Advanced User Manual
318 Pages
Preview
Page 1
Version 4.0
April 2014
QIAxcel® Advanced User Manual For use with QIAxcel ScreenGel® Software v1.3
Sample & Assay Technologies
Trademarks: QIAGEN®, QIAsymphony®, QIAgility®, QIAxcel®, ScreenGel® (QIAGEN Group); Adobe®, Reader® (Adobe Systems Inc.); Excel®, Microsoft®, Windows® (Microsoft Corporation); Intel®, Celeron® (Intel Corporation). Registered names, trademarks, etc. used in this document, even when not specifically marked as such, are not to be considered unprotected by law. 1082215 04/2014 © 2011–2014 QIAGEN, all rights reserved.
Conte nts
3
Contents 1
Safety Information
1-2
1 .1
P r ope r use ... 1 -2
1 .2
Ele... ctr ical safe ty 1 -3
1 .3
Envir onme nt ... 1 -4
1 .4
Che micals ... 1 -4
1 .5
Waste disposal ... 1 -5
1 .6
Me... chanical haz ar ds 1 -5
1 .7
S ymbols on the QIAx ce l Advance d ... 1 -5
2
Introduction
2-2
2 .1
About this use r manual ... 2 -2
2 .2
G e... ne r al infor mation 2 -2
2 .3
Inte... nde d use of the QIAx ce l Advance d 2 -3
2 .3 .1
3
R e... qui r e me nt s for Q I A x ce l A dvance d use r s 2-4
General Description
3-2
3 .1
QIAx ce l Advance d pr inciple ... 3 -2
3 .2
Ex te r nal fe atur e s of the QIAx ce l Advance d ... 3 -3
3 .3
G e... l car tr idge s 3 -4
3 .4
Compute r and softwar e ... 3 -5
4 4 .1
Installation Procedures
4-2
Re quir e me nts ... 4 -2 S i t... e 4-2 P ow e r r e qui r e me nt s ... 4-2 Gr... oundi ng r e qui r e me nt s 4-3
4 .1 .1 4 .1 .2 4 .1 .3 4 .2
Unpacking the QIAx ce l Advance d ... 4 -3
4 .3
Installing the QIAx ce l Advance d ... 4 -3
4 .3 .1 4 .3 .2 4 .3 .3 4 .3 .4 4 .3 .5 4 .3 .6 4 .4
5
R e... l e asi ng t he t r anspor t l ock 4-4 I nst r ume nt se t up ... 4-4 I nst al l at i on of A C pow e r cor d ... 4-4 I nst al l at i on of t he N 2 cy l i nde r ... 4-5 I nst al l at i on of t he Q I A x ce l S cr e e nGe l soft w ar e ... 4-5 Ge... t t i ng st ar t e d w i t h t he Q I A x ce l S cr e e nGe l soft w ar e 4-8
P acking the QIAx ce l Advance d ... 4 -8
Operating Procedures
5-2
5 .1
Unpacking a QIAx ce l K it ... 5 -2
5 .2
S e tting up the QIAx ce l Advance d ... 5 -3
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4
QIAx ce l Advance d Use r Manual P r... e par i ng t he buffe r t r ay 5-3 Loadi ng t he buffe r t r ay ... 5-5 I nst al l i ng a Q I A x ce l ge l car t r i dge and smar t ke y ... 5-5 R e... movi ng a Q I A x ce l ge l car t r i dge 5-7 S t ... or i ng a Q I A x ce l ge l car t r i dge 5-7
5 .2 .1 5 .2 .2 5 .2 .3 5 .2 .4 5 .2 .5 5 .3
Ope r ating the QIAx ce l Advance d ... 5 -8
5 .3 .1 5 .3 .2
T hi ngs t o do be for e st ar t i ng ... 5-9 S t ar t i ng a r un ... 5-9
6 6 .1 6 .1 .1 6 .1 .2 6 .1 .3 6 .1 .4 6 .1 .5
QIAxcel ScreenGel Software
6-2
Conce pts ... 6 -2 Mode s ... 6-2 Use r r ol e s ... 6-3 E nvi r onme nt s ... 6-5 P r... ofi l e s 6-5 Ge... ne r al soft w ar e usage 6-6 Editing... data in tables 6-8 Displaying errors and warnings ... 6-9 Displaying modifications ... 6-11 Getting help ... 6-14
6 .2
Use r authe ntication ... 6 -1 5
6 .3
P r... oce ss 6 -1 9
6 .3 .1 6 .3 .2 6 .3 .3
6 .3 .4 6 .3 .5 6 .3 .6 6 .4 6 .4 .1
6 .4 .2
R... unni ng a pr oce ss w i t h advance d opt i ons 6-20 Provide Sample Information ... 6-27 Modi fy i ng a pr oce ss pr ofi l e ... 6-31 P... r oce ss pr ofi l e opt i ons 6-34 Selecting general process options ... 6-36 Selecting run parameters ... 6-37 Selecting analysis parameters ... 6-40 Selecting marker ... 6-42 Selecting peak calling instructions ... 6-44 Selecting report/export parameters ... 6-45 Run parameters and result structure ... 6-47 Cr e at i ng a ne w pr oce ss pr ofi l e ... 6-51 Vi... e w i ng me t hod de t ai l s 6-52 "S... t at us I nfor mat i on" pane l 6-53
Analysis ... 6 -5 6 Handl i ng sampl e s and e x pe r i me nt s ... 6-57 Meaning of sample icons ... 6-59 Loading sample data ... 6-59 Selecting samples ... 6-61 Selecting samples for analysis or report ... 6-62 Expanding and collapsing ... 6-63 Activating an experiment ... 6-63 Saving an experiment ... 6-64 Closing an experiment ... 6-66 Importing BioCalculator Data ... 6-66 Revising sample information ... 6-67 Handling an incomplete experiment ... 6-67 Vi... e w i ng sampl e dat a 6-68 Adding samples to views ... 6-68 Removing samples from views ... 6-71 QIAxcel Advanced User Manual 04/2014
Conte nts
6 .4 .3
6 .4 .4
6 .4 .5
6 .4 .6
6 .4 .7
6 .4 .8
6 .4 .9
6 .4 .1 0 6 .4 .1 1
6 .4 .1 2
6 .5 6 .5 .1
5
Exporting view to clipboard ... 6-73 Direct... printing view 6-75 Result... table 6-75 Gel view ... 6-81 Electropherogram view ... 6-85 Electropherogram overview ... 6-91 Electropherogram superposition view ... 6-95 Inspecting sample properties ... 6-98 P... e ak de t e ct i on 6-99 Saturated signals ... 6-100 Peak... detection procedure 6-101 Modifying an analysis profile ... 6-104 Creating a new analysis profile ... 6-109 S i z e and conce nt r at i on de t e r mi nat i on ... 6-109 Size ... and concentration determination procedure 6-111 Creating a reference marker ... 6-113 Creating a new size marker table ... 6-116 P e ak Cal l i ng ... 6-118 Modifying a peak calling instruction ... 6-120 Creating a new peak calling instruction ... 6-123 Peak... pattern matching 6-124 A nal y si s of DN A sampl e s ... 6-125 Standard DNA analysis ... 6-126 Fast ... Analysis DNA analysis 6-127 Smear DNA analysis ... 6-127 gDNA analysis ... 6-128 A nal y si s of R N A sampl e s ... 6-129 Standard RNA analysis ... 6-130 RNA... quality control analysis 6-131 A nal y si s of pr ot e i n sampl e s ... 6-133 Low ... complexity sample analysis 6-134 High... complexity sample analysis 6-135 Relative abundance ... 6-135 Absolute quantification ... 6-136 Manual l y modi fy i ng anal y si s r e sul t s ... 6-138 Modifying the threshold ... 6-138 Deleting a peak ... 6-138 Adding a peak ... 6-138 Removing analysis results ... 6-139 Checking alignment marker ... 6-140 Modifying areas of interest ... 6-141 R e anal y si s of mul t i pl e e x pe r i me nt s ... 6-141 Cust omi z i ng e x pe r i me nt s ... 6-142 Creating a new experiment ... 6-143 Modifying an experiment ... 6-144 R e por t / E x por t ... 6-147 Generating a report ... 6-148 Report options ... 6-149 Exporting data ... 6-166 Export options ... 6-167 Modifying a report/export profile ... 6-177 Creating a new report/export profile ... 6-178
S e r vice ... 6 -1 7 8 Cal i br at i ng a car t r i dge ... 6-179
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6 .5 .2
6 .5 .3
6 .6 6 .6 .1 6 .6 .2 6 .6 .3
7
QIAx ce l Advance d Use r Manual Running the calibration wizard ... 6-179 Recalibrating a cartridge ... 6-181 S y st e m Che ck ... 6-182 Complete Check ... 6-182 Detector Test ... 6-183 Filter... Check 6-184 Movement Check ... 6-185 Leakage Test ... 6-186 Mai nt e nance ... 6-186 Purge ... 6-187 Long... purge 6-187 Empty N2 bottle ... 6-188 Setting the instrument ID ... 6-189 Troubleshooting folder and log files ... 6-190
Configur ation ... 6 -1 9 2 S e t t i ngs ... 6-192 P r ofi l e manage me nt ... 6-197 Use r manage me nt ... 6-198
Maintenance Procedures
7-2
7 .1
Cle... aning of the QIAx ce l Advance d 7 -2
7 .2
Minor cor r e ctive mainte nance ... 7 -3
7 .2 .1 7 .2 .2 7 .2 .3 7 .2 .4
8
F use r e pl ace me nt and cl e ani ng ... 7-3 N 2... cy l i nde r r e pl ace me nt 7-3 A l ... t e r nat e N 2 suppl y 7-4 Bl ... ocke d pur ge fi l t e r 7-4
Troubleshooting
8-2
8 .1
S yste m se tup ... 8 -2
8 .2
Ope r ation ... 8 -3
8 .3
DNA applications ... 8 -4
8 .4
RNA applications ... 8 -8
8 .5
P r... ote in applications 8 -1 0
9
Glossary
9-2
10
Appendices
10-2
1 0 .1
Appe ndix A ... 1 0 -3
1 0 .2
Appe ndix B ... 1 0 -7
1 0 .3
Appe ndix C ... 1 0 -1 4
1 0 .4
Appe ndix D ... 1 0 -1 7
1 0 .5
Appe ndix E ... 1 0 -2 1
1 0 .6
Appe ndix F ... 1 0 -2 2
1 0 .7
Appe ndix G ... 1 0 -2 7
1 0 .8
Appe ndix H ... 1 0 -3 2
QIAxcel Advanced User Manual 04/2014
Conte nts
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7
1. Safety Information
Safety Information
1
1-2
Safety Information Before using the QIAxcel Advanced, 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. 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 WARNING/ CAUTION
Proper use [W1] Risk of personal injury and material damage Improper use of the QIAxcel Advanced may cause personal injuries or damage to the instrument. The QIAxcel Advanced must only be operated by qualified personnel who have been appropriately trained. Servicing of the QIAxcel Advanced must only be performed by QIAGEN Field Service Specialists.
Perform the maintenance as described in the Maintenance Procedures section. QIAGEN charges for repairs that are required due to incorrect maintenance.
WARNING/ CAUTION
[W2] Risk of personal injury and material damage The QIAxcel Advanced 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 Do not attempt to move the QIAxcel Advanced during operation.
[W3]
CAUTION
Damage to the instrument Avoid spilling water or chemicals onto the QIAxcel Advanced. Damage caused by water or chemical spillage will void your warranty.
[C1]
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QIAxcel Advanced User Manual
In case of emergency, switch off the QIAxcel Advanced at the power switch at the rear of the instrument and unplug the power cord from the power outlet.
CAUTION
1.2
Damage to the instrument If the "Pressure 1" status is "Low", increase system pressure before performing the "unlatch" command. Removing the cartridge and unlatching with reduced pressure may damage the instrument.
[C2]
Electrical safety Disconnect the line power cord from the power outlet before servicing.
WARNING
[W4] Electrical hazard 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, and opening covers or removing parts is likely to expose live parts.
To ensure satisfactory and safe operation of the QIAxcel Advanced, follow the advice 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. When replacing the main fuse, replace only with the type and current rating specified on the rating label. 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 under unfavorable conditions for a prolonged period. It has been subjected to severe transport stresses.
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Safety Information
1.3
1-4
Environment Operating conditions
WARNING
Explosive atmosphere The QIAxcel Advanced is not designed for use in an explosive atmosphere.
WARNING
[W6] Risk of explosion The QIAxcel Advanced is intended for use with reagents and substances supplied with QIAGEN QIAxcel Kits. Use of other reagents and substances may lead to fire or explosion.
CAUTION
Damage to the instrument Direct sunlight may bleach parts of the instrument and cause damage to plastic parts. The QIAxcel Advanced must be located out of direct sunlight.
CAUTION
[C4] Damage to the cartridge When in use, the gel cartridge should not be left out of the "Wash park" position of the buffer tray for more than 15 minutes. Failure to do so will cause the capillary tips to dry out, affecting correct function of the cartridge. Dry tips will void the warranty. The capillary tips are made of glass and are very fragile. Take care not to knock the tips on any hard surfaces. Failure to do so will cause the capillary tips to break, affecting correct function of the cartridge. Broken tips will void the warranty.
1.4 WARNING
[W5]
[C3]
Chemicals [W7] Hazardous chemicals Some chemicals used with this instrument may be hazardous or may become hazardous after completion of the 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).
WARNING
[W8] Risk of fire When cleaning the QIAxcel Advanced with alcohol-based disinfectant, leave the QIAxcel Advanced doors open to allow flammable vapors to disperse.
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QIAxcel Advanced User Manual
1.5
Waste disposal Used labware and containers may contain hazardous chemicals. Such wastes must be collected and disposed of properly according to local safety regulations. For information about how to dispose of the QIAxcel Advanced, see Appendix A.
1.6
Mechanical hazards The cartridge door and sample door of the QIAxcel Advanced must remain closed during operation of the instrument.
WARNING
1.7
[W9] Moving parts To avoid contact with moving parts during operation of the QIAxcel Advanced, the instrument must be operated with the cartridge door and sample door closed. If the door sensors are not functioning correctly, contact QIAGEN Technical Services.
Symbols on the QIAxcel Advanced Symbol
Location Type plate on the back of the instrument Type plate on the back of the instrument
Description CE mark CSA listing mark for Canada and the USA
Type plate on the back of the Legal manufacturer instrument Type plate on the back of the Waste Electrical and Electronic instrument Equipment (WEEE)
Type plate on the back of the FCC mark of the United States instrument Federal Communications Commission
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Safety Information
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1-6
2. Introduction
Introduction
2
2-2
Introduction Thank you for choosing the QIAxcel Advanced. We are confident it will become an integral part of your laboratory. Before using the QIAxcel Advanced, 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.
2.1
About this user manual This user manual provides information about the QIAxcel Advanced in the following sections: Safety Information Introduction General Description Installation Procedures Operating Procedures QIAxcel ScreenGel Software Maintenance Procedures Troubleshooting Glossary Appendices
The appendices include the following: Technical data QIAxcel Advanced methods and accessories Data analysis algorithm descriptions Warranty liability clause
2.2
General information Technical assistance At QIAGEN, we pride ourselves on the quality and availability of our technical support. Our Technical Services Departments are staffed by experienced scientists with extensive practical and theoretical expertise in sample and assay technologies and the use of QIAGEN® products. If you have any questions or experience any difficulties regarding the QIAxcel Advanced or QIAGEN products in general, do not hesitate to contact us. QIAGEN customers are a major source of information regarding advanced or specialized uses of our products. This information is helpful to other scientists as well as to the researchers at QIAGEN. We therefore encourage you to contact us if you have any suggestions about product performance or new applications and techniques. For technical assistance and more information, please see our Technical Support Center at www. qiagen.com/goto/TechSupportCenter or call one of the QIAGEN Technical Service Departments or local distributors (see back cover or visit www.qiagen.com).
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QIAxcel Advanced User Manual
Policy statement It is the policy of QIAGEN to improve products as new techniques and components become available. QIAGEN reserves the right to change specifications at any time. In an effort to produce useful and appropriate documentation, we would appreciate your comments on this user manual. Please contact QIAGEN Technical Services.
Version management This document is the QIAxcel Advanced User Manual, version 4.0.
2.3
Intended use of the QIAxcel Advanced The QIAxcel Advanced is a multicapillary electrophoresis instrument, designed to perform fast and fully automated DNA fragment analysis, qualitative and quantitative RNA analysis, or protein size and concentration analysis. The QIAxcel Advanced instrument is intended to be used only in combination with QIAxcel Kits for applications described in the respective QIAxcel Kit handbooks. The QIAxcel Advanced instrument is intended for use by professional users, such as technicians and physicians trained in molecular biological techniques and the operation of the QIAxcel Advanced instrument.
QIAxcel Advanced User Manual 04/2014
Introduction
2.3.1
Requirements for QIAxcel Advanced users This table covers the general level of competence and training necessary for transportation, installation, use, maintenance, and servicing of the QIAxcel Advanced.
Task
Personnel
Training and experience
Transportation
No special requirements
No special requirements
Installation
Laboratory technicians or equivalent
Appropriately trained and experienced personnel familiar with use of computers and automation in general
Instrument administration
Laboratory technicians or equivalent
Appropriately trained and experienced personnel familiar with use of computers and automation in general
Routine use Laboratory technicians or (running profiles) equivalent
Appropriately trained and experienced personnel familiar with use of computers and automation in general
Analyzing data
Laboratory technicians or equivalent
Appropriately trained and experienced personnel familiar with use of computers and automation in general
Instrument maintenance
Laboratory technicians or equivalent
Appropriately trained and experienced personnel familiar with use of computers and automation in general
Servicing
QIAG EN F ie ld S e r vice S pe cialists only
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3. General Description
General Description
3
3-2
General Description The QIAxcel Advanced system performs fully automated separation of DNA fragments, as well as RNA and proteins according to their molecular weight and can process up to 96 samples without user intervention. The QIAxcel Advanced system consists of the QIAxcel Advanced instrument, a QIAxcel Kit (containing a QIAxcel gel cartridge and reagents), a computer, and QIAxcel ScreenGel® software, which have been optimized to work together across a wide variety of applications and provide unmatched resolution, speed, and throughput for DNA, RNA, and protein analysis. The QIAxcel ScreenGel software supplied with the QIAxcel Advanced provides both electropherograms and gel images of the nucleic acid and protein separation and can be used to perform the following types of analysis: Determination of the size and concentration of DNA fragments Determination of the ratio, concentration, and quality of total RNA, and the quality of cRNA/ cDNA and fragmented RNA/DNA Determination of protein size and concentration Note: We do not recommend determining nucleic acid concentration with the QIAxcel DNA Fast Analysis Kit.
3.1
QIAxcel Advanced principle The QIAxcel Advanced uses capillary electrophoresis to enable high resolution and sensitive separation of DNA, RNA, and protein samples. This 12-channel capillary electrophoresis instrument uses disposable, multiple-use cartridges for cost-effective analysis of up to 96 samples in as little as 25 minutes. 1.
The QIAxcel Advanced is set up with a gel cartridge, running buffer, and wash buffer, and calibrated using intensity markers.
2.
The samples for analysis (in a 96-well plate or 12-tube strips) are placed onto the sample plate holder.
3.
Required data collection settings are selected and the samples pass through the capillaries of the QIAxcel gel cartridge.
4.
Data is analyzed using the QIAxcel ScreenGel software.
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3.2
QIAxcel Advanced User Manual
External features of the QIAxcel Advanced
External features of the QIAxcel Advanced.
1
Sample door
8
N2 door
2
Cartridge door
9
Transport lock and buffer tray location
3
Service door
10
Sample plate holder
4
Power connection for AC connection
11
Cartridge bay
5
Tube fitting for external N2 supply
12
Slot for smart key
6
RS232 connection
13
Digital pressure display
7
N2 regulator and cylinder
14
Purge filter
Note: If using an external N2 source, the output pressure must not exceed 75 psi. The QIAxcel Advanced is equipped with an internal regulator that will regulate the pressure provided by the external N2 source to approximately 40 psi (37–45 psi), which is the instrument’s operating pressure.
QIAxcel Advanced User Manual 04/2014