AmpXpress™
Contents
1. 4 4 1 1 One Step Start segment Suggested usage First denaturation step in the temperature profile Position in segment panel First position only Setpoint 1 Temperature Time es Blo Si Setpoint 1 Temperature 40 to 98 C Time 0 to 5999 seconds 4 4 1 2 Two Step Start segment Suggested usage Reverse transcriptase RT with a RT step followed by denaturation step Position in segment panel First position only Setpoint 1 Setpoint 2 Temperature Time Temperature Time 50 Moo Mes cio df Setpoint 1 Temperature 40 to 98 C Time O to 5999 seconds Setpoint 2 Temperature 40 to 98 C Time O to 5999 seconds Note Always use setpoint 2 with a higher temperature value than setpoint 1 for correct function Page 46 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 4 1 3 Two Step Cycle segment Suggested usage Two step cycle sequencing Position in segment panel Position 2 to 8 Setpoint 1 Setpoint 2 Temperature Time Temperature Time E Number of cycles 95 Em Mep E a i Setpoint 1 Temperature 40 to 98 C Time O to 5999 seconds Setpoint 2 Temperature 40 to 98 C Time 0 to 5999 seconds Number of cycles 2 to 99 Note Always use setpoint 2 with a higher temperature value than setpoint 1 for correct function 4 4 1 4 Three Step Cycle segment Suggested usage Three step cycle sequencing Position in segment panel Posit2. Do not to deposit any potentially hazardous materials within 30 cm from AmpXpress A warn ING The product must never be moved during operation A warn ING The product must never be used close to water baths or flooding water WARN ING Do not open the cover panels Some parts inside the instrument have high voltages capable of causing injury or death Refer servicing to personnel authorized by AlphaHelix Molecular Diagnostics AB Page 12 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT ZA WARNING For continued protection against risk of fire ensure that any replacement fuses are of the specified type and current rating Always disconnect the power cord before carrying out any service task WARNING AmpXpress does not have a bioseal Therefore materials used with it must not be toxic radioactive or contaminated with pathogenic microorganisms according to IEC EN 61010 2 020 CAUTION Always use counterweights Le tubes filled with the appropriate volume of water to fill up all empty positions in the sample tray Note The PCR process is extremely sensitive to contamination Always wear protective clothing when handling reagents samples and amplified material 2 2 4 Grounding and electrical safety AmpXpress must be grounded for protection against electrical shock 2 2 5 Safety mechanism Hardware interlocks ensure that the user can only open the instrument lid once the rotor has come to
3. Temperature Sequence Segment control Segment temperature window Segment choice Figure 18 AmpX main window 4 2 1 1 Menu bar The menu bar access actions to save and open program files with temperature sequences you have created in AmpX software Opening the program automatically open a new file and you can start creating your temperature sequence right away The Tools menu is used to customize your segment pre settings and working directory as well as setting USB options 4 2 1 2 Temperature sequence window The temperature sequence window shows the total temperature sequence based on the information in each segment located in the segment panel Note the difference compared to the segment temperature window 4 2 1 3 Segment Temperature window The segment temperature window only shows the temperature profile for the selected segment in the segment panel 4 2 1 4 Segment panel The segment panel show the order of segments used to build the temperature sequence When empty it can only be populated with the highlighted segments in the segment choice panel When populated buttons in the segment choice and segment control will be highlighted to show possible actions for the populated segments in the segment panel Page 41 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 2 1 5 Segment control The buttons in segment control panel is used to change move or delete the highlighted segment in the seg
4. 42 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 5 Left click the number of cycles and change 35 to 30 by using down arrow or entering the number with the keyboard Setpoint 1 Denaturation Setpoint 2 Annealing setpoint 3 Extension r Temperature Time Temperature Time Temperature Time Number o ciples eae aea r a rar ae e Tres ecgsersst Hoover your mouse icon over the Isothermal step button without pressing the button A label will appear after a few seconds with an explanation of the segment function Also note there is a space between the three step segment and end segment indicating that the segment will be inserted on position 3 in the segment panel Se figure below Left click segment choice button Isothermal step The segment will be added to the right of the three step segment Your AmpX software screen should look as below AmpX Modified File Tools Help Total Temperature Sequence 11 40 13 37 15 33 17 30 Temperature Sequence Setpoint 1 Temperature Time 40 lte Ss Note that the last segment added has a red ring around the icon in the segment panel This is the active segment The active segment can be edited in the set point field and changes will be updated directly in the graphical fields Total Temperature sequence and Temperature sequence To change active segment and edit Set point values Right click the segment in the
5. Firmware version Press OK to show SW 1 10 Internal instrument Release version Build 445412 Internal instrument build version 3 8 2 Select Rotor Each rotor has a unique identification number Do the following in case the rotor has been changed 1 Choose Select Rotor 2 Check the rotor id shown on the display and the id number found underneath the rotor Figure 15 3 Edit the rotor id using the control buttons so that it agrees with the id number found underneath the rotor Enter rotor id 00019508C3ED 3 8 3 Setup buzzer Allow to turn On Off the instruments buzzer Turn the run ready signal On Off Press OK key to acknowledge choice Note that no warning signals will be heard when buzzer is turned off Setup buzzer ON Page 31 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 8 4 Ambient overtemp continue A too high ambient temperature room temperature negatively affects the performance of the instrument If the temperature is higher than 32 C the instrument will not perform according to its specifications Therefore the instrument is programmed to notify the user in such case either by a message only or by shutting down the instrument The Ambient overtemp continue function allows the user to select the desired response by allowing the instrument to 1 continue despite a too high ambient temperature ON or 2 shut down OFF The following message appea
6. PARAMETERS When creating a program time and temperature values are defined plus the number of cycles and when applicable also touch down settings Time is defined in two consecutive windows first minutes and then seconds see page 35 section 3 10 3 3 RUN PROGRAM The Run program menu is used to select which program to run among the programs that are stored internally in AmpXpress Press OK to enter the menu and then the up or down arrows to toggle between the different programs Q Press OK to enter the menu Select program using the up or down arrows O semi Ga Press OK to select program Q Return to main menu 19 Continued on next page Page 24 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Continued from previous page Close the lid to start the run Program is running Press OK if you wish to terminate the run The instrument cools down automatically at the end of the run The instrument idles at 40 C for 20 seconds before turning off Total run time is presented at the end of the run Page 25 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 4 LIST PROGRAM The List program function is for viewing program settings only Enter the menu by pressing OK Then use the left and right arrows to select which program to view among programs stored in AmpXpress Press OK to select p
7. User Manual DRAFT 6 ERROR MESSAGES In case a software or hardware error occurs an error message is presented on the front display and the buzzer will sound Errors messages and what action to take is explained in the table below 6 1 ERROR MESSAGE DURING OPERATION Message presented on AmpXpress front panel Explanation Action to take Aborted by user Program aborted during run by the user Press OK to return to main menu Bluetooth error Bluetooth communication error Turn the instrument OFF and then ON again unplug power cord Call for service if the problem persists Incorr set temp Temperature setting is out of range Correct temperature setting Int error nnnn see table above Various internal errors Turn the instrument OFF and then ON again unplug power cord Call for service if the problem persists The outer lid is open Close the lid Lid not locked The outer lid is not locked Open and close the lid Press the lid downwards to lock it No RPM data No temp data FRO No temp data TMO No temp data CON No temp data COM Rotation speed data from the centrifuge Turn the instrument OFF and then ON is lost again unplug power cord Call for service if the problem persists Probe data is frozen Le not changing with Turn the instrument OFF and then ON again unplug power cord Make sure that the temperature probe is properly positioned Replace the temperature probe if
8. a complete stop No moving parts can be accessed without opening the lid Condition Rotor is turning Lid opening is disabled by a hardware relay which is controlled by speed sensing electronics Power interrupted by disconnecting the power cord Lid opening is disabled mechanically Opening the lid requires the power to be restored or manually unlocking the lid locking mechanism accessible via a hole on the left side using a 1 mm screwdriver see 0 Table 3 Interlock conditions preventing opening of the instrument lid 2 2 6 Emergency shutdown In a situation with risk of personal injury stop AmpXpress as quickly as possible by unplugging the power cord 2 2 Power failure In the event of a power failure the rotor will slow down and come to a complete stop The PCR process is thereby interrupted The instrument lid remains locked until power is restored 2 2 7 1 Main after power failure Make sure that the rotor has come to a complete stop The instrument lid can be opened once power has been restored 2 2 8 Alarms 2 2 8 1 Buzzer A buzzer sounding for 5 seconds with 20 second intervals indicates that the run has ended The signal keeps sounding until the message is cleared by pressing any of the five control buttons on the front panel of the instrument Another more intense buzz with a higher pitch is activated in the case of an instrument error and sounds for 10 seconds with 20 second intervals 2 2 8 2 Warning L
9. by the difference in density between warm and cold parts Convection is normally driven by the earth s gravitation 1 x g In a conventional PCR instrument the force driving convection is 1 x g In AmpXpress convection 1s driven by a centrifugal force of more than 3000 x g where the centrifugal force acts upon the denser i e colder subset of a sample The convectional movements resulting from differences in densities between hot and cold parts of the liquid are greatly increased in AmpXpress and result in instant temperature homogenization throughout the sample ar ew ZC a ei DG Figure 1 Principle of convection effect of different driving forces F1 F2 1 1 1 Centrifugal force A tube that is subjected to centrifugation is continuously accelerated towards the center of rotation This 1s called centripetal acceleration The acceleration depends on the rotation speed and the radius of the movement The force acting on a tube subjected to centrifugation depends on the mass of the tube including sample This is the centripetal force which is directed towards the center of rotation The force that we experience when traveling around sharp bends in a car or train is called centrifugal force The experienced force is actually the result of the centripetal force pulling the car or train towards the center of the curve In your frame of reference the seat is pressing you outwards from the center of movement This is also the
10. case for a sample contained in a tube that rotates in a centrifuge We therefore speak of the centrifugal force acting on the sample In AmpXpress the centrifugal force induces SuperConvection i e enforced convection which ensures rapid and homogenous distribution of temperature changes within the reaction volume This in turn enables rapid temperature ramping Page 8 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 1 1 2 Rotational speed The centripetal acceleration is determined by the rotational speed and the radius of the movement through a simple relation de r 2nf where 1 ac acceleration r radius of movement f rotational frequency For calculations all three parameters must be measured in the same system of units for example SI units m s and Hz The centrifugal force Fc 1s according to Newton s second law directly proportional to the acceleration Fo mac where 2 m the mass of the sample The centripetal acceleration is expressed in e where 1 x g equals the gravitation at the surface of the earth g 9 81 m s 1 1 3 Example typical rotational speed and centrifugal force When describing a centrifuge we simply refer to the centrifugal force expressed in x g e The rotational frequency or speed is measured in rpm revolutions per minute This figure is divided by 60 to get the frequency in Hz e The calculated acceleration is divided by 9 81 for expre
11. label as indicated above To forward the products to recycling or proper disposal use an authorized collection system or return the products to AlphaHelix Molecular Diagnostics AB 7 4 CONTACT INFORMATION For help or questions please contact your local dealer or AlphaHelix directly at AlphaHelix Molecular Diagnostics AB Kungsangsvagen 29 SE 753 23 Uppsala Sweden Phone 46 18 120701 E mail info alphahelix com www alphahelix com To place an order contact your local distributor or AlphaHelix at sales alphahelix com Page 55 Document number 70 0001 Rev 2
12. new file will automatically get the file name Untitled_Year_Mounth_day_time ahx Example Untitled 2011 11 08 101040 4 4 3 2 Open Allow the user to open an existing temperature sequence file on the computer Note It 1s not possible to open a temperature sequence file stored on the instrument via AmpX software 4 4 3 3 Save Save the temperature sequence file currently in use directly with the given name If the existing file has been altered without giving a new file name the program will bring up the Save as dialogue box This behavior is to prevent accidental overwriting of a temperature sequence file 4 4 3 4 Save As Save as bring up the dialogue box Save as with the previously saved name or by the software suggested name 4 4 3 5 Ext Exit the program and any unsaved work is prompted to be saved Page 50 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 5 QUESTIONS AND ANSWERS 5 1 PROBLEMS AND QUESTIONS RELATED TO THE OPERATION OF THE INSTRUMENT Q How can I tell if the temperature probe is OK A The following criteria must be met to ensure proper function of the probe and AmpXpress 1 Both sensors must be submerged in the liquid and centered in the tube to avoid contact with the walls see Figure 1 ll The connecting socket should slide onto the connecting pins of the rotor without difficulty Q How can I tell if the liquid volume of the temperature probe is correct A Chec
13. next page Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Continued from previous page Press OK again to finish the program IS Return to the previous segment i Use up and down arrows to toggle between different letters and numbers Then use the right arrow to add more characters Press OK to finalize the program name Page 38 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Continued from previous page 3 10 1 Deletion of Segments Segments can be deleted by pressing the is then presented key from the first position of the segment The following option 3 10 2 Touch down PCR To program a touch down PCR enter the number of cycles for the touch down Use one segment for the touch down settings and a separate segment for the subsequent cycles First enter the number of cycles for the touch down Then enter the desired number of degrees per cycle see below Touch down only allows for annealing down to 40 C If the touch down settings result in a final annealing temp below 40 C the following error message appears TD gives a final temp below 40 Page 39 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 AMPX SOFTWARE MANUAL 4 1 INTRODUCTION This manual is written for AmpX software version 2 0 4 1 1 Definitions Term Explanation Main window The main window is defined as the window that includes t
14. the problem persists Probe data timeout Clean the electrical contact surfaces underneath the rotor Figure 15 Inspect carbon pins and make sure they are not stuck Replace the temperature probe if the problem persists Probe data is not available because there is Inspect carbon pins to see if they are no connection with the rotor stuck Make sure the rotor is correctly positioned Probe data cyclic redundancy check Make sure that the temperature probe is CRC error properly positioned Replace the probe if the problem persists Probe error faulty probe Replace the temperature probe Probe overtemp Prog bad index Prog bad descr Program bad data Bad checksum Program error RAM memory low Page 53 Probe is too hot Temperature gt 99 C Inspect probe thermistor Make sure thermistors are not in contact with tube wall Various program checks Turn the instrument OFF and then ON again unplug power cord Delete the program Re program and make sure the program settings are properly entered A critical program error has occurred Turn the instrument OFF and then ON again unplug power cord Not enough RAM memory left Turn the instrument OFF and then ON again unplug power cord Call for service if the problem persists Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Ramping too slow Temperature ramping is too slow Check the water level of the temperature probe Make sure the IR radia
15. this might make it difficult to loosen the screw after the run has completed Page 17 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 4 8 Buzzer A buzzer sounding for 5 seconds with 20 second intervals indicates that the run has ended The buzzer keeps sounding until the message is cleared by pressing any of the five control buttons on the front panel of the instrument Another more intense buzz with a higher pitch is activated in the case of an instrument error and sounds for 10 seconds with 20 second intervals 2 5 PERIODICAL MAINTENANCE 2 5 1 Temperature probes For proper function of the instrument it is important to visually check the water level of the temperature probe before each run Both gold plated thermistors should be submerged If not the water level is too low In this situation refill the probe using distilled water Handle the probe very gently when opening and closing to avoid damage to the gold plated thermistors If the thermistors become bent realign them very gently using gloved hands Probes are fitted with a handle to facilitate handling Note If there is not enough water to cover both gold plate thermistors temperature regulation will not work properly and may cause the instrument to shut down and terminate the run Pi alah Aa TNT Figure 9 Visually inspect the position of the thermistors to make sure they are placed in the middle of the tube and are not in contact with tube walls
16. 0 S r Default path C Documents and Settings AmpXpress Programs By choosing a segment from Select segment type drop down list set point values can be edited and saved by left clicking the Save button The setting you have altered will now be displayed as pre setting every time you select that segment in the Segment choice panel 4 4 2 2 Default path If you save all your temperature sequence files on a specific library a default path can be set for the program to open this folder as pre set library to save your program files Page 49 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 4 2 3 Com port Help Com port options for connection to AmpXpress are available under the Tools menu by selecting Com port Default settings Select Com port in the tools menu to bring up the below window Com Port Automatic O Fixed Save Cancel Select option Automatic to have AmpX program automatically searching for a connected AmpXpress instrument This is default option and recommended setting Select option Fixed to force AmpX program to connect to the instrument at the specified COM port 4 4 3 File menu Tools Help New Open Save Save S Exit 4 4 3 1 New Creates a new temperature sequence file If the existing file 1s modified the program will prompt the user to save current work prior to opening the new file The
17. 50 or 100 uL Handle the probe very gently when opening and closing to avoid damage to the gold plated thermistors If the thermistors become bent realign them very gently using gloved hands CAUTION All probes are delicate and fragile and must be treated with utmost care Do not under any circumstances tamper with or modify the probes since this would negatively affect the control of the instrument thereby affecting the outcome of the PCR and may also damage the instrument Note When not in use temperature probes should be stored in a refrigerator 4 C to minimize evaporation of the liquid 2 4 7 Loading samples 2 4 7 1 Loading samples into the rotor 1 Position the hinge of the tubes downwards facing the rotor with the opening flange pointing upwards The positions of the rotor are labeled 1 to 28 2 Fill up all empty spaces with dummies i e tubes with water containing the same volume as the sample tubes Note Make sure that the tubes are correctly and uniformly placed in the rotor by grabbing each tube one by one using gloved hands and pulling them outwards 2 4 7 2 Positioning the rotor in the instrument 1 Place the rotor onto the rotor axis The rotor has three guide pins to correctly orientate the rotor which in turn has guide slots that fit the guide pins Figure 6 2 Tighten the locking screw and close the instrument lid Note Do not use excessive force when tightening the locking screw as
18. AmpXpress User Manual AmpXpress User Manual DRAFT AlphaHelix Copyright 2011 AlphaHelix Molecular Diagnostics AB All rights reserved No part of this manual may be reproduced or transmitted in any form or by any means electronic or mechanical for any purpose without the expressed written permission of AlphaHelix AlphaHelix Molecular Diagnostics AB Kungsangsvagen 29 SE 753 23 Uppsala Sweden Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT WARRANTY AND LIABILITY AlphaHelix Molecular Diagnostics AB AlphaHelix warrants that the product supplied has been thoroughly tested to ensure that it meets its published specifications The warranty is only valid if the product has been installed and used according to the instructions provided by AlphaHelix AlphaHelix makes no warranties expressed or implied including without limitation the implied warranties of merchantability and fitness for a particular purpose regarding the product AlphaHelix does not warrant guarantee or make any representations regarding the use or the results of the use of the product in terms of its correctness accuracy reliability or otherwise The entire risk as to the results and performance of the product is assumed by the user Since the exclusion of implied warranties is not permitted by some jurisdictions the above exclusion may not necessarily apply AlphaHelix shall in no event be liable for any direct indirect sp
19. E EE E E E AEE E E E EEE E E E 10 1 2 5 E E EE E E E E Si E E E S 10 2 AMPXPRESS INSTRUMENT MANUA eege 11 Zeke IMPORTANT NOLE saer E S 11 22 SAFELY INFORMATION D 11 Dk AOAECOY O VAMOS ee Ee 11 PA T ae K 2d e en E IK 224 rounding and Te y snoin a Ei ai arian 13 e DEEN E 13 Da ENEE 13 Dh WOW EW EE 13 E E 13 sec UNPACKING AND INSTALEING NEE Eeer 14 GE a ee 14 2 MSU C AN E 14 Zoo MVC CIC AN PCG IGE CIES apres sereia aa Sent EA E EE A E A EE 14 24 OPERATING THE INSTRUMENE sssicecccetisnspecsnasecvacsices aiee ina a aia i aina a osaa 14 2 4 1 BEER 14 242z Samples Eege 14 Zu EE 15 ZA TAO WS Open E 15 die Ree age se ye to rere E te secs sues cc cna tne eget sec ct he ara en oe se steels oe ct tp EA EE E E tacts gst 16 240 PM TEMA PEP AM Ie EE 16 e MOAT AN ON pecs cat noses ne E O E E E 17 PA SE EE 18 25 PERIODICAL MAINTENANCE cirrosis ooer a aaaea a 18 2 5 1 Lop eae eege 18 2 5 2 How to refill the temperature probe rer ee ceea eee an rrene arara nan eenan cena rereneenaaavo 19 2 5 3 Howto assemble the temperature probe ccccccseccccseeeneeeceeececeeeeccaseeeseeeessensaesesseeeessuseessuseesausessaesaanes 20 2304 NS CC E E 20 MANS CCEA Een Ee 20 250 Me ONTGCT SURIACCS Ob TNS MOLI parada paia O DR AU a sees 20 Dee AMC Ant MC THiS te ING EE 21 Page 5 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 258 Decontammanne CAS aC eege 21 TN EH NL ATION KE 22 5 AMPXPRESS USER INTERFACE MANUA iesscscc
20. ED When there is an instrument error that causes the instrument to terminate a run the red Warning LED will be lighted together with an error message showing up on the screen Consult the manual for detailed information regarding the nature and cause of the error see chapter 6 Error messages Page 13 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 3 UNPACKING AND INSTALLING AMPXPRESS Unpack and install the AmpXpress instrument according to the Unpacking and installation instructions provided with the instrument 2 3 1 Inspect AmpXpress Inspect AmpXpress and its supplied parts for any damage that might have occurred during shipment If AmpXpress appears to have been damaged during transit report such damage to the carrier and AlphaHelix within one week from receipt of the instrument 2 3 2 Physical requirements Place the instrument on a workbench that is stable enough to take the weight of the instrument as well as any instrument vibrations Allow 30 cm of clearance on all sides of the instrument Make sure there is sufficient room to allow the instrument lid to be fully opened Note Do not block air vents Allow 30 cm of clearance on all sides of the instrument CAUTION Neglecting the importance of an adequately stable bench table may cause serious damage to the instrument in the event that the bench table should collapse ZA WARNING To prevent the instrument from moving sliding AmpXpress
21. If thermistors are out of position remove the tube see 2 5 2 and realign thermistors gently using gloved hands Figure 10 Visually inspect the water level of the temperature probe prior to each run using the level measuring stick provided with the instrument Both gold plated thermistors should be submerged If they are not refill the probe with distilled water see below Page 18 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 5 2 How to refill the temperature probe Figure 11 Detach the probe by grabbing the handle and gently pulling it towards the rotor axis Figure 12 Slide the probe towards the rotor axis and lift it to get it out of the rotor Figure 13 Grab the upper part of the probe the handle with one hand and the plastic tube with the other Page 19 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Figure 14 Separate the upper and lower part of the probe Refill the tube with 20 appropriate volume of distilled water 2 5 3 How to assemble the temperature probe Assemble and install the probe in the reverse order see Figure 11 to Figure 14 To ensure proper contact and alignment of the probe gently push the probe outwards so that the tube rests properly against the edging of the rotor 2 5 4 Changing the external fuses WARNING For continued protection against the risk of fire replace fuses only with the same type and rating as those currently installed in t
22. ON OF THE INSTRUMENT 51 5 2 PROBLEMS AND QUESTIONS RELATED TO THE OPERATION OF AmpkX Software 52 Page 6 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT OTRO RV DAGE weskseseccciesesesacccteeteavessararesuecoaanasiuennecsaeseseocntiecanssansinindusavists aes ceapiessacesuesinantesndievecaacnerereeieaeens 53 61 ERROR MESSAGE DURING OPERA TION vesissscssesccssasntesnctsnssscndecestasdennessisuctuaossenesnseossstterssxasnteesiedesnsoenes 53 7 A SGENERAL INFORMA TION BEE 55 Za DECLARATIONOFCONFORMITY scinn 55 7 1 1 POODE E O E e E E A N E E O E E R EEEE 55 ke OL GE KE 55 jo NELE EECHELEN REENEN enee eaa adada aai 55 7 3 VALID FOR CUSTOMERS IN EU COUN EISCHEN 55 Ze CONTACT INFORMATION HE 55 Page 7 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 1 TECHNICAL DESCRIPTION AmpXpress enables rapid temperature cycling while maintaining thermal homogeneity The following modules contribute to this e A high speed rotor system 7000 rpm enabling SuperConvection e A powerful heating system using an IR radiator and a reflector e An efficient cooling system that uses high speed rotation to create a wind chill effect that efficiently cools the samples e A sophisticated in tube temperature measurement system that measures sample temperature in real time 1 1 SUPERCONVECTION When a sample is heated the temperature change is distributed throughout the sample by convection caused
23. Page 54 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 7 GENERAL INFORMATION 7 1 DECLARATION OF CONFORMITY AmpXpress meets the requirements of the following directives and standards 7 1 1 European directives AmpXpress has CE mark and complies with the requirements of Low Voltage Directive 73 23 EEC It also complies with the EMC directive 89 336 EEC including amendments by the CE marking directive 93 68 EEC AmpXpress has been tested and complies with the requirements of EN 61010 1 2001 EN 61010 2 020 1994 and Al Exclusive part 7 and 13 EN 61326 1 2006 EN 61326 2 6 2006 EN 301 489 1 V1 6 1 2005 09 and EN 301 489 17 V1 3 1 AmpXpress complies with the requirements of e WEE 2002 96 EC e ROHS 2002 95 EC 7 1 2 UL and CSA directives AmpXpress complies with the requirements of UL 61010 1 second edition 2004 and CAN CSA C22 2 NO 61010 1 7 2 WEEE COMPLIANCE STATEMENT 7 3 VALID FOR CUSTOMERS IN EU COUNTRIES We are committed to be a good corporate citizen As part of that commitment we strive to maintain an environmentally conscious manufacturing operation The European Union EU has enacted a directive on product recycling Waste Electrical and Electronic Equipment WEEE and over time this directive will be implemented in the national laws of each EU member state Products falling under the scope of the WEEE directive will be identified with a crossed over Wheelie bin symbol on the product
24. ce Devices Device Manager Sy IDE ATA ATAPI controllers D Storage amp IEEE 1394 Bus host controllers Removable Storage 38 Imaging devices EN Disk Defragmenter BB Jungo Disk Management ae Keyboards E a Services and Applications Mice and other pointing devices E Modems 3 Monitors EH Network adapters D Other devices E PCMCIA adapters a PCMCIA and Flash memory devices Y BSE ECP Printer Port LPT1 a7 USB Serial Port COM20 B Processors SCSI and RAID controllers 3 Secure Digital host controllers e Smart card readers Sound video and game controllers System devices z Universal Serial Bus controllers lt p V50 devices PEK Ports COM amp LPT jd ECP Printer Port LPTI USB Serial Port COMZO Make sure that the COM number has the same number as the Fixed Com Port setting in the Tools Com Port setting or Automatic option is used Com Port Automatic O Fixed 2 Note Windows enumerates a new COM port number to the USB port if another USB connector than used before is connected to the instrument Therefore it is strongly recommended to use the Automatic option under the Tools Com port setting Try to reinstall the enclosed USB to Serial driver For more information please refer to the readme txt file on the Installation CD ROM Page 52 Document number 70 0001 Rev 2 AmpXpress
25. cssssctvsnsnassccsteseceudesoesssseeusnsasisasbsscassadsuasseeceesersuabatanasessseseess 23 SS INTRODUCTION D 23 3 2 DESCRIPTION OF PROGRAMMING RUN PARAMETERS sssssccccccccccccsscssccceccsssssccseeees 24 Sd SHEET 24 dd MAST PROGRAM siccovercccsssesivacsieesessscssracessasaccvasuvaswediesvecisesabacoeessescvauesavasdaviees sosceaadsusseesestuasivasbaevsesavacemeceslesas 26 33 LOAD PROGRAM E 27 do TONE Eege 28 Sete DELETE DIO GR AWM H 30 do OUP AVA DEE 31 3 8 1 EE 31 o2 CNC e EE 31 3 8 3 NS CEN Zs soca hairs se seers E EQ a DD O o DE api 31 3 84 HEIEREN eeh 32 EE EEN 32 Se EENEG 32 Oe Ee 32 o O TT E EE E E Ge 33 SSC Mm ic E E A E A E T 33 DS KE HK CRL 33 3 9 1 EE 33 EE EE 34 S O CREATECPROGRAM ee 35 Se PELTO EEN 39 OZ ern yy RC aoe dicts oust ria Ra COR RO ARC OU nai ia rasa ae 39 a AMPASOFEWAREMANUAL sociso oio a 40 AL INTRODUCTIO N esi E E E E S 40 4 1 1 DC OS sagas gens a a Uai di oe duna dead ad 40 Eos AUT AUS SYS CC TI ip sit shea se en pae ace sunnnauutnetue cece macau R E 40 4 1 3 Install Uninstall AmpX software 40 diz START THE AMPA SOFTWARE E 40 4 2 1 El OD sas ca RR RA QD RR RR OR RR RR eh mene bouamin creamer nlsnd au 41 4 2 2 Creatine a Temperature UE 42 ds LOADING A TEMPERA TURE SHOU EN Eeer 45 4 4 Detailed function description eege ENEE 46 4 4 1 RS TN SIN EE 46 Be GOONS MCU E 49 BAS CR CIN EE 50 S OUBSTIONS AND ANSWERS isapan OE 51 5 1 PROBLEMS AND QUESTIONS RELATED TO THE OPERATI
26. cular Diagnostics AB have been tested to withstand the elevated g forces Recommended 0 2 ml sample tubes need to be used together with AmpXpress to ensure proper and trouble free operation of the instrument AlphaHelix 0 2 ml tubes Product No 61 0001 and 61 0003 has been tested to withstand the elevated g forces thereby ensuring trouble free operation in AmpXpress A special rotor also needs to be used with the instrument These items are available from AlphaHelix Molecular Diagnostics AB see Contact information 2 2 SAFETY INFORMATION Important Before using AmpXpress it is very important to read and understand the complete AmpXpress User Manual Negligence may increase the risk for instrument failure and or personal injury To avoid any risk of injury AmpXpress should only be operated by properly trained personnel and always in accordance with the instructions of this manual 2 2 1 Safety symbols The following safety labels are attached to the AmpXpress instrument All users must read and understand the warnings before using the instrument Inside instrument cover Indicates potentially hot parts Manual before operating AmpXpress Non compliance with instructions may cause damage to the instrument Under the instrument on Consult the AmpXpress User Manual product label see Figure 3 R l A ie a No user serviceable parts inside Do not open covers Read the User Table 2 Safety labels on the AmpXpress instr
27. ecial or consequential damages including without limitation damages for loss of business income business profits business interruption loss of business information and the like arising out of the use or inability to use the product Since the exclusion of implied warranties is not permitted by some jurisdictions the above exclusion may not necessarily apply TRADEMARKS AND PATENTS AlphaHelix AmpXpress and SuperConvection are trademarks of AlphaHelix Molecular Diagnostics AB SuperConvection is a patented technology covered by US patent 6783993 European patent EP 1173284 B1 and foreign counterparts Microsoft and Windows are registered trademarks of Microsoft Corporation Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT CONTENTS This manual was written for AmpXpress and AmpX software version 2 0 It is divided into seven parts 1 TECHNICAL DESCRIPTION 2 AMPXPRESS INSTRUMENT MANUAL 3 AMPXPRESS USER INTERFACE 4 AMPX SOFTWARE MANUAL 5 QUESTIONS AND ANSWERS 6 ERROR MESSAGES 7 GENERAL INFORMATION Page 4 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT TABLE OF CONTENTS L KI Ch UL ADS CARP TON RE 8 Dee ORC ON EC KE 8 Cil EE 8 Ee MROUALIOIA SCC WEE 9 1 1 3 Example typical rotational speed and centrifugal force 9 EZ AMEXPRES ar E E E T 10 12 1 ROLOS VS D 10 My MMC MUTI E og pra S EE EAE EA E E E AEE E T A A S 10 LoS R UE OE een a PS E seexohecusatt 10 ee ASO TAOS S E
28. for carrying out appropriate decontamination Page 21 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 6 SPECIFICATIONS Mains voltage 100 240 VAC 50 60 Hz Maximum 600 VA Equipment class Class 1 equipment Enclosure safety class IP 20 Sample capacity 24 samples Sample volumes 20 ul 50 ul and 100 ul PCR cycle time Typically below 20 min when performing 40 cycles 20 ul samples Operating temperature 4 32 C Performance measured at 20 C Operating humidity to meet performance RH 50 80 Weight Approx 8 kg Dimensions WxDxH 19 x 35 x 15 5 cm Maximum noise level 70 dB Connection to Personal Computer USB 2 0 USB to Serial driver on host computer Page 22 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 AMPXPRESS USER INTERFACE MANUAL 3 1 INTRODUCTION The five control buttons on the AmpXpress front panel Figure 16 are used to program the instrument i e to enter run parameters user interface is made up of a simple entry level menu structure Figure 17 and basic control buttons The left and right arrows are used for to toggle between the different menus Control buttons Warning LED o 7 SIOS o w AlphaHelix S Figure 16 Control buttons and Warning LED Figure 17 AmpXpress user interface menu Page 23 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 2 DESCRIPTION OF PROGRAMMING RUN
29. get the impression that the rotational speed is not constant Is there something wrong A No this is perfectly normal AmpXpress runs at a variable rotational speed between 4000 to 7000 rpm where the higher speed is used during cooling Page 51 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 5 2 PROBLEMS AND QUESTIONS RELATED TO THE OPERATION OF AmpX Software Q I get the following message when I try to load a temperature sequence to the instrument Amp press could not be detected Make sure that the USB cable is properly connected and that mprpress is in Load Program mode EE A Make sure the instrument is in Load program mode Note that the instrument will exit the mode after 1 minute 1f no program has been sent If the USB cable is connected and the instrument is in Load Program mode there might be a problem with the USB to Serial windows driver Check that the USB to Serial connection is identified by Microsoft Windows in the Device Manager Check that there is a USB Serial port COM port number connection under Ports COM amp LPT See figure below g Computer Management m File Action View Window Help es EI 8 DS Computer Management Local Batteries E CH System Tools 4 Computer gj Event Viewer a Disk drives H k Shared Folders EI Display adapters z Local Users and Groups DVD CD ROM drives Performance Logs and Alert ig Human Interfa
30. he instrument TSA H 250V see Figure 3 2 5 5 Inspect for damages Inspect the rotor protective lid and centrifuge axis for any damages on a weekly basis 2 5 6 Contact surfaces of the rotor Clean the electrical contact surfaces underneath the rotor using a damp cloth before use see Figure 15 Page 20 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Rotor ID Figure 15 Clean the electrical contact surfaces underneath the rotor using a damp cloth moistened with isopropanol 2 5 7 Cleaning the instrument The instrument is cleaned using a damp cloth or sponge and a mild detergent water solution Blot dry Note Before using other cleaning or decontamination methods than those recommended in this user manual user should check with AlphaHelix or distributor that the method will not damage the equipment 2 5 8 Decontaminating the instrument In the event of tube breakage and amplicon contamination decontaminate the interior of the instrument using DNA ExitusPlus from AppliChem www applichem com Apply DNA ExitusPlus to a paper towel and wipe all surfaces of the instrument that may have come into contact with the sample The cleaned parts should be subsequently wiped with a paper towel moistened with water and then allowed to air dry Before use of any other decontamination method please contact AlphaHelix N B If hazardous material is spilt onto or inside AmpXpress the user has the responsibility
31. he temperature sequence setup This is the window that appears when the AmpX application is started 4 1 2 Operative system The application works with the following operative system Microsoft Windows XP Professional 32 bit Service Pack 3 Microsoft Windows 7 32 bit and 64 bit Please use the regional setting English United States as language in Windows regional options 4 1 3 Install Uninstall AmpX software AmpX software installation is normally started automatically when the installation disc is inserted in the CD DVD drive Please refer to the readme txt file on the installation disc for additional information on installation procedures and last minutes changes before you start the installation procedure 4 2 START THE AMPX SOFTWARE Open the application from the Windows Start menu All Programs AlphaHelix AmpX 2 0 or double click on the ampX icon on your windows desktop Page 40 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 2 1 Main window AmpX software starts with an empty program file The first window presented to the user is the main window Figure 18 The main window comprises Menu bar Temperature Sequence window Program button Segment panel Segment control Segment temperature window and segment choice Sun mme Menu bar Total Temperature Sequence Temperature Sequence window Program button Segment panel
32. hold temperatures 2 step start segment suited for e g RT PCR or whenever more than one initial hold temperature is utilized The subsequent segments are preprogrammed for up to three hold temperatures denaturation annealing and elongation Finish anytime by pressing OK a E Continued on next page Add segment Enter number of minutes oS Oo Oo LU ees he Gi Gei O oO Enter number of seconds O eo O 6 2 0 od Continued on next page Page 35 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT O SL TE Kor Kor Return to the first segment Continued from previous page Q O O O Q O Q O O O Enter number of cycles IS Three hold temps may be added per segment Page 36 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 Temp degC 2 60 Continued from previous page Exit anytime by pressing OK a ic i Slo Q Segment 2 Program done Y O Time min 2 O SNS IS O Segment 2 Save program Y O Time s 2 10 Sil O Add hold temp Y Enter program id O elongation M rogram 1 IS IG O Segment 2 Enter program id Q SE bel Sei D IS H Temp degC 3 72 M rogram 1 o O O Segment 2 Continued on next page Q Time min 3 O SIS Segment 2 Time s 3 3 em Three hold temps may be added per segment Page 37 Continued on
33. ion 2 to 8 Setpoint 2 Annealing Temperature Time Setpoint 1 Denaturation Temperature Time Se ice als ajc fo Si Touch Down 1 Licence Setpoint 1 Temperature 40 to 98 C Time O to 5999 seconds Setpoint 2 Temperature 40 to 98 C Time 0 to 5999 seconds Touch Down 1 to 9 C cycle Setpoint 3 Temperature 40 to 98 C Time 0 to 5999 seconds Number of cycles 2 to 99 Temperature Time bk Setpoint 3 Extension Number of cycles ace HP E ka Note Always use setpoint 2 with a higher temperature value than setpoint 1 for correct function Always use setpoint 3 with a higher temperature value than setpoint 2 for correct function Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 4 1 7 Isothermal step segment E Suggested usage Isothermal step to finalize extension Position in segment panel Position 2 to 8 Setpoint 1 Temperature Time fe gc a Setpoint 1 Temperature 40 to 98 C Time 0 to 5999 seconds 4 4 2 Tools menu 4 4 2 1 Segment pre settings Hel l e 2 All segment buttons are pre set with values to facilitate fast method set up Pre settings for the segment buttons can be altered under the Tools menu om port by selecting default settings Left clicking Default settings will bring up the below window E Default Settings Select segment type One step start Setpoint 1 Temperature Time Bs A SR 2
34. ion 2 to 8 Setpoint 7 Denaturation Setpoint 2 Annealing Setpoint 3 Extension Temperature Time Temperature Time Temperature Time Number of cycles SS E ass Eno se E als s gl Setpoint 1 Temperature 40 to 98 C Time 0 to 5999 seconds Setpoint 2 Temperature 40 to 98 C Time 0 to 5999 seconds Setpoint 3 Temperature 40 to 98 C Time 0 to 5999 seconds Number of cycles 2 to 99 Note Always use setpoint 2 with a higher temperature value than setpoint 1 for correct function Always use setpoint 3 with a higher temperature value than setpoint 2 for correct function Page 47 Document number 70 0001 Rev 2 AmpXpress User Manual 4 4 1 5 4 4 1 6 Page 48 Two Step Cycle segment DRAFT Suggested usage Two step cycle sequencing with touch down temperature Position in segment panel Position 2 to 8 Setpoint 1 Setpoint 2 Temperature Time Temperature Time op a sp 3 aj ZU ERES O E Touch Down 1 Ctcucle Setpoint 1 Temperature 40 to 98 C Time O to 5999 seconds Setpoint 2 Temperature 41 to 98 C Time O to 5999 seconds Touch Down 1 to 9 C cycle Number of cycles 2 to 99 Number of cycles a SE Note Always use setpoint 2 with a higher temperature value than setpoint 1 for correct function Three Step Cycle segment Vv Suggested usage Three step cycle sequencing with touch down temperature Position in segment panel Posit
35. k the volume of the temperature probe using the water lever measuring stick Alternatively keep track of the weight of the temperature probe after filling it with the correct volume of distilled water by measuring it on scale It is recommended to check the amount of liquid of the probe tube before each run If the water level is low refill the probe using distilled or de mineralized water see 2 5 1 Handle the probe very gently when opening and closing to avoid damage to the gold plated thermistors Q The total run time of my PCR was shorter compared to what it usually is and there was less product when I analyzed the PCR reactions on a gel A Make sure that the gold plated thermistors are centered in the tube and have not become bent If the thermistors are bent so that they are touching the inside of the plastic tube temperature regulation will not work properly Realign the thermistors very gently using gloved hands Q When I try to start the instrument I get an error message saying Terminated No temperature data What is wrong A It may result from poor contact between the electrical contact surfaces underneath the rotor and the carbon pins that supply the rotor with electricity Clean the electrical contact surfaces underneath the rotor using a damp cloth Figure 15 and make sure the carbon pins are moving freely Then try again Call for service if the problem persists Q Judging by the sound coming from AmpXpress I
36. king mechanism Grab the instrument lid to fully open the lid and to access the rotor Figure 5 Figure 4 Insert a small 1 mm screw driver into the Figure 3 Grab the instrument lid to fully open it hole to manually open the lid Page 15 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 4 5 The rotor The rotor Figure 6A is detachable and allows the user to load samples outside of the instrument Once the rotor has been fully loaded it is positioned in the instrument using the guide pins Figure 6A and fastened using the rotor locking screw Figure 6B A The rotor 1 Liquid temperature probe 2 Sample tubes 3 Guide pins B Rotor locking screw Figure 6 A The 24 sample rotor showing the position of the temperature probe B The rotor locking screw 2 4 6 The temperature probes In a rapid instrument such as AmpXpress it is important to accurately measure and control the temperature to avoid over or undershooting of sample temperature In AmpXpress this is achieved using a temperature probe thermistor placed inside a sample tube which is positioned in the rotor to mimic a real sample This enables exact control of actual sample temperature in real time throughout the run contrary to other systems that rely solely on measuring the temperature of a metal block or air surrounding the samples Another advantage of the temperature probe is that it ensures that every individual run is temperature co
37. l be set OFF when leaving the menu 3 9 STATISTICS Select Statistics to enter the statistics views Statistics menus can be viewed by pressing right and left arrows Press OK key to leave the statistics menus 3 9 1 Last program runtime Show the program name and total run time of the last run Page 33 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Note The instrument only save the run time from the latest run The information cannot be viewed after power down If the menu is selected directly after the instrument is powered up the following display will be shown 3 9 2 IR On time The display shows the total on time of the IR heater Note that the time does not match the running time of a program but the time a current is flowing through the IR radiator Page 34 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 10 CREATE PROGRAM A total of more than 100 programs may be stored in AmpXpress Programs are created either using the control buttons or optionally using an external PC and the AmpX software see section 4 The Create program function is used for creating programs i e to define temperature and time settings using the control buttons Press OK to enter the Create program menu Then use the up and down arrows to define settings Use the right arrow to proceed to the next step The initial segment allows for two different
38. ment panel 4 2 1 6 Segment choice The buttons in the segment choice panel is used to put the corresponding buttons segment in the segment in the segment panel By left clicking on the highlighted button the segment will be put in the segment panel with pre set values An additional set of parameters for the selected segment is displayed below the Segment temperature window The parameters can be changed directly in the parameter field and the changes are displayed both in the Temperature Sequence window and Segment temperature window By selecting a new segment the values in the previous segment are stored as displayed on the screen 4 2 1 7 Program button The Program button is used to down load the temperature sequence in AmpX software to AmpXpress Make sure that the USB cable is connected between the computer and AmpXpress before the program button is pressed Also AmpXpress must be set in Load program mode before it can retrieve the program from AmpX software Please refer to 3 5 Load Program for an explanation on the topic 4 2 2 Creating a Temperature sequence This section will guide you through a temperature sequence setup step by step Start AmpX software on your computer Your AmpX software screen should look as below File Tools Help RESET M N SEGMENT os d ALL Temperature Sequence 1 Left click segment choice button One step start 2 Left click segment choice button Three step cycle Page
39. must never be installed close to where water is being used CAUTION It is important that the instrument is placed on a horizontal bench table Make sure that the bench table is correctly leveled using a spirit level CAUTION Not allowing enough ventilation space around the instrument or in any way obstructing or restricting the ventilation may cause the instrument to work under sub optimal conditions or in the worst case to overheat and shut down 2 3 3 Electrical requirements AmpXpress must be connected to a grounded power outlet rated according to the product label located on the bottom of the instrument Figure 3 Importantly only ever use the power cord delivered with the instrument CAUTION Do not extend the power cord or in any other way alter the power cord as this might result in blow out of fuses 2 4 OPERATING THE INSTRUMENT 2 4 1 Operating conditions AmpXpress will meet performance specifications when the ambient temperature is 15 to 25 C and the relative humidity is within RH 50 80 2 4 2 Samples and tubes The instrument is intended for PCR analysis of RNA and DNA samples Always use AlphaHelix 0 2 ml tubes Product No 61 0001 or 61 0003 to ensure trouble free operation Page 14 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT CAUTION Use of any tubes other tubes than AlphaHelix 0 2 ml tubes Product No 61 0001 or 61 0003 will potentially damage the instrument Failure to foll
40. n the right side of the window Figure 19 is used to transfer the temperature sequence program to the instrument The instrument must be in the correct mode before this button 1s clicked see section 3 5 Load Program otherwise the temperature sequence will not be received by AmpXpress The temperature sequence is saved in the instrument library with the same filename as the file on the external PC 1 Connect the enclosed USB cable between AmpXpress and the computer with AmpX installed 2 Set the instrument in Load Program mode See 3 5 LOAD PROGRAM 3 Select Tools menu and Com Port Default settings 4 Select radio button Automatic and left click Save button Com Port e Automatic O Fixed 21 Save Cancel 5 Left click Program button The instrument will display Load succeeded when the program 1s loaded AmpX Modified File Tools Help Total Temperature Sequence i 11 40 13 37 15 33 17 30 19 26 Temperature Sequence Setpoint 1 Temperature Time 40 C feo Page 45 Document number 70 0001 Rev 2 Program button AmpXpress User Manual DRAFT 4 4 Detailed function description 4 4 1 Segment description Segment buttons are located in the Segment choice panel Once left clicked the segment symbol will appear in the segment panel The order of segment in the segment panel will give the final temperature sequence Figure 19 Segment Panel
41. next page Page 28 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Page 29 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 7 DELETE PROGRAM The Delete program function is for deleting programs Press OK to enter the menu Then use the up and down arrows to select which program to delete among programs stored internally in AmpXpress Press OK to delete and then use up or down arrow to select Y to confirm Finish by pressing OR N B Delete Program only deletes programs stored internally in the AmpXpress library It will never delete programs stored on the external PC connected via USB Page 30 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 8 SETUP HARDWARE The Setup Hardware menu covers the following Firmware version presents the currently installed firmware version prior service call Select Rotor rotor ID Setup buzzer turn buzzer ON OFF Ambient overtemp continue ambient over temp shut down shut down override Reinit BT chip re initialization of the Bluetooth chip Clear memory deletes all programs stored internally in AmpXpress Test valve test valve functionality prior service call Test Lid test lid functionality prior service call Test Fan Set the internal fan on off prior service call 3 8 1 Firmware version Displays the currently installed firmware version
42. ntrolled The temperature probe fits into a dedicated slot on the rotor from where it is easily removed and re inserted when the probe needs to be refilled Probes are built for and calibrated with 20 50 or 100 uL of distilled or demineralized water See figure 8 20 ul probes are labeled 20 ul 50 ul probes are labeled 50 ul and 100 ul probes are labeled 100 ul Note Always use a 20 ul probe for 20 ul samples a 50 ul probe for 50 ul samples and a 7100 ul probe for 100 ul samples If a 100 ul probe is accidentally used together with 20 ul samples sample tubes may burst from the intense heat Note In order to run 25 ul PCR reactions simply fill up the 20 ul probe to 25 ul of distilled or demineralized water Page 16 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Gol Figure 7 The temperature probe Figure 8 20 50 and 100 ul probes are available and should be used for corresponding PCR reaction volumes Since the liquid volume tends to decrease over time due to evaporation it 1s important to check the liquid volume of the temperature probe prior to each run Check the amount of liquid in the probe tube visually using the level measuring stick or alternatively using a balance Oe weigh the temperature probe Both thermistors should be submerged If they are not the water level is too low In this situation refill the probe using distilled water to the appropriate level 20
43. ow this recommendation will void all warranty CAUTION Always secure the rotor using the rotor locking screw to prevent damage to the instrument CAUTION Do not use any other rotors than the one supplied with the instrument from AlphaHelix Product No 60 0005 WARNING Do not centrifuge any flammable or explosive mater or any material that could react chemically with sufficient vigor to cause a hazard 2 4 3 User interface The instrument is controlled and programs are created using the five buttons on the front panel of the instrument Run parameters may also be set and loaded to the instrument using the AmpX Software installed on an external PC see section 4 AmpX Software Manual The Display is lit when the power cord on the back of the instrument is plugged into a power outlet The Warning LED is lit if there is an instrument error that causes termination of a run see 6 Error messages 2 4 4 How to open the lid The lid is opened by pressing the up arrow control button followed by OK In a situation where lid opening via the control buttons is disabled the lid may be opened manually Always disconnect the mains power cord before following the below instruction failure to disconnect the mains power cord may result in damages of the locking mechanism Insert a small 1 mm screw driver into the hole located on the left hand side of the instrument 0 Inserting the screwdriver will unlock the lid loc
44. rogram and then use the left and right arrows to view program settings Exit by pressing OK Exit by pressing OK Page 26 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 5 LOAD PROGRAM The Load program function is used when sending programs from an external PC to AmpXpress Press OK to activate the USB port located on the back of AmpXpress so that it may receive programs from the external PC Then press the Load button from within the AmpX software on external PC see section 4 3 K Press the Load button on the external PC screen within the AmpX software If the upload is not completed in I min the following error message appears Exit by pressing OK Page 27 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 3 6 EDIT PROGRAM The Edit program function is for editing program settings Press OK to enter the menu Then use the up and down arrows to select which program to edit among programs stored internally in AmpXpress Press OK to select program and then use the left and right arrows to toggle between the program settings Edit settings using the up and down arrows Exit by pressing OK If the program has not been edited kd O To the end of the program no O more segments can be added O Continued from previous page Continued on
45. rs in case the ambient temperature instrument is higher than 32 C Note If the Ambient overtemp continue is set to OFF the instrument will shut down automatically 3 8 5 Reinit BT chip This function is used to reinitialize the Blue tooth communication circuit in the instrument Should normally only be used after service 3 8 6 Clear memory Selecting Clear memory by pressing OK will delete all programs stored internally in AmpXpress 3 8 Test valve Select Test valve by pressing OK and use the up and down keys to test the valve functionality O arrow Valve OPEN Op arrow Valve CLOSED Page 32 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT Depending on the valve position when entering the valve test the other key needs to be pressed before the valve reacts This is normal Leave the menu with OK key 3 8 8 Test Lid Select Test lid by pressing OK and use the up and down keys to test the lid functionality O Up arrow lid OPEN Op arrow lid CLOSED Depending on the lid position when entering the lid test the other key needs to be pressed before the lid reacts This 1s normal Leave the menu with OK key Lid will be set OPEN when leaving the menu 3 8 9 Test fan Select Test fan by pressing OK and use the up and down keys to test the fan functionality O Up arrow fan ON O arrow fan OFF Leave the menu with OK key Fan wil
46. segment panel If you want to move the active segment in the segment panel press the Move button Ei in the segment control panel Depending on the segment properties and position in the segment panel move buttons will be inactive Page 43 Document number 70 0001 Rev 2 AmpXpress User Manual A temperature sequence always starts with One step start DRAFT d or Two step start segments These segments will always be located on the first position in the segment panel and cannot be moved from this position 8 Left click File Menu and select save Tools Help Neu Open Save Save Os Exit AmpX software suggests the file name Untitled_2011 11 04_161932 ahx since this is a new program not saved before You can change the name and location by using standard Windows functionality Remember The name you select will be the file name also in AmpXpress run program menu when transferring the sequence file to the instrument Savein O AmpXpress Programs v ki gt m 4 My Recent Documents My Documents gs My Computer e File name Untitled_2011 11 04_161932 ahx My Network Save as type Text Files Tabu Cancel The program is now ready to be transferred to AmpXpress instrument via the USB interface Page 44 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 4 3 LOADING A TEMPERATURE SEQUENCE The Program button located o
47. ssion of centrifugal force in x g The radius of the rotor in AmpXpress is 58 mm from center of the rotor to the tip of the tube As shown in expression 1 the centripetal acceleration is proportional to the square of the rotational frequency A 10 fold increase in rotational speed results in a 100 fold increase in centrifugal force Rotational speed Radius Centrifugal force Instrument 7000 rpm 58 mm 3100 x g AmpXpress 400 rpm 65 mm 10x g Competitor A Table 1 Centrifugal force for AmpXpress and a competing instrument Page 9 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 1 2 AMPXPRESS 1 2 1 Rotor system The rotor is driven by a powerful brushless DC motor mounted at the bottom of the instrument operating at a variable rate between 4000 and 7000 rpm 1 2 2 Heating system The AmpXpress heating system comprises a circular infrared IR radiator surrounded by a reflector The IR radiator together with the reflector efficiently delivers infrared power that enables very rapid heat ramps The size of the reaction chamber is minimized to maximize energy transfer from the IR radiator to the samples 1 2 3 Reflector A heat resistant reflector is used to maximize the reflection of IR light from the IR radiator to the sample tubes Figure 2 Heating system The circular IR radiator is surrounded by a reflector 1 2 4 Cooling system AmpXpress utilizes high speed rotation to provide efficient cooling of the rotor
48. system The samples are cooled by an air flow drawn into the instrument Warm air then exits through vents on the side and back panel The reflector and the IR radiator are lifted during the cooling phase to maximize the cooling wind chill effect created by the high speed rotation The miniaturized size of the reaction chamber minimizes the volume that needs to be heated which in turn favors a rapid cooling rate 1 2 5 Sample capacity Number of samples per run 24 full rotor Sample volumes 20 ul 50 ul and 100 ul Page 10 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 AMPXPRESS INSTRUMENT MANUAL AmpXpress is intended for research use only AmpXpress is only intended for amplification of genetic material AmpXpress performs rapid temperature cycling of PCR samples using SuperConvection technology Elevated g forces generated by a high speed centrifuge together with a powerful heating system ensure instant thermal equilibration within the samples The PCR run is programmed using the buttons on the instrument or optionally using the AmpX software and an external PC The temperature is monitored during the run and displayed in real time on the display A rapid 40 cycle PCR typically takes 20 minutes 2 1 IMPORTANT NOTICE Use of any tubes other than recommended by AlphaHelix may damage the instrument Failure to follow this recommendation will void all warranty Tubes recommended by AlphaHelix Mole
49. tor wire is not broken Call for service if the problem persists Reflect overtemp Reflector temperature is too high Make sure the ambient temp is within specifications below 40 C and that Ambient overtemp continue is turned OFF see 3 8 4 Room T too high Ambient temperature is too high Move the instrument to a colder Rotor crash Accelerometer crash detected Inspect the rotor for any damage Make sure the rotor locking screw is securely attached Rotor imbalance Accelerometer excessive movement Check that the rotor is properly positioned a detected and correctly balanced with tubes Rotor power err No rotor power Clean the electrical contact surfaces a underneath the rotor Figure 15 service Temp data lost Corrupt temperature probe data Make sure that the temperature probe is properly positioned Replace the probe if the problem persists Terminated No rotor data There is no power to the rotor Inspect carbon pins and make sure they are not stuck Clean the electrical contact surfaces underneath the rotor Figure 15 Call for service if the problem persists Terminated Probe error No probe is sitting in the rotor Insert a temperature into the rotor Terminated Lid was The lid was opened after a program was Open and close the lid properly opened started Undefined error Others unhandled errors Turn the instrument OFF and then ON again unplug power cord Call for service if the problem persists
50. ument Page 11 Document number 70 0001 Rev 2 AmpXpress User Manual DRAFT 2 2 2 Safety notices A warnin G The Warning notice is used for an instruction that must be followed in detail in order to avoid personal injury Users should not proceed until they clearly understand the instructions and all stated conditions are met CAUTION The Caution notice is used for an instruction that must be followed in detail in order to avoid damage to the product or other equipment Users should not proceed until they clearly understand the instructions and all stated conditions are met mal AlphaHelix Molecular BA FOR LABORATORY USE ONLY Diagnostics AB Instrument 100 240 VAC SE 753 23 Uppsala SE EN Tel 46 0 18 120701 Model AmpXpress REF Figure 3 AmpXpress product label located under the instrument The Note symbol is used to indicate information that is important for trouble free or optimal use of the product 2 2 3 Safety precautions A warn ING Before using the product make sure the proper fuse is installed according to the instructions found on the product label located on the bottom of the instrument see Figure 3 ZA WARNING AmpXpress must always be connected to a grounded mains outlet rated minimum 5 A using the power cord delivered with the instrument Do not use any other power cord A warn ING Keep a safety distance of at least 30 cm from AmpXpress during operation A warn ING
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