BiOptic Qsep Series User manual

BiOptic Inc.,
4F., No.108-3, Minquan Rd., Xindian Dist., New Taipei City 23141, Taiwan (R.O.C.)
www.bioptic.com.tw
Revolution
Qsep


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Welcome
Thank you for purchasing Qsep Series capillary electrophoresis system. Now you can
experience this high-performance, fully-automated and easy-to-use system.
Copyright and Trademarks
Copyright ©BiOptic Inc.
All rights reserved. Reproduction, adaptation, or translation of this manual is
prohibited without prior written permission of BiOptic Inc., except as allowed under
the copyright laws.
Qsep™ and Q-Analyzer™ are registered trademarks of BiOptic Inc.
Microsoft Windows is registered trademarks of Microsoft Corporation.
Product and company names listed are trademarks or trade names of their respective
companies.
Symbols ofQsepSeries
Symbol
Description
CE mark for European Conformity.
FCC mark of the United States Federal Communications Commission.
Underwriters Laboratories (UL LLC) Safety Certification

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Welcome ........................................................................................................................... 2
Copyright and Trademarks ............................................................................................... 2
Symbols of Qsep Series.................................................................................................... 2
Applications...................................................................................................................... 7
Packing List ...................................................................................................................... 7
Cautions............................................................................................................................ 8
1. System Overview........................................................................................................ 10
1.1 Pre-program Method and Cartridge.......................................................................11
1.1.1 Pre-program Method .......................................................................................11
1.2 System Installation ............................................................................................... 12
1.2.1 Software Requirements .................................................................................. 12
2. Q-Analyzer Installation Instruction............................................................................ 13
2.1 Software Installation............................................................................................. 13
2.2 Software Mode ..................................................................................................... 18
2.2.1 USB Software Key ........................................................................................ 20
2.2.2 Q-Editor License............................................................................................ 23
3. Start to Use Qsep™ Series ......................................................................................... 26
3.1 Operation of Qsep™ Series.................................................................................. 27
3.1.1 Connection Assistance................................................................................... 28
3.1.2 Sequence and Method Setting ....................................................................... 32
3.2 Cartridge Calibration ............................................................................................ 40
3.3 Edit Sample Position Settings .............................................................................. 42
3.4 Recalibration......................................................................................................... 44
3.5 Capillary Clog Check ........................................................................................... 45
3.6 Purge Check Function .......................................................................................... 48
3.7 Home Function ..................................................................................................... 50
4. Q-Analyzer™ User Interface...................................................................................... 51
4.1 Main Window ....................................................................................................... 51
4.1.1 System Overview........................................................................................... 52
4.1.2 System Status Column................................................................................... 53
4.2 Function bar and Toolbar...................................................................................... 54
4.2.1 Instrument...................................................................................................... 54
4.2.2 Results ........................................................................................................... 59
4.2.3 Comparison.................................................................................................... 65
4.2.4 Real Time....................................................................................................... 66
4.3 Menu..................................................................................................................... 67

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4.3.1 File................................................................................................................. 67
4.3.2 Edit ................................................................................................................ 70
4.3.3 Tool................................................................................................................ 74
4.3.4 View............................................................................................................... 77
4.3.5 Window.......................................................................................................... 78
4.3.6 Setting............................................................................................................ 78
4.3.7 Language ....................................................................................................... 79
4.3.8 Help ............................................................................................................... 80
4.4 Control Panel ........................................................................................................ 82
4.4.1 Main............................................................................................................... 82
4.4.2 Method........................................................................................................... 84
4.4.3 Direct Control (Partial Advanced Only)........................................................ 86
4.4.4 Board Setting (Advanced Only) .................................................................... 87
5. Result/Data Analysis .................................................................................................. 88
5.1 Result for Data Display ........................................................................................ 88
5.1.1 Calculation..................................................................................................... 91
5.1.2 Reference Marker Table ................................................................................ 93
5.1.3 Improve Calculate Accuracy ......................................................................... 95
5.2 Comparison........................................................................................................... 96
5.2.1 Export the Report of Compare Result ......................................................... 103
5.3 Total RNA Quality Analysis ............................................................................... 105
5.4 Smear DNA Analysis (gDNA QC for NGS) ...................................................... 107
5.5 Peak Calling Function for Clinical Testing ........................................................ 109
Appendix A-Troubleshooting ........................................................................................112
1. Unpacking, packing process and Installation ............................................................112
Q1：How to unpack the cargo and what should we notice when move the
instrument? ................................................................................................................112
Q2：What are the minimum computer requirements and recommendations? .........112
Q3：What is the size of the result file?.....................................................................113
Q4：Do we need to install the software first or connect the cable first?..................113
Q5：Can power adaptors be used alternately?..........................................................113
2. Instrument not working or working abnormally........................................................113
2.1 Before use................................................................................................................113
Q1：Pressing the machine power, but have no response? ........................................113
Q2：How should we do when PC cannot detect the connection of Qsep100?...........114
Q3：How should we do when PC cannot connect with Qsep1 WiFi mode? ............114
Q4：What does the light of Qairbox mean? ...............................................................115
2.2 During use ...............................................................................................................115

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Q5：If the buffer tray can’t move smoothly, how should we do? ............................115
Q6：The Qairbox works frequently, over 3 times/min...............................................117
Q7：Jet error window pop-out..................................................................................117
3. Cartridge issues .........................................................................................................118
3.1 Before use................................................................................................................118
Q1：HV check failed or Calibration failed...............................................................118
Q2：What’s wrong with the pop-out error window?................................................119
3.2 During use ...............................................................................................................119
Q3：How to check if the cartridge is clogged or not and how to rescue the dry out
cartridge? ...................................................................................................................119
Q4：What if the cartridge has expired, but still has runs left? ................................ 120
Q5：What if the cartridge has sucked the mineral oil? How to recover it?............. 120
Q6：Anything needs to notice during insert or take out the cartridge?................... 121
3.3 Storage.................................................................................................................... 122
Q7：How to store the cartridge? And relative buffer?............................................. 122
4. Questions of operation.............................................................................................. 123
Q1：How do I place the Qsep400 Alignment marker and size marker? ................... 123
Q2：How do I prepare the unknown sample before Qsep analysis? ....................... 123
Q3：The minimum volume of sample? ................................................................... 123
Q4：The sample consumption (per run)? ................................................................ 124
Q5：What is the air pressure range of each instrument? ......................................... 124
Q6：What if we use the wrong buffer?.................................................................... 124
Q7：Will dye or organic solvent influence cartridge? How to pretreat the sample?125
Q8：What is the difference between Basic key and Advance software key?.......... 125
Q9：What is the difference between Q-AnalyzerTM, Q-EditorTM and Q-viewerTM?126
Q10：Why should I do recalibration?...................................................................... 127
5. Unexpected results.................................................................................................... 128
Q1：What kind of conditions will cause unstable current? ..................................... 128
Q2：What to do if alignment marker and samples are migrating too slowly and the
upper alignment marker does not appear on the result? ........................................... 128
Q3：Identify wrong alignment marker or size marker ............................................ 129
Q4：The calculated size is wrong............................................................................ 131
Q5：Is the concentration display in result table reliable?........................................ 131
Q6：The current is stable, but there is no signal at all, even the alignment marker
does not appear. RFU near zero................................................................................ 131
Q7：The current is stable, but there is no signal except the alignment marker....... 132
Q8：One of the 4 Channel shows different result with others................................. 132
6. Specific application issues (RNA, Protein …) ......................................................... 133

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6.1 R1 RNA cartridge ............................................................................................... 133
Q1：When running RNA samples, are there any special things to consider? ......... 133
Q2：What is the criteria of RQN? ........................................................................... 133
Q3：Why the result shows “N/A” in RQN?............................................................ 134
6.2 P2 Protein cartridge ............................................................................................ 135
Q4：What Protein Alignment marker should I use?................................................ 135
Q5：Which instrument can I use to analyze protein sample? Or what labeling dye
should I choose? ....................................................................................................... 136
Q6：How to do the labeling process?...................................................................... 136
7. Maintenance.............................................................................................................. 136
Q1：How often should I change the Marker and Buffer? ....................................... 136
Q2：What happens if I don't change the filter for a long time??............................. 136
Q3：How to clean the instrument regularly?........................................................... 136
8. Others ....................................................................................................................... 137
Q1：Should we turn off the instrument and pump every day?................................ 137
Q2：How should we do before discard the cartridge?............................................. 137
Report to BiOptic ..................................................................................................... 138

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Limitation of Liability
Qsep Series, Q-Analyzer™software, and all related reagents are designed for the use of
electrophoresis analysis in general biochemistry laboratory. If you use it for profit,
diagnosis, or other non-research purposes experiments, the company is not responsible
for the accuracy and reliability of the result and the safety of operation.
BEFORE ATTEMPTING TO OPERATE THE INSTRUMENT, READ ALL PRODUCT
MANUALS AND FOLLOW THE INSTRUCTIONS.
BiOptic Inc. assumes no liability whatsoever for any personal injury, property damage,
or other loss resulting from not complying or familiar with the manuals, or improper
operation of the devices.
Applications
Genetic Profile Screening
Amplified Fragment Length Polymorphisms
Bacterial/Viral Genotyping and Identification
DNA Fragment/PCR Product Analysis
Rapid Analysis of Genomic DNA Samples
RNA Analysis
Protein Analysis
Packing List
Each Qsep™ Series Instrument package comes with the following:
Qsep™CE Instrument
Qsep™ Standard and High resolution cartridge Kit (C105200)
Power Cord with Adapter
USB Cable
Software Key (Basic edition)
Installation Disc including Q-Analyzer™and Qsep™ Operation Manual
: The Software key contains 8GB storage space, Q-Analyzer™ and Qsep™ Series
Operation Manual, including Hardware version and Software version.

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Cautions
Qsep™ Seriesare capillary electrophoresis instruments driven by high voltage.
Carefully read and thoroughly comply with the following instructions to maintain the
integrity of the equipment, the reliability of results, and the safety of operation.
Keep Qsep™ Series away from other electronic device and voltage sources.
1. Only the components and consumables provided by BiOptic Inc. are
suggested to use.
2.  perform the following actions:
•Disassemble Qsep™ Series instrument and its associated parts
•Bumps or jolts to Qsep™ Series
•Move the instrument or remove any connected external equipment,
such as computers and air pumps, while Qsep™ Series are in action
•Open the sample door or cartridge door while Qsep™ Series are in
action
•Remove the cartridge while Qsep™ Series are in action
•Power off Qsep™ Series before confirming Qsep™ Series are inactive
3. Store the cartridge upright; do not lay the cartridge on a table horizontally or
place it upside down.
4. Store the cartridge in the calm-shell container (Cartridge needs to be stored
in a proper environment as the instructions of cartridge unpacking guide to
maintaining its lifetime and quality).
5. Ensure the cartridge is taking out from Qsep™ Series before shutting down or
disconnecting instrument. Or ensure the cartridge is placed at  position
before shutting down or disconnecting Qsep™ Series. Failure to do so will
cause dryness of the gel at the cartridge tip, which will damage the cartridge.
6. Before operating Qsep™ Series, ensure the buffer tray is placed properly.
7. Dilute the PCR DNA test sample to 1
20 with our dilution buffer before
running the test for obtaining better result and retaining the lifetime of the
cartridge. You can adjust the dilution ratio after primary test runs.
8. Ensure that the test sample, alignment marker, cartridge, and buffer tray
have been removed from the instrument before transporting or shipping.
9. If the buffer solution spills out on the platform inside the instrument, wipe it
with tissue and clean it up immediately.
10. Ensure that the main power of the instrument has been shut down and all

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the test materials have been removed before cleaning Qsep™ Series.
11. User can also use N2 gas as an air source to ensure the air quality and prevent
damages to the devices caused by dirty air.
12. Make sure to press the plastic connection ring before pulling the air tube out
from the back of the instrument.
13. Release the condensation water in the external air pump periodically and
check the water level before each use to avoid the mist damage the devices
of Qsep™ Series.
14. To cut off the power, please disconnect the power plug.
15. Please clean the instrument with a dry cloth. For other maintenance, please
contact the local distributor.
16. Please use the MAINS power cord within the adequate rating.
17. The conditions of transportation and storage: Temperature -30 to +60°C.
Humidity 20 to 80% RH, non-condensing.
: Strongly suggest performing this step whenever you start to operate Qsep™
Series.
Qsep™ Series are high-voltage Multiple-channel electrophoresis
system. Please follow the operation manual and laboratory safety guidelines for
system operation. Do not remove covers. For operation and safety questions,
please contact BiOptic Inc. at the official website or with your local BiOptic
representatives.

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1. System Overview
Qsep™ Series are a fully automated CE system developed by BiOptic Inc., which uses
pen-shaped disposable gel-cartridges to improve efficiency. Time-consuming manual
procedures such as gel preparation, sample loading, and capillary changing are no
longer required. Further, the information will be obtained easily with the fully-
automated Qsep™ Series. Qsep1™, Qsep100™and Qsep400™ are designed to
accommodate the standard 96-well and 8 & 12 well PCR strip, respectively.
Qsep™ Series’s compact design helps you to set up and operate the instrument
intuitively. The disposable gel-cartridge with integrated pre-programmed test
methods makes capillary electrophoresis experiments no longer a painful procedure
that requires well-trained operators. No more worries about the operation and human
errors caused by different operators which affect the accuracy and reproducibility of
the results.
The following sections will describe the product overview, the functions of Qsep™
Series instruments and the gel-cartridge. Please read through this section and get
ready to be at amazed with the power of Qsep™ Series.
 The operator of this instrument is advised that if the equipment is
operated in a manner not specified in this manual, the protection provided by the
equipment may be impaired.

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1.1 Pre-program Method and Cartridge
1.1.1 Pre-program Method
Qsep™series are designed to work with the special-designed cartridges provided by
BiOptic Inc.. The modularization design of cartridges makes the time-consuming gel
preparation no longer be required. For the cartridges, we provide a various specific
testing protocol, so-called “Method” which integrates the sequential steps to accomplish
the test. The various cartridges and pre-programmed Methods are utilized in performing
the CE experiment that corresponds to the size range and concentration of the sample.
Additionally, users can create their own Methods according to their preference.
In the Method selector (Figure 1-1), the user can check the Methods corresponding to
suitable size range, alignment marker, and the cartridge type. If the latch function is done,
Qsep™ series will automatically detect the type of the cartridge in use and only display
the suggested Methods according to the selected cartridge type.
Figure 1-1 Method Selector Tab

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1.2 System Installation
1.2.1 Software Requirements



Microsoft® Windows 7 32-bit or 64-bit
Microsoft® Windows 8 32-bit or 64-bit
Microsoft® Windows 8.1 32-bit or 64-bit
Microsoft® Windows 10 32-bit or 64-bit

500 MB
1 GB

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2. Q-Analyzer Installation Instruction
A suitable operating environment is essential to ensuring the best performance of Qsep™
Series.
2.1 Software Installation
Q-Analyzer™, including Q-Analyzer and Q-Analyzer for Qsep400, are the software that
specially designed to operate Qsep™ series. The software key will be found in the
package. Click “” for Qsep1™ or Qsep100™ and “ 
” for Qsep400™ to begin the installation.
: Please close all the other applications before installing Q-Analyzer™. In addition,
 connect Qsep ™series to the computer while installing Q-Analyzer™.
The installation steps are as follow:
Step 1. Click Q-Analyzer-Setup.exe to start Setup Wizard

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Step 2. Specify the default data archive folder
Step 3. Select the program destination

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Step 4. Create a desktop icon and select the driver you wish to install
Step 5. Verify the settings of the installation and click Install to start the installation

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Step 6. Q-Analyzer™ installation is in progress
Step 7. The installation is completed and Q-Analyzer™is ready to be launched
After launching Q-Analyzer™, the Main Window appears on the screen. The
instrument page is used to communicate with the device (Figure 2-1). For the different
instruments, the picture of instruments will show the corresponding pictures when
connecting Qsep Series.
The software will create a default project named according to the date automatically.

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Figure 2-1 Software overview

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2.2 Software Mode
Q-Analyzer/Q-Editor/Q-Viewer are integrated into the installed software.
Q-Analyzer™ Setup has combined with these three programs, so there is no need to
install them separately. Please double-click the icon and follow the on-screen
instruction to install it.
When double clicking Q-Analyzer™ icon, the software will automatically detect the
status and launch the respective program according to the condition below. (Q-
Analyzer,Q-Editor, or Q-Viewer)
Software Level table








 
Q-Editor




Q-Analyzer


Q-Analyzer 


Q-Editor

Q-Viewer










Q-Analyzer




Create
Method
Q-Analyzer



Q-Editor


License
binded to the
PC
Q-Viewer

Without Qsep™ Series or the software key, user can click to start the Q-Viewer,
after launching Q-Analyzer™. The Q-Viewer is only used to display the result file.

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2.2.1 USB Software Key
⚫
A software key is required, if the user operates the software in Q-Analyzer mode
without Qsep™ series.The software key must be activated first before its initial
usage. Insert the software key into an available USB port on the computer before
launching Q-Analyzer™.
Figure 2-2 Software Key
The system will automatically lead you to the activation page while starting Q-
Analyzer™. Enter your Company Name, User ID, and Password. After confirming the
password, you will be directed to the Login page.
Figure 2-3 Login page
*Note: Password comprises 8characters (6characters for the previous version of
software key) in length contained characters and/or numbers and is case-sensitive.
If the user wants to change the password of the software key, go to Change Password