWER³ auto and qTOWER³ 84 auto.
Fig. 4: Front panel qTOWER³ auto, 10-3107-822-11
Front panel qTOWER³84 auto, 10-3107-926-11
Fig. 5: Front panel, pulled them from the housing in service cases
Fig. 6: Position of 6 magnetics on the metal housing

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 16 to 116
4.2.3 Basic housing- locking screws
To remove the upper housing, remove the two screws located behind the front panel. The housing
can be pulled off to the rear after the 2 screws have been removed.
Fig. 7 Position of housing screws
4.2.4 Basic housing- mounting
To remove the rear panel unscrew the 6 screws fig. 8. Then the housing can be pulled. Upper rear
panel, 10-3107-818-51, Basic upper housing, 10-3107-810-61 fig. 9
Fig. 8Fig. 9

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
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Page 17 to 116
Fig. 10 shows the Basic unit from the front after the housing has been removed.
Fig. 10 Basic lower housing,10-3107-802-61
Fig. 11 shows the Rear panel with cable
Fig. 11 Basic lower housing rear panel,10-3107-808-51
Fig. 10Fig. 11
Power cable, 10-3108-160-91, distance 3 m, position left see Fig.11
Data 1 cable, 10-3108-159-91, distance 3 m, position middle see Fig. 11
Data 2 cable, 10-3108-161-91, distance 3 m, position right see Fig.11
4.2.5 Basic housing- Rear panel overview
Rear panel
Fig. 12 Upper rear panel, 10-3107-818-51 rear side with USB hub

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
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Page 18 to 116
Fig. 13 Fan, 10-3108-173-96 mounted on the rear panel
Fig. 14 USB hub, 10-3108-170-83 mounted on the rear panel
4.2.6 Basic housing- Base mounting
Since the fans in the base assembly can become clogged with dust, they must be cleaned from time to
time. They can be cleaned with a hoover or compressed air. The fans are mounted on the chassis,
which is enclosed by the housing. To be able to replace the fans, they must be removed from the base
assembly.
For this replacement of the fans or a repair inside the enclosure, the 4 enclosure device stands,
10-406-222, must first be unscrewed, see Figure 15. Then the 6 enclosure screws, see Figure 16,
must be removed. Then the housing of the lower assembly can be removed, see Fig.17.

Rev. 01-2021 Service Manual of the
qTOWER3 auto
Valid from: 06.05.2021
Service Manual qTOWER3Auto Rev. 01 / valid from: 06.05.2021 Page 1 of 125
Page 19 to 116
Fig. 15Fig.16
Fig. 17

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qTOWER3 auto
Valid from: 06.05.2021
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4.2.7 Basic housing- Base boards and plugs
Figs. 18 to 21 show the circuit boards in the base assembly, which can be seen after disman-
tling the housing.
On the right side is the USB board
(SPI-RS485-LP board), 10-3108-140-83 see Fig. 19. It is
responsible for amplifying and booting the internal USB signal. Th
e board is equipped with DIP
switches, which are shown in Fig. 2
0. In the basic position, the switches S2 point downwards.
Fig. 18 Fig.19
On the left side is the high
-current connection for the block, see Fig. 21. The Peltier elements
in the block of the base module are controlled by the power module via this
connection. Fig.
22 shows the opened rear panel with the three electrical connections to the power module.
Fig.2
0Fig. 21
Fig. 2
1shows the mounted high current cable, 10-3108-172-91 on the right side of the basic
module.
The states of the Peltier elements can be checked at these connectors.