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Matrix Platemate 2x3 - User Manual

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1. Move the deck to the right Reset To Factory Default Settings Selecting this button will reset all field values for the current position configuration to those originally set as the factory default values Any changes that have been made via this dialogue will be overwritten Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate Plates To provide accurate positioning functionality for each stage the vessel type whether it is a plate tip wash or even a reagent reservoir must be defined in the plates library This option is used to set dimensional and positional parameters for each vessel type The detail and number of entries depends on how accurate the stage positioning is required either by defining a vessel plate type for each specific type or by a generic group for example by defining one vessel type group that represents all 96 well plates that are likely to be used It is important to remember that the parameters entered in this dialogue play an important part in the positioning of plates on the device at the tips and at the stackers and whether plate filling is to be enabled by setting the correct values for non plate vessel types such as reagent reservoirs and tip wash units To amend information for an existing vessel type select the respective vessel description in the drop down and then change the required parameters Read further on in this topic for information on how to add and copy vessel t
2. P Wash Station Sensor Port Contact Liquid Level detects liquid overflow using Sensor on Wash Station a conductive contact sensor and serves as a safety backup in case the vacuum pump stops P Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 4 Insert one end of the wash tubing into the Supply Inlet place the tubing into the lower peristaltic pump then insert the other end of the tubing into the wash container 5 Insert one end of the waste tubing into the Drain Outlet and the other end into the waste bottle The system pumps clean wash liquid into the tip wash station through the lower peristaltic wash pump The system then removes Tubing from Wash the waste liquid from the tip Container Tubing to Waste wash station using a vacuum Bottle pump internal not shown The waste liquid exits from the Drain Outlet to the waste container User Manual 91 Chapter 4 System Operation 6 In ControlMate select Move to Position from the Toolbox Toolbox gt Move to Position e Inthe Move to Position drop down menu select Pipettor Stage 2 e In Vessel Type select Tip wash 96 well or Tip wash 384 well Note To dispense waste liquid into the waste bath instead of the washing channels select the tip wash into waste bath option e In Height select a preset filling height or enter a height 7 Select
3. Tip magazines specifically designed for serial dilutions are available Z Ti m oe Figure 4 6 96 ch Serial Dilution Magazine Figure 4 7 384 ch Serial Dilution Magazine The tip magazines above are for portrait orientation for row wise access Other configurations are also available Catalog No Pipettor Head D A R T s Tips Type 301 30020 501 20001 5516 5517 5518 or 5536 5537 5538 301 30021 501 20004 5506 5507 5508 or 5501 5502 301 30022 Portrait 501 20002 5316 5317 5318 5416 5417 5418 or 5326 5327 5528 5901 30020 501 20001 9516 5517 5518 or 5536 5537 5538 501 30021 5506 5507 5508 or 5501 5502 500 10015 5301 5302 500 10020 5311 5312 500 10025 5321 5322 500 10030 Landscape 501 20002 5316 5317 5318 5416 5417 5418 or or 501 20005 5326 5327 5528 Thermo Scientific Matrix PlateMate 2x3 aenal diyhon using 344 ipe 4 3 Running Pipetting Program The following screen shows the steps for a serial dilution program a Kein Sequence to i Oe ae Sen FI l g treagan for diuin im 384 Serial d e Hase a Pigetor Stage Aspirate Tiu es Hase Pigetor mage 3 Calumna l 1 Lt Dispense All with blowout arii Senal dition 23 lerabans e howe Pieter Stage 3 Column I i Aspirate Tiu t Hae a Pigetor Stage 3 C lumi z Z ii Drpenie All with blowout e Hase a Pigetor Stage 3 Columi z Z Mis 2 Others with linet arii remove etre 1 0ul iori beet column e Hase a Pigetor mage 3 Calu
4. Allow column incremental movements fw Allow row incremental movements Reset To Factory Default Settings Note Refer to the ControlMate help file for information on each field entry and command button In this screen you can enter X and Y values then press Move to position the pipettor head Use the Test height to move the pipet head to a safe level after pressing the Move button You can also use the arrow keys in the Manual movement box to apply incremental changes directly to the pipettor head The pipettor head responds to each tap of an arrow button The distance for each tap can be adjusted using the Steps slide bar 4 Visually check the alignment of the pipet tips to the wells after entering the X and Y values or while using the arrow keys 5 Repeat the previous steps for each stage position User Manual 99 Chapter 4 System Operation 4 3 Running Pipetting Program 100 Before starting a pipetting program review the steps below Open pipetting program in Contro Mate Check instrument setup Attach Reagent Reservoir if needed stage 1 and or stage 2 Attach Tip Wash Station if needed stage 2 only Load microplates Insert or change tip magazine Add ancillaries reagents buffers wash solution waste container OOOCOUOD When you are ready to start the pipetting program return to the Contro Mate screen and perform the following steps To run a pipetting program 1 Check the Notepad
5. Blank Plate QC 5400 00 5300 00 5200 00 5100 00 5000 00 4900 00 4800 00 4700 00 4600 00 4500 00 4400 00 que Plate Average Column Average A Row Average Value 012345 67 8 9 101112131415161718192021 Row or Column Number User Manual 141 Appendix C Precision Data C 4 Precision at 5 0ul into a wet 384 well plate 1 3 4 6 9 10 14 10431 10375 9918 10187 9774 9979 10342 10084 10320 10065 9780 10087 10005 9634 9839 10260 10062 10098 9724 9697 9795 9844 10156 9952 10082 10126 9844 10124 9490 10161 9996 9698 10313 9878 10206 9950 9962 10183 10110 10061 10501 9838 10218 10305 10209 10450 10222 10966 10137 9920 10178 9878 10011 10284 10310 10225 10050 10040 10141 10234 10034 11056 10294 9803 9939 9708 10083 10209 10175 10026 9673 9994 9609 9860 10165 10174 10268 9531 9959 9622 9848 10098 9991 10414 9875 9943 9882 10296 10137 10423 10504 9606 10042 9788 10022 10151 10196 10242 9593 9922 9854 9548 9833 10260 10212 9654 10273 9956 9743 10127 9977 10431 VOZSErTFAC LTONMIININS Volume 5 0ul Plate average 10072 9 Plate SD Plate C V 2 52 Stats calculated from Control Wells Only Column Column Column Column Row Plate or Row average SD CV Average Row CV average Value 9847 56 259 77 2 64 9973 15 2 68 10072 94 High Control 10062 16 3xSD 707 171674 9933 00 208 43 2 10 9905 85 2 54 10072 94 High Control SD 235 72 mean 3SD 10769 33 10114 31 157 19 1 55 9969 10 1 62 10072 94 Low Control 1005
6. EXT SXT 02H Start of message EXT 03H End of message Any message not included in SXT and EXT should be ignored as noise Transmission Protocol a Transmit _ Correct receive lt 4 ACK b Transmit Incorrect receive No response 2 seconds delay Re transmit Correct receive tm _ ACK c Transmission error with repeated no response is to be judged by the transmitting side d PC does not return ACK against R transmission from Thermo Scientific Matrix PlateMate 2x3 Common Message a Positive Response STX ACK ETX ACK 06H User Manual 127 Appendix A Host PC Communication A 1 1 Basic Message Specification 1 STX Discrimination DATA ETX A 2 Control Commands A 2 1 PC gt Thermo Scientific Matrix PlateMate 2x3 i Opening COM port You can find the information about the version of the last page a Reset for all axis After the initialization is done R is sent Reset for the specified axis Numbers are shown for each axis X Y Z S This command will initialize only the axis for the value you enter 3 SX Y Both X and Y axis will move to the point where you address at the same time psem ooo O psen psem Setting Speed on S axis same as Thermo Scientific Matrix PlateMate 2x3 Upper comp External Piping OFF Upper Pump External Piping ON Supply Upper Pump External Piping ON Drain Setting Speed on M1 1010
7. The system moves the tip wash Tip washing sequence or station up to the D A R T s tips until they are inserted into the es wash channels Refer to the diagram on the right or into Bah Step 1 The wash fluid enters n ae Sa rae Step5 Step 6 through the wash channels to da a a ee ee een clean the outside of the pipet tips and spills into the P epths surrounding basin The pipet Step 1 3 and 5 at dispense depth tips expel any liquid remaining in oes aspirate depth l the tips tep 4 and b at wash dept Repeat steps 4 and 5 Aspirate and Dispense depths can be set in Tools Options Plates Note If the waste bath option Wash depth set in Add In Change Pipettor or Tips is selected the tips move to the outside of the channels before expelling waste liquid Steps 2 and 3 At the same time the system aspirates and dispenses wash fluid into the channel or waste bath to clean the inside of the tips Steps 4 and 5 Fluid aspiration CO and dispensing is repeated for each wash cycle Step 6 The tips expel any remaining liquid Step 7 i Lower stage to zera height and then Step 7 The pipetting head reset piston to home position rises while the vacuum pump drains the waste fluid from station The tips are clean and ready to be used in the next pipetting routine CAUTION Although tip washing significantly reduces sample carryover by rinsing both the internal and external walls of the D A
8. 1050 MI pump is not available with the other axes at the same time due to the relation to the hardware 6 Lower Pump Internal Piping OFF 17 M3 Lower Pump Internal Piping ON Supply 10 11 12 13 14 15 16 17 128 Thermo Scientific Matrix PlateMate 2x3 A 2 Control Commands Lower Pump Internal Piping ON Drain 8 22 DC Output right OFF 25 DC Output left O z JMC i 35 Setting Delay Time 001 250 10mS 2 500mS User Manual 129 Appendix A Host PC Communication The Teaching commands Stages The center position of each stage will be changed depending on which type of plate you use therefore you need to redo teaching and enter new value each time you use a different type of plate 1 Move 0 1mm to right on X axis Ponoi ormona oo E 70 menim somara These are the commands required for teaching Obtain the address by using QX QY and QZ Both X and Y Move commands can be used at the same time A 2 2 Thermo Scientific Matrix PlateMate 2x3 gt PC e o irese or s p pescon p Peson z ron s fsc 7 p Emaseo w p m semon 8 130 Thermo Scientific Matrix PlateMate 2x3 A 2 Control Commands Amount of movement on each axis X 0 05mm 1 address Y 0 05mm 1 address Z 0 005mm 1 address S Same as Thermo Scientific Matrix PlateMate 2x3 Other commands Version Pause Reset a Version information STX O ETX STX ACK ETX STX 1 0
9. Done in the ControlMate screen The motor will move the pipettor head down for removal m 14 Read the next set of steps described in the screen Select Pipettor or Tips Replace Pipettor or Tips Step Selection show steps to change Pipettor and tips C Tips only M Remove tip magazine Done M Loosenpipettor head camps Done M Replace pipettor head M Tighten pipettor head clamps M Inserttip magazine lM Home pipetor Action 1 Disen gage piston head alignment knobs 2 Remove and replace the piston head 3 Re engage the piston head alignment knobs A Select the Done button when finished this will cause the motor to move Done 78 Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 15 Pull out the alignment knobs on both sides of the pipettor housing and turn Knobs approximate 1 4 turn in either direction to unlock the pipettor head Alignment Knob 16 Lift the pipettor head housing door 17 Grasp the front end of the pipettor head firmly and slowly pull it out of the frame 18 Insert the replacement pipettor head Warning Lift the screws at the back of the pipettor head to keep them clear of the piston mechanism as you push the pipettor head into place 19 Turn both alignment knobs until they slip into the pipettor head and lock it in place 20 Close the pipettor head housing door
10. F 96 deep well to 38 4 cms Title 96 deep well to 38 well l Editlock F Runlock I Move to Position Position Pipettor stage 1 Vessel toe 96 deep well 2 0 ml 4221 4222 T Height o Freset aJ Aspirate Specific fisioo Wi Quadrant O 1 Tip welloffset m Predefiend fq cina a 0 amn Open files 1 ee correct Off Current file Sb deep wellta 304 cms A After you create a program you can validate it in Contro Mate before running it on the Thermo Scientific Matrix PlateMate 2x3 Thermo Scientific Matrix PlateMate 2x3 2 3 Software Interface ControlMate 2 3 3 Running a Program Before running a program you can check for setup instructions or last minute notes in the Notepad This feature is ideal for documenting any assumptions that are made during the creation of a pipetting program It serves as a reference for the user when the program is implemented Matrix Technologies Corp ControlMate File Edit View Bun Tools Add Ins Window Help CY a ted e Ba JA Command f a fat DF est T Editlock F Run lock gy Notepad OS Aspirating from 96 deep well block to 384 well plate Change 96 deep well black after aspiration Repeat this program twice Execute Sequence File sequence file E deep wellto 384 cms 000 Last run date 2409 2002 Last run duration 0 00 49 Estimated time remaining 0 00 39 Frogress oe start Help Checking tip magazine
11. In cases where liquids of varying specific gravity are to be pipetted the instrument can be recalibrated accordingly This feature ensures accurate liquid delivery no matter what fluids are being dispensed Calibration for specific liquids can be performed quickly in the lab Many calibration settings can be stored in memory and applied when needed Volume calibration is a feature found on all Thermo Scientific Matrix liquid handling systems About this Manual To use your new Thermo Scientific Matrix PlateMate 2x3 properly and safely read this Operation Manual Due to changing technologies and product enhancements this manual may be changed without notice However if you want to receive product updates on the Thermo Scientific Matrix PlateMate 2x3 please contact your local sales representative We have made every effort to ensure that this document is accurate and comprehensive However if you discover an error or omission please contact your local distributor or Thermo Fisher Scientific Hudson New Hampshire immediately at the address on the cover of this manual Thermo Fisher Scientific will not be responsible for any damage or claims of loss suffered as a result of use of this equipment in any application or in any manner other than that for which it was originally and expressly designed Any transfer of all or any part of this manual to a third party without permission is prohibited Chapter 1 Introduction 1 3 Manual Conve
12. MATRIX PLATEMATE 2x3 User Manual 1 Introduction The Thermo Scientific Matrix PlateMate 2x3 Liquid Transfer Device is a member of the Thermo Scientific Matrix PlateMate line with 8 interchangeable air and positive displacement pipetting systems A small footprint and unprecedented operator safety mechanisms make it the instrument of choice for a wide range of liquid handling applications This platform offers all the tools and flexibility for assay development and low to medium throughput The device can easily be implemented as a core pipetting system in any integrated robotic environment The Thermo Scientific Matrix PlateMate 2x3 combines a stepper motor controlled stage X and Y motion with a vertically adjustable pipetting head enabling reliable tip access into all standard lab ware 96 1536 It also has the added capability to perform serial dilutions in both portrait or landscape layouts 96 and 384 well plates With user friendly software running under MS Windows Contro Mate PlateMate 2xY ver 1 1 2 or newer operators in chemical biological physical and in vitro medical laboratories can quickly and easily customize specific laboratory protocols 1 1 System Features The Thermo Scientific Matrix PlateMate 2x3 base unit provides a universal platform upon which a flexible automated workstation is built This platform supports a deck offering simultaneous vessel placement for up to six vessels in any user defi
13. SepraSeal piercing station User Manual 97 Chapter 4 System Operation 98 The microplate deck is controlled by two stepper motors which enable the stage to be moved both laterally x and front to back y to position various vessels under the pipet tips IMPORTANT All instruments are calibrated at the factory and should not require adjustment Before running a pipetting program you must calibrate the platform stages to the microplates you plan to use The calibration procedure aligns the x y and z positions of the pipetting head to each stage position This procedure is critical to pipetting accuracy The Thermo Scientific Matrix PlateMate 2x3 instrument must be calibrated for each stage position and the minimum and maximum limits for each axis at each stage position This procedure is normally performed during instrument installation however if you change microplate types then the platform positions should be checked and possibly recalibrated to ensure optimal pipetting performance Each position on the device has been mapped to a specific stage location for example Stage 1 positioned at the pipetting head Each stage allows for the positioning along 3 axes which allow for the two X and Y associated with the deck positioning and for the tip position Z axis These are shown in the following diagram Z Z The platform positions are calibrated by using the Options Positions dialogue in the ControlMate software
14. f Pipettorandtios Tips only M Remove tip magazine M Loosen pipettor head clamps i Replace pipettor head M Tighten pipettor head clamps M Inserttip magazine M Home pipettor 28 Insert the new tip magazine Note Seat the tip magazine firmly behind the Tip Magazine Stop to ensure that the limit switch back of the clamping frame is activated by the tip magazine 29 Select Done The system resets the pistons to the home position Dione Dione Done Done Action 1 Insert the new tip magazine 2 Select the Done button when finished this will cause the motor to move Tip Magazine Stop N AE Tip Magazine Clamping Frame The Thermo Scientific Matrix PlateMate 2x3 is ready to run your pipetting program User Manual 81 Chapter 4 System Operation 4 2 2 Changing Pipet Tips Only Pipet tips can be replaced quickly and easily in the Thermo Scientific Matrix PlateMate 2x3 Tips can be changed before a run or during a run The ControlMate software guides you through each step For details on each screen refer to Chapter 4 ControlMate Software Use the following procedure to manually change pipettor tips Each step is described in the left column and illustrated with picture or screen in the right column Note For details on each option or field shown in the screens refer to Chapter 4 ControlMate Software 82 Start the Thermo Scientific Matrix PlateMate 2x3 and C
15. for setup instructions or last minute notes Matrix Technologies Corp ControlMate File Edit View Bun Tools Add Ins Window Help De ee t i m XfAdacommend Aaaa ee T Editlock PF Run lock G Notepad y Change b deep well block after aspiration Repeat this program twice la E a Bee la G 4 o ane rc ae alinan Geta TOA T Open files 1 Auto correct Off Current file 6 deep well to 304 cms 2 Prime buffer or reagent lines Note You can use the Test feature in the Move command to prime buffer or reagent lines 3 Select Run then Start from the Tools Menu i Matrix Technologies Corp ControlMate File Edit View Pun Tools Add Ins Window Help oO Thermo Scientific Matrix PlateMate 2x3 E spirating from 46 deep well block to 384 well plate re el validate File x Add Command A G eet 4 3 Running Pipetting Program 4 Review the program information in the Execute window and click Start a Execute Sequence File sequence file PE deepwellto384cms 00 Last run date 4 09 2002 Last run duration 00 00 49 Estimated time remaining 00 00 39 Frogress Start Checking tip magazine status 2 You can watch the percentage completion of the program in the Progress field Note At any time during the pipetting sequence you can click Stop to interrupt the program The
16. programmed dispense volume Conversion factor This is a factor used for converting milligrams of weight to microliters at a specific barometric pressure i e sea level 14 7 bar Weight grid This is used to enter the gravimetric values for each test sample The volume associated with the weight calculated by using the conversion factor is displayed alongside the entry Motor Steps factor This calculated field represents the value that will be used for all commands if the current entry is selected in the command as the volumetric entry to use 68 Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Calibrate Device Addin Calibr at O X This Add In feature will calibrate the and axis motor positions Start Stop E The device must first be calibrated to set the X and Y axis settings within the EPROM memory This option will perform this automatically in 0 01 increment steps and need only be done once for each device Fields Start Starts the calibration process Stop Will stop the current calibration process If the process is stopped before it completes then X and Y position accuracy will be compromised User Manual 69 Chapter 3 ControlMate Software 3 5 Previewing Pipetting Programs 3 5 1 Print Preview The print preview dialogue menu is used to view and produce a printed report of the current sequence file The name of the current sequence file is shown in a p
17. 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 8 Remove the tip magazine then select Done on the n ControlMate screen j ermo The piston motor moves down to loosen the tip magazine clamp The software screen briefly describes each instrument action as it is performed Acton Releasing the tip magazine clamp 9 Read the next set of steps described in the screen Select Pipetor or Tips Replace Fipettor or Tips Step Selection Action Show steps to change 1 Open the pipettor head housing door Loosen and disengage the 4 top piston head clamps 3 Close the pipettor head housing amp Pipettor and tips C Tips only M Remove tip magazine Done 3 oor vie see peed eiatee 4 Select the Done button when finished M Replace pipettor head this will cause the motor to move i Tighten pipettor head clamps i Inserttio magazine W Home pipettor Done 10 Lift the pipettor head housing door of the Thermo Scientific Matrix PlateMate 2x3 User Manual 77 Chapter 4 System Operation 11 Loosen the four clamps that secure the pipettor head to the frame Turn the clamps counter clockwise to loosen Once loosened the front screws will swivel forward and the rear screws will Swivel to the back Caution Move the screws so that they are clear of the piston mechanism rear screws and clear of the front cover front screws 12 Close the pipettor head housing door 13 Select
18. 4 E 7 je m 0 Washer Pump W P X Y Z Stage position 7 Reagent Pump R P S Syringe position F 2 ay ENTER R_P Reagent Pump position n Syringe Pipettor Stage W_P Washer Pump position Down Head Down Forward S Z Y 4 Use the numeric keypad to move each component Call your Matrix representative for additional information on the external keypad 107 User Manual Chapter 5 Alternate Computer Options 5 2 5 3 5 3 1 PC Command line Host PC Communications Thermo Scientific Matrix PlateMate 2x3 can be PC controlled using commands from the command line instead of the ControlMate software Command line control includes stage movements stacker sensors and barcode communication The following communication settings are required 9600 bps Stop bits 1 Parity Even Flow control None Data bits 7 All ASCII Refer to Appendix A Host PC Communications for more detailed specifications a listing of control commands and instructions on their use ControlMate OLE Introduction ControlMate provides an application developer with an ActiveX COM automation interface for the ControlMate device control application The component will enable an application to initiate an object that can load modify and execute ControlMate Sequence files The calls made to the ControlMate components do not involve the need to load the ControlMate application in memory A very powerful and useful feature of the Cont
19. 8 96 channel 125mL Sterile Polypropylene Attaching Fill Reservoir 1 86 Place the Reagent Reservoir on platform Stage 1 or 2 Stage 2 Stage 1 Note If the Tip Wash Station is used it must be placed on Stage position 2 Insert the filling nozzle of the reagent tube into the hole in the non contact sensor bracket and secure it by turning the adjustment screw Non contact sensor bracket Adjustment screw Filling nozzle Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 3 Manually fill the reagent reservoir to the desired fill height 4 Use the Move command to move the filled reservoir under the liquid level sensor Note The closer the level sensor is to the liquid the more accurate the level sensing Adjust the liquid level sensor with a small screwdriver Turn the screw clockwise until the sensor light turns on red LED in sensor turns on when it detects liquid Turn the screw slightly in both directions until the light turns off then back on to fine tune the sensor To double check the sensor rock the reagent reservoir slightly The sensor light should remain on Once set the liquid level sensor will stop reagent filling when the reagent reaches this fill height 5 Place the reagent tubing into the peristaltic pump top for left sensor bracket or bottom for right sensor bracket then into the reagent or buffer
20. C Note Failure to observe these cautions may invalidate your warranty If you have questions about any aspect of operating the Thermo Scientific Matrix PlateMate 2x3 safely please contact Thermo Fisher Scientific 24 Thermo Scientific Matrix PlateMate 2x3 3 3 1 3 1 Minimum System Requirements ControlMate Software Contro Mate is a Windows based application that provides a graphical user interface for creating and running pipetting programs From this application you can create and run a variety of pipetting operations from repetitive liquid transfers to complex pipetting sequences Because the ControlMate software is tightly integrated with the Thermo Scientific Matrix PlateMate 2x3 instrumentation you can control all Matrix PlateMate 2x3 functions from the software such as changing tips and pipettor heads or fine tuning plate movements to handle delicate pipetting operations e g transferring or mixing liquids in1536 microwells This chapter covers software installation and setup It also provides basic steps to understand and use the software as well as a reference section of all Contro Mate functions Refer to the following chapters for instrument procedures using ControlMate Chapter 4 System Operation Includes software steps used in starting the instrument changing pipettor tips or pipettor heads setting up reagent reservoir and tip wash station and creating and running common pipetting sequences Ch
21. Catalog 501 20004 501 20001 501 20002 501 20005 501 102810 501 102811 501 102890 501 102891 Channels 96 96 384 384 96 96 384 384 Volume Range 0 5 30 ul 5 0 300 pl 0 5 30 ul 1 0 100 ul 0 1 50 pl 0 1 50 pl 0 1 50 pl 0 1 50 pl Air or Positive Pipetting Technology Air Air Air Air Positive Displacement Stainless Steel PTFE Positive Displacement Duraflex Positive Displacement Stainless Steel PTFE Positive Displacement Duraflex Accuracy 2 0 or 0 15 ul 2 0 or 1 0 ul 2 0 or 0 15 ul 2 0 or 0 5 ul 2 5 or 0 01 ul 2 5 or 0 01 ul 2 5 or 0 01 ul 2 5 or 0 01 ul Precision 1 5 or 0 1 ul 1 5 or 0 75 ul 1 5 or 0 1 pl 1 5 or 0 25 ul 1 5 or 0 02 ul 1 5 or 0 02 ul 1 5 or 0 02 ul 1 5 or 0 02 ul Table 2 2 Thermo Scientific Matrix PlateMate 2x3 Accuracy and Precision User Manual 21 Chapter 2 System Overview 2 6 Hazards and Precautions There are no known hazards associated with the Thermo Scientific Matrix PlateMate 2x3 when it is operated in accordance with the instructions in this manual However you should be aware of situations that can result in serious injury Note Do not perform troubleshooting procedures on the internal components unless instructed by Matrix Technologies service personnel 2 6 1 Warnings The following warnings describe conditions or situations that can cause personal injury Throughout
22. Pipetting speed slower is better for small volumes Plate height tip should be 0 1 0 3 mm above the well bottom and Dwell times at the dispense step Slower pipetting speed prevented droplets that formed at the ends of the tips from contacting the sides or top of the wells as the plate was raised Optimal plate height ensured that the droplets made contact with the well bottom and were removed from the tip during the dispense step Longer dwell times allowed liquid drop formation at the end of the pipet tip Piston Speed Slow piston speed is recommended for small volume aspiration and dispensing Plate Height Plate height requires some trial and error to determine the optimal distance from the well bottom A height that places the tips too deep in the wells will seal the tip to the well bottom and not allow the liquid to leave the tip If the tips are not deep enough the dispensed droplet will not make contact with the well bottom and will not remove the droplet from the tip see the following diagrams a 4 Pipet tip Pipet tip Hicrowell Mictowell 0 1 0 3 mm Figure 6 3 Position of the tip in the plate before Figure 6 4 Position of the pipet tip during dispense dispense of liquid and air blowout When positioning the plate under the tips for a small volume dispense allow approximately 0 1 0 3mm of space above the well bottom prior to executing the dispense step to allow the droplet to contact the bottom of
23. Plate Max value 1486 1299 06 140 84 10 84 1323 00 69 61 1303 53 Whole Plate Min value 729 1260 81 75 89 6 02 1295 70 66 00 1303 53 1245 69 115 73 9 29 1307 15 63 22 1303 53 1296 00 53 96 4 16 1253 50 132 26 1303 53 1326 56 60 90 4 59 1292 05 64 63 1303 53 1318 25 82 76 6 28 1282 55 112 05 1303 53 1285 25 134 01 10 48 1304 35 73 36 1303 53 1302 81 128 69 9 88 1303 53 1306 63 65 86 5 04 1303 53 1308 69 75 86 5 80 1303 53 1299 81 82 41 6 34 1303 53 Blank Plate QC 1600 00 1400 00 pee 1200 00 Trt eet 1000 00 qu Plate Average 800 00 Column Average A Row Average Value 600 00 400 00 200 00 0 00 012345 67 8 9 101112131415 161718192021 Row or Column Number 139 Thermo Scientific Matrix PlateMate 2x3 Appendix C Precision Data C 2 Precision at 1 0pl into a dry 384 well plate 1 1957 1908 1790 1998 1836 1878 1993 1967 1911 1857 1755 1796 2076 1997 1883 1976 VOZZrAc LTOA mMVIUADD Volume 1 0ul Plate average 1996 46 Plate SD Plate CV 5 26 Stats calculated from Control Wells Only Column Column Column Column Row Row Plate or Row average SD CV Average CV average Value 1911 13 89 82 4 70 2013 15 6 18 1996 46 High Control 2030 63 3xSD 280 288 1956 69 113 92 5 82 1946 60 5 26 1996 46 High Control SD 93 43 mean 3SD 2310 91 1981 69 100 77 5 08 1902 00 5 08 1996 46 Low Control 2014 66 Mean 3SD 1750 34 1941 94 92 84 4 78 1950 70 6 50 1996 46 Low C
24. R Ts the Thermo Scientific Matrix PlateMate 2x3 provides fast flexible and precise automated liquid delivery while ensuring zero carryover thereby greatly reducing the risk of contamination The Thermo Scientific Matrix PlateMate 2x3 is also compatible with a selection of positive displacement syringe based pipetting heads in 96 and 384 well format for liquid handling tasks that involve viscous solutions or low volume pipetting Instrumentation System Configuration This section summarizes the standard components in the base system The Thermo Scientific Matrix PlateMate 2x3 Base Units Two base unit models are available Both models share the following list of standard features e flexible six position deck e high resolution linear microplate movement e two peristaltic pumps stepper motor controlled with integrated non contact liquid level detection e one vacuum pump e one 24VDC input output switches e universal operating voltage 100 240VAC e bar code reading capability using the barcode reader accessory e Stepper motors for plate positioning Supports 96 384 864 and 1536 well plates also supports deep or shallow wells e Keyboard unit for manual control e ControlMate Windows based PC interface software for sequence based program creation and editing plus OLE option for robotic integration Chapter 2 System Overview The Standard Base Unit The standard base unit is designed with operator safety as a
25. The Positions dialogue allows you to reset the minimum and maximum values that a stage can travel on any one of the three axes at any of the defined stage positions These values will be used within the sequence file editor for each respective command Platform Calibration Procedure Note Ensure that the instrument is on and connected to the PC Also ensure that the correct pipetting head is installed 1 Insert the D A R T magazine you plan to use 96 well tips nN 2 Inthe first stage position insert a microplate 384 well plate 1 Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 Note To ensure positional accuracy use a 384 well plate with 96 well tips or 1536 well plate with 384 well tips By aligning the D A R T s tips over the intersection of 4 wells of the 384 well plate the tips will be correctly centered for the 96 well plate see figure 3 Inthe Contro Mate software select Tools gt Options Select the Positions tab to display the following screen Position Fipettor Stage 1 Y Adjust physical location Changing any ory home values or using the Manual Movement buttons Will cause the pipettor head to move home 100 1 100 mm home O 14100 mom Manual movement Steps mm p Test height 5700 1 700 mm Offset limits offset 450 to 450 17100 mm Yoffset o to 450 1 700 mm Z offset p to 60000 1100 mm
26. Use this dialogue to load new or edit existing pipettor and tip parameters The information set up here will be used in any sequence file command so it is important that the information is accurate The information loaded must correctly reflect the physical characteristics of the pipettor head and tips currently loaded Height settings within this dialogue can be tested by selecting The stage can be reset by selecting Configuration Single row 12 tips Sul 300ul long Tip count fiz Tip diameter 83 Wash depth 2400 12100 mm Volume range 5 to 300 Increment 0 1 ul Piston diameter 350 1 100 mm Incremental column movement p Incremental row movement r Aspirate overstroke fio ul Max blow out volume hs ul Tip removal height 1050 1100 mm Tip bottom height ate 10900 1 100 mm gt ie Piston clamp height 1050 110mm l Ej Piston remove height 200 E 1100mm ge Reset To Factory Piston lock height 8000 1100 mm F MELTS AE aT Piston speed Slow 4 Fast 1095 Fields Configuration Selects the actual tip and pipettor head configuration required Tip count Physical number of tips in the tip magazine Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Tip diameter Physical measured tip diameter This is useful since it is used in positioning movement such as tip touch and well offsets Wash depth This value represents a physical measurement as to how far the respective tips
27. a rule to check a rule but not set a register value Example The Thermo Scientific Matrix PlateMate 2x3 Aspirate command applies the following sequence_Rule_Check MINVOL MAXVOL ASPIRATEMOVE In this example the rules declared as MINVOL MAXVOL and ASPIRATEMOVE will be applied See previous examples for reference User Manual 137 Appendix B ControlMate Rules Definitions B 4 Rule Validation B 4 1 Field Bounds Rules Field Bounds rules are validated during the edit process Whenever the Set button is clicked the rules are applied if applicable If the Auto Correct checkbox is checked within the Tools gt Options gt Limits tab then a failed field value will be corrected as follows e lf the value is less than the minimum rule value then it will be set to the minimum value e Ifthe value is greater than the maximum rule value then it will be set to the maximum value e f auto correction is not required then a message will be displayed for each field rule failure The text displayed will be that as defined within the rules parameters along with the field minimum and maximum limits for reference File execution will not be allowed if a Field Bounds rule has failed B 4 2 Sequential Sequence Rules The Run gt Validate File option will apply the Sequential Sequence rules The process is also applied whenever the file execution Start button is selected If a sequence fails validation then the f
28. can be pushed into the wash station chimneys during the tip wash cycle Volume range Identifies the minimum and maximum values used for checking the piston movement for volume limits Increment This field is used for determining the increment value associated with the volume increment and decrement buttons in a number of sequence commands Incremental column movement If the selected tip magazine allows for incremental column movement across a plate for example when performing serial dilution then this field when checked will enable the correct fields within the Move command Aspirate overstroke This identifies the amount of overstroke that is applied if the option is selected in the Aspirate command Tip removal height This height is used to determine the amount of travel the piston has to move in order to release the tip magazine can be used to test this field value Tip bottom height This field value is used to determine the reference point from which all height movements are calculated when positioning stages at the pipettor head The value is measured from top surface of a stage at the home position at the lowest point to the end of the tips when the magazine is loaded Getting this value wrong will cause all height movements to be inaccurate Piston clamp height This field value is used to set the travel distance the piston has to move in order to expose the 4 piston clamps This is used when the Change Pipettor and T
29. clean wash fluid and waste vacuum line to remove the used fluid Through the Contro Mate software you can specify the number of wash cycles and the wash volume The Tip Wash Station comes with a separate area to receive waste liquid thereby minimizing contamination during the wash step Tip Wash Channels k hax Fa Sensor Cable Figure 4 3 Tip Wash Station 96 Channel Tall Tip Wash Stations are available for 96 channel and 384 channel pipettor heads in two different heights Short for standard tips and Tall for extended length tips and positive displacement heads All tip wash stations are made of PTFE with Stainless Steel Chimneys Refer to the following table for order information 801 20961 96 channel Standard Height PTFE Stainless Steel 801 20962 384 channel Tall Height PTFE Stainless Steel 801 2384 1 96 channel Standard Height PTFE Stainless Steel 8011 23842 384 channel Tall Height PTFE Stainless Steel User Manual 89 Chapter 4 System Operation Attaching the Tip Wash Station 1 3 The Tip Wash sensor 90 Place the Tip Wash Station on platform stage 2 Ensure that the sensor cable is to the front The inlet and outlet barbs on the bottom will automatically engage with their corresponding ports Note The Tip Wash Station can only be used on platform stage 2 Tip Wash Station Insert the contact sensor cable from the Wash Station into the sensor port in the deck
30. container To unlock Tension Note Both pumps can be j Levers used to fill either of the two i a it reagent reservoirs as long a ae as the tip wash station is not o amp Ma required HN et ordy MAETERPLEN pecinan kating wri ASTEA Fimi iG baduna eo To insert tubing unlock the pump by moving the locking Reagent tubing User Manual 87 Chapter 4 System Operation pump lever to the left side of the pump Return the lever to the right side to lock the tubing in place If necessary adjust the tension levers on both sides of the pump to prevent slippage 6 In Contro lMate select m JE Move to Position from the Toolbox Toolbox gt Move to Position e Inthe Move to Position drop down menu select Reagent Reservoir Stage 1 e In Vessel Type select l the appropriate reagent Rmss daei reservoir During a pipetting sequence the system pumps reagent through the filling nozzle The liquid level sensor prevents overflow by signaling the pump when to stop The reagent reservoir is ready to be used in the next pipetting sequence 88 Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 4 2 4 Using the Tip Wash Station The Tip Wash Station allows you to wash both the interior and exterior walls of D A R T tips positive displacement pipetting heads and stainless steel probes It connects to the wash peristaltic pump to dispense
31. deep well to 384 well l Editlock F Run lock 4 i Move to Position M P Position Pipettor stage 1 BA i Vessel type 96 deep well 2 0 ml 4221 4222 sd I Height a Preset LJ Aspirate cy Specific isso 1 100 mm Quadrant O 1 disp into 38404 Tip wellofiset Mf T Piedefiene FiSidetoplet gt a Procedure Library o speciic ce 1 100 mm E enm Start we End UO Increment At Row E Sgn LUE End LOR Increment i i disp into 364 Q3 Column S Thermo Scientific Matrix PlateMate 2x3 4 3 Running Pipetting Program All steps that will be performed are checked If you want to skip steps during a pipetting run you can uncheck a Group Command to skip all steps in that group or uncheck an individual step F 96 deep well to 384 cms Title 196 deep well to 384 well Editlock F Run lock Group Commands disp into 364 C1 Loop f iterations W E pimo 33401 disp into 384 G2 a disp into 384 03 T Editlock P Run lock ii Dispense Volumetric Distilled water 20 22 5 Celsius Volume C i All All with blowout on H a oe specific foo 4 ul Dwell time bo 1 100 seconds Tiptouch TO Action Sey E E Changed E sequence unchecked z Commands OF Lastrun 24 09 2002 E User Manual 103 Chapter 4 System Operation 4 3 2 Sample Serial Dilution Program 104 In this sample program liquid is aspirated from a deep well block and dispensed into a 384 well microplate
32. diagram The Positions dialogue allows the setting of the minimum and maximum values that a stage can travel on any one of the three axes at any of the defined stage positions These values are then used within the sequence file editor for each respective command Position Fipettor Stage 1 s Adjust physical location Changing any ory home values or using the Manual Movernent buttons Will cause the pipettor head to move home 100 17100 mm Yhome 0 1 100 mm Hanual movement Steps mm Offset limits x offset 450 to faso 1 100 mm Voffset fo 4 to a50 1 100 mm Z offset p to E0000 1 100 mm Allow column incremental movements v Allow row incremental movements E Reset To Factory Default Settings Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate Fields Position The required stage position Adjust physical location X and Y home Use these fields to directly enter the respective axis value in 1 100 mm increments to set the required position Manual movement The manual movement buttons are used to directly control the deck motors to move the required position The deck will move in the direction specified by one motor step increment the value for which is set by the Steps mm slider For example if the slider is set to 1mm steps and the move to the back button is pressed then the deck will move 1mm backwards Test height This is t
33. dust or dirt on the power plug e Inspect the instrument thoroughly for broken or loose components e Perform general maintenance and cleaning procedures Prior to using the instrument after extended storage have it inspected by a Thermo Fisher Scientific service engineer Thermo Scientific Matrix PlateMate 2x3 7 2 Service 7 2 ZN 7 2 1 User Manual Service WARNING Always turn off the power switch and unplug the power cord when servicing the device Contact with internal components or other components connected to the line power can cause severe shock hazard Perform only service procedures that are described in the manual or authorized by Thermo Fisher Scientific Service Department service personnel Replacing Tubing The Thermo Scientific Matrix PlateMate 2x3 is designed with Easy Load peristaltic pumps and quick disconnect fittings to easily replace Reagent tubing Tip Wash Inlet and Waste Outlet lines The Thermo Scientific Matrix PlateMate 2x3 uses two basic fluid systems e Reagent fill e Tip Wash The sections that follow describe tubing replacement for each fluid system 117 Chapter 7 Maintenance and Service Reagent Fill Two reagent filling nozzles are available to fill plates on both sides of the microplate deck if the Tip Wash Station is not used In the following diagram Reagent 1 flows through the upper peristaltic pump and filling nozzle in the left sensor bracket to stage position1 Reage
34. following rule Sequence Rule Set MINVOL txtVolume MAXVOL txtVolume DISPENSEVOL txtVolume chkAirGap 1 MINVOL txtAirGap chkAirGap 1 MAXVOL txtAirGap chkAirGap 1 DISPENSEVOL txtAirGap e The MINVOL register is incremented with the value of the txtVolume field Notes A command s field value is referenced by its name and is prefixed with the symbol This is a fixed assignment i e the register will always be changed and is not logic based e The MAXVOL register is incremented with the value of the txtVolume field e The DISPENSEVOL register is incremented with the value of the txtVolume field e The MINVOL register is incremented with the value of the txtAirGap field if the chkAirGap value is 1 this means that if the Air Gap checkbox is checked then the register is incremented e The MAXVOL register is incremented with the value of the txtAirGap field if the chkAirGap value is 1 e The DISPENSVOL register is incremented with the value of the txtAirGap field if the chkAirGap value is 1 Using a register s value Each command can have a setting which identifies which rule to apply Note Commands do not have to apply rules It is feasible for a command to set register values but not check them For example a Move command can set a register value that identifies that a stage has been positioned at the tips yet has no sequence rule check Similarly it is feasible for
35. following sections describe two sample pipetting procedures 4 3 1 Sample Dispense Program In this sample program liquid is aspirated from a deep well block and dispensed into a 384 well microplate hatri Tathnolioges Comp Conirat iate Editieock F Main Sequence C ey Aypirabe from deeper Tide le the alt Comniand aeni The commands ho in this sacton will be execuied saquantnly trom the alle hice t Fepetio head aeta F Agpeahs Sul nija ca ie disp inte sia Ll of m disp into 36402 zija ayia disp into S42 cay i disp into 36404 rye Frogu Library oes ng E Ge amg sE p E wro 1 Sequence unchecked Commands OF Lest run 2409 2002 User Manual 101 Chapter 4 System Operation 102 Steps can be grouped according to their function using the Group Commands icon Group commands with descriptive titles make the program easy to follow fe 96 deep well to 384 cms Title 96 deep well to 384 well l Editlock F Funlock Group Commands Apirate from deepwel Title Apirate from deepwell block Taller Mave to Pipetta Apirate from deepwell black Loop fi iterations ii Aspirate Jiul Sag disp into 38401 disp into 364 Qz Plateklatezxz 9 Sequence unchecked Commands OK Lastrun 24 09 2002 q 2 The first step in the group commands is to move to the 96 deep well microplate te 96 deep well to 384 cms Title 196
36. pees ane show steps to change Select the steps required in Replace Pipettor and Selection left then use the Pipettor and tips Tips only tips to start the process The prac Remove tip magazine be stopped at any time via th 6 The steps required to i Loosen pipettor head clamps Sutin M Replace pipettor head replace both the pipettor M Tighten pipettor head clamps head and the tips are I Inserttio magazine shown in the Step M Home pipettor Selection box in the order they should be performed z All the steps are required ji for this procedure therefore they are all automatically checked Note Do not lift the pipettor head housing cover until instructed to do so The pipettor head housing contains a safety sensor that stops pipettor head move ment when the hood is opened Contact sensors on back of hood door and top of hood 7 Click Start The screen will remain displayed as the instructions in the Action box shown in blue text guide you through each step Select Pipettor or Tips Replace Fipettor or Tips Step Selection gt Action show steps to change 1 Remove the tip magazine Pipattor and tips C Tips only 2 elect the Done button when finished M Remove tip magazine w Loosen pipettor head clamps M Replace pipettor head W Tighten pipettor head clamps M nserttip magazine W Home pipettor Done 76 Thermo Scientific Matrix PlateMate 2x3
37. pipettor head obstructed or moved out of its physical range Check for obstructions in piston shafts Check piston settings in Add in gt Change Pipettor or Tips screen Unable to read barcode Unable to communicate with Barcode reader is not Check for loose or faulty the barcode reader connected cable connections Barcode label is covered Check for obstruction or or damaged damaged barcode vessel Command ai Device receives command Check for faulty data cable transmission error it does not recognize Command timeout is set Increase command timeout too low setting ACK timeout Instrument does not respond Check that the cables are to Control Mate commands correctly connected and that the power is switched on and available Command timeout Device begins or performs Check PC connection to an action but does not device respond to software Timeout is set too low Increase timeout setting 124 Thermo Scientific Matrix PlateMate 2x3 8 2 Error Messages Z axis obstruction safety mechanism activated The device has not been configured Unable to establish communication with the device Press OK to resume or Cancel to abort the run execution Please ensure that a tip magazine is loaded User Manual Pipettor head housing door opened during pipettor or piston head movement Light curtain detects motion or obstruction during pipettor or piston head movements User a
38. significantly different from waiter 6 2 1 Introduction 112 The calibration feature defines the number of steps that the piston motor uses to raise or lower the pipetting pistons during a pipetting cycle A liquid type with high viscosity requires more time to move through the pipet tip By increasing or decreasing the number of motor steps the pistons aspirate and dispense more or less liquid dependent on that liquid s characteristics specific gravity Liquids exhibiting higher specific gravity than water require fewer motor steps and liquids exhibiting lower specific gravity than that of water will require more motor steps Through Contro Mate you can define and save calibration values for a library of liquid types These settings will be available as choices when you insert an aspirate or dispense command The calibration procedure is performed by obtaining five volumetric weights using Contro Mate to run a dispense program The weights as well as the liquid s conversion factor are entered in the Contro Mate Volumetric Calculation program Contro Mate converts the weights to volume averages the results and calculates the motor steps factor This feature is also useful to determine if you need to define calibration values for a specific liquid After obtaining the volumetric weights you can compare the weights to the Thermo Scientific Matrix PlateMate 2x3 accuracy specifications If the results are outside of the accuracy spec
39. the electronic controls The Base Unit includes the following components Refer to Figure 2 3 1 Pipettor Hood Houses pipettor head and tips magazine Front panel can be raised to allow access to the internal components 2 Safety Shields Plastic covers on both sides of the instrument provide safety to the operator and reduce possible contamination of the work area 3 I O Connector One connector on either side of the deck allow for additional externally operated devices Power to the connector is software controlled 4 Stepper motors Stepper motors move the 6 position microplate deck vertically and horizontally 5 Vacuum pump Removes waste fluid from the tip wash station 6 Power switch Rocker switch turns Thermo Scientific Matrix PlateMate 2x3 on or off User Manual 7 Chapter 2 System Overview 7 6 Position Microplate deck Microplate deck contains six microplate positions Platform is SilverStone PTFE coated for easy cleaning Supports 96 384 864 and 1536 well plates also supports deep or shallow wells Supports a variety of standard SBS conforming labware microwell plates and reservoirs Stage 1 microplate deep well block tube rack or reagent reservoir Stage 2 microplate deep well block tube rack reagent reservoir or tip wash station Stage 2 only Stage 3 microplate deep well block tube rack manually filled reservoir vacuum manifold or sepraseal piercing manifold Stage 4 microp
40. tips Tip touch This action causes the tips to be touched against the top of the well after dispensing to remove liquid which may have adhered to the side or bottom of the tips User Manual 51 Chapter 3 ControlMate Software 52 Note Tip touch is executed near to the chosen vessels well top the height of which can be adjusted via the Tip Touch Z offset value in Tools Options Plates Move Command This command is used to position the deck to any of the positions defined in the Position Library created via the Positions tab of the Tools Options menu option The vessel positions stages on the deck are numbered from 1 back left 2 back right 3 center left 4 center right 5 front left and 6 front right The movements are grouped into six position types by default however it is possible to defined any position within the position library editor a Position a vessel under the pipetting head a Position a vessel for plate placement or removal a Position a vessel for barcode reading a Position a vessel under the dispensing location for the use of the Reservoir Pump Control command The move command is a very important command in the collection of commands since all actions require the positioning of a stage somewhere on the device It is therefore possible to test the actions of a move command when editing a sequence file by selecting _Test mode within the Sequence File Editor dialogue window a Mo
41. view Run Tools Add Ins Window Help Toolbar m ry S GH 8 MM X Add Commend oI BO e 96 deep well to 384 cms Title 96 deep well to 384 well T Editlock F Runlock Q Main Seque J Apirate f d Il black E aaa This is the main comma Toolbox Pa ali gt gt an gies Move to Pipettor Stage 1 y Ae be exe floating palette Aspirate Jiul disp into 304 01 disp into 384 G2 disp into 384 O53 i disp into 384 G4 Child Dialog j Window a Procedure Library set Undo Stat PlateMate2x2 E Changed E sequence unchecked lv Commands OF Last run ed atus 40 Bars Open files 1 Auto correct Off Current file b deep well to 384 cms Menu bar The Menu Bar shows the major software operations such as Opening and saving sequence files editing files running or validating a pipetting sequence and changing tips or pipettor head Toolbar The Toolbar provides icons that represent the operations in the Menu bar Toolbar Icons Creates New sequence file Opens existing sequence file Shows or Hides toolbox window Saves the current sequence file Saves all open sequence files Cuts the highlighted command onto the clipboard Copies the highlighted command onto the clipboard eo Koy oO Pastes the contents of the clipboard below the current command node Thermo Scientific Matrix PlateMate 2x3 Toolbar Icons 3 4 Creating Pipetting Programs EA Views the clipboard contents Del
42. 1 F10 F20 WO MO TO ETX STX ACK ETX STX OK ETX STX ACK ETX b Pause Reset STX P ETX STX ACK ETX STX P ETX STX ACK ETX sending Reset individually STX R ETX STX ACK ETX User Manual 131 Appendix A Host PC Communication Note R command is not available in Reset command after Pause Barcode Communication 1 Connect the bar code reader to COM2 2 The power supply for the bar code reader is supplied from the COM2 port and the DC motor revolves when the machine is turned on Under these conditions even if the reader is not used the motor revolves and the life of the bar code reader is shortened When the reader is not used transmit BO so that it stops 3 Transmit the following telegram for bar code reading This is an example of how it looks when reading the ZD code X8BRZD ETX ETX Telegram ends By X8 stage ZD moves under the head By BR the bar code reader laser turns on By ZD ZD reads the bar code when it moves to address after moving to the address transmit the data to the PC After receiving the data transmit the following operation Barcode Reader en 70000 Position Align the laser as shown above so that it reads the data as the stage moves up 4 The bar code reader is generally used with the default value Only cord types can be changed Use carefully to avoid changing the setup 5 E11 is transmitted when the bar code r
43. 1 0 uL It also provides the actual programming conditions under which optimum precision can be obtained by using 12 5 pL and 30 0 uL pipet tips for 384 well plates and 12 5 uL pipet tips for 1536 well plates Materials and Methods All data and results included in this procedure were obtained using the following materials Thermo Scientific Matrix PlateMate 2x3 Base Unit Cat No 501 1 10001 384 30 uL Pipetting Head Catalog No 501 20002 384 30 uL Tips Catalog No 5311 384 12 5 uL Tips Catalog No 5301 Matrix 384 Flat bottom Plates Catalog No 4318 Matrix 1536 Plates Catalog No 4512B Tecan Ultra Microplate Reader ControlMate for Thermo Scientific Matrix PlateMate 2x3 WellMate dispenser A 384 channel head was used to pipet 1 0 uL and 0 5 pL Rhodamine Green R110 fluorescent dye into pre weighed 384 well plates The plates were weighed again before adding 100 uL of PBS Phosphate Buffered Saline to each well with a calibrated Multidrop CV 1 8 at 100 uL The 384 well plates were then read using a Tecan Ultra that uses an excitation A 485 nm emission A 535 nm with 3 flashes per well The following table summarizes the precision results that were obtained Table 6 1 Precision Results With 12 5 uL Pipet Tips DISPENSE VOLUME PRECISION C V Mean for 3 plates User Manual 109 Chapter 6 Pipetting Techniques Software programming The following Contro Mate programs were written for 0 5 uL and 1 0 uL dr
44. 2 3 6 Controlling Reservoir Pumps The reservoir pumps can be used to fill reservoir vessels and can also provide finite control over the speed at which the liquid flows in either direction fill or empty Typically there are two pumps and their respective outlets available these are positioned on either side of the pipetting head The pumps can be controlled by either filling until a reservoir liquid level sensor is activated or by filling for a fixed length of time Using a sensor rather than a fixed duration to control pump motor activation will reduce the operating time of a process if the reservoir is to be used many times during a run The Overfill timeout option serves as a backup to the pump sensor The pump shuts off after the specified time default is 60 seconds in case the non contact sensor fails The Empty option reverses the direction of the pump and returns any liquid in the tubing to its container The Duration in seconds depends on the length of the tubing Reservoir Pump Control Speed Slow 4 aoe Direction e Fill 1050 Untilfull Overil timeout E000 H 1 100 seconds fe Lett sensor f Right sensor f Duration E 1 100 seconds f Empty Duration fo E 1 100 seconds User Manual 15 Chapter 2 System Overview 2 3 Connecting to External Devices One connector exists in the rear center of the deck by which additional externally operated devices can be attached This command will control
45. 9 69 Mean 3SD 9354 98 9926 44 183 60 1 85 10020 85 1 78 10072 94 Low Control SD 278 03 9978 56 199 48 2 00 10034 20 2 19 10072 94 Signal window 5 97 To find values outside 3 SD of 10003 13 240 59 2 41 10156 95 2 15 10072 94 zZ 623 31 control wells press CTRL m 9779 25 179 36 1 83 10297 60 2 30 10072 94 Signal Noise 0 01 10115 44 128 00 1 27 10202 25 1 74 10072 94 Signal Background 1 00 10084 06 170 59 1 69 10250 05 3 04 10072 94 Whole Plate Max value 11056 10214 50 377 46 3 70 9990 65 1 70 10072 94 Whole Plate Min value 9361 10038 38 156 38 1 56 10028 05 2 23 10072 94 10216 56 261 80 2 56 10010 30 2 63 10072 94 10304 75 212 69 2 06 10219 60 2 43 10072 94 10168 25 240 43 2 36 10079 35 2 34 10072 94 10047 00 191 08 1 90 9979 20 2 97 10072 94 10068 13 239 13 2 38 10084 35 2 69 10072 94 10163 44 328 46 3 23 10072 94 10269 31 229 85 2 24 10072 94 10125 44 260 81 2 58 10072 94 10104 38 169 38 1 68 10072 94 10063 88 2842 13 28 24 10072 94 10065 38 2870 59 28 52 10072 94 10264 13 2855 89 27 82 10072 94 9855 25 2985 16 30 29 10072 94 Blank Plate QC 10800 00 10600 00 10400 00 10200 00 e Plate Average Column Average A Row Average Value 10000 00 9800 00 9600 00 9400 00 012345 67 8 9 101112131415161718192021 Row or Column Number 142 Thermo Scientific Matrix PlateMate 2x3 143 Warranty and Customer Service Contact Us With Your Questions and Commen
46. Note If you do not close the housing door prior to the next step you will receive an error message 21 Select Done User Manual 79 Chapter 4 System Operation 22 Read the next set of steps described in the screen Select Pipettor or Tips Replace Pipettor or Tips Action 1 Open the pipettor head housing door 2 Re engage and tighten the 4 top piston head clamps Step Selection Show steps to change Pipettorandtios C Tips only M Remove tis magazine Done 3 Close the Pipettor head housing M Loosen pipettorhead clamps Done door 4 Select the Done button when finished M Replace pipetior head Dane this will cause the motor to mowe W Tighten pipettor head clamps Inserttip magazine i Home pipettor Done 23 Lift the pipettor head housing door 24 Hand tighten all four knobs Turn the clamps clockwise to tighten 25 Close the pipettor head housing door 26 Click Done Caution To avoid damage to the instrument ensure that the clamps are securely fastened and that the pipettor head housing door is closed before clicking Done The system releases the tip magazine clamp to receive the new tip magazine 80 Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 27 Read the next set of steps described in the screen Select Fipetor or Tips Replace Pipettor or Tips otep Selection show steps to change
47. R T s tips carryover is never completely eliminated To ensure zero carryover it is recommended that D A R T tips be replaced between sample transfers This can be done manually by an operator or automatically by using the Thermo Scientific Matrix Tip Tower an automated tip changing device User Manual 93 Chapter 4 System Operation 4 2 5 Overview of Fluid Lines Previous sections showed specific fluid line attachments for the reagent reservoir and tip wash station This section provides an overview of fluid lines in the Thermo Scientific Matrix PlateMate 2x3 94 The following illustration shows the pathway of the various fluid lines throughout the instrument Solid lines represent tubing outside of the instrument broken lines represent tubing inside the instrument Tip Wash Supply Inlet Line Tip Wash n Container Waste LIne Waste Container Reagent 2 Reagent 1 Figure 4 4 Overview of Fluid Lines Fluid Line MM Reagent 1 C1 Reagent 2 Tip Wash Ee Waste Description Reagent 1 flows from the Reagent 1 flask through the top peristaltic pump into the left filling nozzle and to the reagent reservoir on stage position 1 Reagent 2 flows from the Reagent 2 bottle through the bottom peristaltic pump into the right filling nozzle and to the reagent reservoir on stage position 1 or stage position 2 if Tip Wash Station is not used Tip Wash solution is drawn into the Supply Inlet b
48. Tip Wash from the Toolbox Toolbox gt Tip Wash e In Cycles select the number of wash cycles e In Volume select the wash volume e Adjust Pump speed according to tip size e Specify dispense location for waste liquid into chimneys or into waste bath e Select Blowout if you want to expel the remaining liquid 8 Click Set to save the settings 92 fe Move to Position Fasition Pipettor stage 2 Vessel type Tip wash 96 well T Height eE Freset Well top specific 172050 1 100 mm Quadrant Ci t Move to Position Position Pipettor stage 2 ee Ee Vessel type Tip wash 96 well into waste bath Height i Freset C Specific fi2050 Quadrant 1 Tip well offset p Predetiend F Side top lett c Specific x i 1700mm 1 100 mrm Wash Tips Cycles Volume 0 100 ul Fump speed Slow r Fast 1050 Dispense r Into chimneys Into waste bath j Volume ja 100 ul Blow out lv Vest mode Help Note Do not use the dispense option Into waste bath if you selected Tip wash 96 or 384 well in the Move to Position command The tip wash cycle will not operate This dispense option works only when you select Tip wash 96 or 384 well into waste bath in the Move to Position command Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 Tip Wash Sequence
49. VOL which will compare a register value with the field bounds rule LIMIT_01 and if found to be less than the minimum setting for this field bounds rule will display the message Total volume too low The Thermo Scientific Matrix PlateMate 2x3 configuration file has the following rule declarations Sequence 01 MINVOL lt LIMIT 01 MIN Total volume too low Sequence 02 MAXVOL gt LIMIT 01 MAX Total volume too high Sequence 03 DISPENSEVOL lt 0 Total volume after dispense too low Sequence 04 ASPIRATEMOVE lt 1 No Move to tips prior to Aspirate Sequence 05 DISPENSEMOVE lt 1 No Move to tips prior to Dispense User Manual 135 Appendix B ControlMate Rules Definitions Comparison with a literal value Example Sequence_03 DISPENSEVOL lt 0 Total volume after dispense too low This example creates a rule DISPENSEVOL which will compare a register value with zero If it is found to be negative will display the message Total volume after dispense too low B 3 2 Applying a Rule 136 A sequence rule is applied in one of two ways selectively for each command A command does not have to apply a rule or change a register s value Changing a Register s value A command can change a register s value by applying a SET instruction Example The Matrix PlateMate 2x3 Dispense command will apply the following rule Sequence Rule Set optDispenseAll 1 MINVOL O optD
50. al with tips in the tips magazine Pipettor heads L A are available with 96 and 384 channels 8 Thermo Scientific Matrix PlateMate 2x3 2 2 Instrumentation Tips Magazine Aluminum or plastic frame that holds 96 or 384 pipette tips Disposable tips magazines D A R Ts can be used with the Thermo Scientific Matrix SS PlateMate 2x3 Tips magazines with PTFE coated stainless steel tips and partial row tips are also available Tips transfer tool not shown Transfers D A R T s tips from a container to the tips magazine Tip wash station Used for washing disposable or PTFE coated stainless steel pipet tips both interior and exterior walls It is mounted on a microplate stage and connects to the buffer and waste lines liquid level sensor prevents overflow Tip wash stations are available in 96 and 384 format tall and standard height versions Reagent reservoir Reagent vessel for dispensing lt I limited volume of reagent Automatic fill reservoir is EP dap a mounted on a microplate stage A separate buffer line ae JF connects to the peristaltic pump and buffer bottle The a LF reservoir provides a continuous supply of reagent liquid a level sensor prevents overflow iig Barcode reader Optional component that is mounted to the ell side of the pipettor hood and reads the barcode label on the side of a microplate when it is moved in position for pipetting The barcode reader supports the following barc
51. anel at the foot of the main application window Toolbar Buttons e First Page Displays the first page of the report e 4 Previous Page Displays the previous page e Next Page Displays the following page e Last Page Displays the last page of the report o amp Print Sends the report to the selected printer e Printer Setup Allows the user to change the printer properties 0 Y Help This help page 70 Thermo Scientific Matrix PlateMate 2x3 3 6 Processing Programs 3 6 Processing Programs 3 6 1 File Validation Command values and relationships are checked for errors using the File Validation option Any individual field errors and relationship errors are listed It is possible to highlight an error and then display the command in the sequence file editor window in order to make corrections Command Buttons e OK Closes the dialogue window e Show Jumps to the highlighted command in the sequence file editor window e Help This help page 3 6 2 File Execution The File Execution dialogue controls the Thermo Scientific Matrix PlateMate 2x3 device using the sequence file from the current Sequence File Editor window The name of the file for the current window is shown on the status bar at the foot of the main application window Execute Sequence File IOl x sequence file E ernalD lute cms Last run date fi8 Oct 2000 Last run duration 00 06 11 Estimated time remaining 00 05 38 Progress i
52. apter 6 Pipetting Techniques Includes software controlled calibration sequences Minimum System Requirements e Computer configuration requirements a Pentium PC 400 MHz Processor 64 Mb RAM a Microsoft Windows 95 98 NT NOTE For Windows NT Contro Mate Service Pack 6 0 or higher is required a CD ROM drive for installation a VGA or Super VGA video display card a Microsoft or IBM PS 2 compatible mouse e Computer interface requirements a Serial RS 232C 16 byte FIFO memory UART16550AFN 9600 bps 7 data bits 1 stop bits Even parity 0DODOO Note For details on computer interface connection see Section A Host PC Communication User Manual 23 Chapter 3 ControlMate Software 3 2 Installation 3 2 1 Connecting the Computer Connect the serial cable to the serial or COM port in the back of the computer and the COM port in the side panel of the Thermo Scientific Matrix PlateMate 2x3 Keypad Controller COM2 Port barcode reader COM1 Port Computer Main Power Fuse Power Outlet 3 0 AMPS s Electrical Panel Serial Cable Thermo Scientific Matrix PlateMate 2x3 back view PC back view Figure 5 Computer Connection 3 2 2 Installing Control Mate 1 Start Windows and insert the Control Mate CD into the CD ROM drive The installation program will begin automatically If your installation program does not launch automatically use the following steps a From the Windows Star
53. ased around vessel placement will show a different set of fields specifically related to the control of plate placement or removal Fields Position Sets the stage position Other field parameter availability is dependent on the position selected for example Selecting a pipettor position will only show fields applicable for pipetting Vessel type Specifies the vessel type which is situated at the target location Different vessel types have different settings for the other fields within this command The values for this drop down list a created via the Options Plates window dialogue Place vessel During file execution the deck will be positioned at the location specified by the position field The user will then be prompted to place a vessel the type of which as specified in the vessel type field The user will then be required to select the OK button to continue Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Remove vessel During file execution the deck will be positioned at the location specified by the position field The user will then be prompted to remove the vessel the type of which as specified in the vessel type field The user will then be required to select the OK button to continue Mix Command lf dry tips are used more time is required to saturate the dry air with moisture while vapor pressure increases above the liquid inside the tips As a result dry tips may cause liqui
54. ate 2x3 and ControlMate software 2 In ControlMate select F Matrix Technologies Corp ControMiate Add Ins gt Change De Edt yew Bun Took addins Window bip Pipettor or Tips from the O BS a ORS ea Voimat Caer 4 Calibrate Device 3 Select the pipettor head select Pipettor or Tips Replace Pipettor or Tips configuration and tip combination you Will be Configuration 304 0 1ul 12 5ul standard tips 5301 5302 installing Tip count 384 Tip diameter 48 Wash depth f 200 Important Be sure to select mer nge 01 to fi25 Increment fo ul the correct tip combination Piston 1501 1700 mm that corresponds to the Incremental column movement M Incremental row movement M ipettor head configuration pip g Aspirate overstrake bo A ul Max blow out volume f Many preset height Uae o elias movements are based on the Tip botam height A fisa 1 100 mm physical characteristics of the tips Using the incorrect Piston clamp height 500 H 1 100mm D A R T combination will z Fist height 300 H 110mm cause the microplates and e aaah ra Ed Sss T stages to crash into the tips Piston lock height eooo H 1 100mm an and will result in improper Fiston speed Slow J Fast volume accuracy 4 Click OK to save the selection User Manual 15 Chapter 4 System Operation 5 Select Add SO Select Fipettor or Tips Replace Pipettor or Tips Ins gt Pipettor and Tips again and select the tab e epeen
55. be filled or for tubes connected to pumps to be emptied by operating the associated pump for a fixed duration User Manual 61 Chapter 3 ControlMate Software I O Switch One connector exists in the center of the deck by which an additional externally operated device can be attached This command will control the activation of the DC supply to the connector This supply can be switched on or off and also constant or momentarily E 1 0 Switch Connection f Left C Right f Constant C Momentary i seconds r Off Fields Connection One Connection Two Selects the outlet to use when using the Thermo Scientific Matrix PlateMate 2x3 use Connection One only Connection Two is available for Matrix PlateMate 2x2 only Action On Off Specified whether to switch on the DC supply or to switch off the DC supply Switching Off would normally be selected after a previous command which had switched on the supply for constant use Constant Selecting this option will cause the DC supply to be switched on constantly Another I O Switch command will be required later in the file sequence to switch off the supply Momentary Selecting this option will cause the DC supply to be switched for the duration specified in the seconds field and then switched off again 62 Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Sequence rules There are a few simple steps to follow when creating sequence f
56. be used to control a device Unless a command is changed added deleted moved or a field amended it does not need further validation This reduces start up time when issuing the sequence to the device Thermo Scientific Matrix PlateMate 2x3 Appendix B ControlMate Rules Definitions B 2 Field Bounds Checking 134 These rules are known as LIMIT rules The minimum and maximum field values field bounds for a number of fields within Control Mate commands can be set via the Tools gt Options gt Limits tab within the application This in turn updates the respective module configuration file The values that can be set are listed below the example values are actual values for the volume fields within the Thermo Scientific Matrix PlateMate 2x3 module Caption A textual value that is displayed to the user Aspirate or Dispense volume Unit Unit of measurement Edit lock Read only locking flag used to allow value 1 of 0 or disallow value of 1 editing via the Tools gt Option gt Limits tab External parameters may change the values within the rules set For example changing a Thermo Scientific Matrix PlateMate 2x3 head type would change the Volume rules settings Thermo Scientific Matrix PlateMate 2x3 B 3 Sequential Sequence Checking B 3 Sequential Sequence Checking The relationship between commands within a programmed sequence are validated by applying the sequential sequence rules This allows
57. ch step Using Online Help If you need help using the Contro Mate software program select the Help button 23 in the Toolbar menu for a list of help topics Double click the color highlighted topics to read the topic descriptions For faster access to the desired topic select the Search button in the Help menu Enter the topic to be searched and press the ENTER key to begin the search The help program will display the topics related to the search topic Select the desired topic and press Go to display the help information To get help on an open dialog window click the Help button To get context sensitive help getting help on any commands showing in the open window click on the icon The mouse pointer changes to match the icon Position it over the command of interest and press the CTRL key together with the right mouse button All software commands are available through the window menus The most commonly used commands are also available through the icons in the icon bar User Manual 39 Chapter 3 ControlMate Software 3 4 2 Understanding the Main Application Window The main application window provides function dialogues in the form of child windows The main operations of the windows are carried out by either selecting an option from the menu bar at the top of the window or by clicking on a toolbar icon Matrix Technologies Corp ControlMate Menu bar Fie Edit
58. cientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Dispensing with blow out on the last dispense of a cycle ensures that the piston is reset to the home position T Dispense Volumetric fan liquid types all temperatures bi Volume fe Al All with blowout o 000 e ul Specific 5 O00 ul Dwell time la a 17100 seconds T ip touch E Acton Gide left Fields All If checked this will dispense all liquid in the tips This does not perform a piston reset at the end of the action This is important to remember use All with blowout if a piston reset is required All with blowout This will dispense all volume in the tips plus an additional air blowout The blowout volume can be defined in the adjacent volume field After the blow out has completed the stage moves to position the tips at the top of the well out of liquid where the piston will return to it s home position Specific Selecting this option will dispense the specified volume in the adjacent field Note Choose this option when dispensing small aliquots after an aspiration with overstroke The increment and decrement buttons will change the volume value accordingly The increment for these actions can be set via Change Pipettor or Tips Add In Dwell Time The dwell time is used to specify a period of time over which to leave the tips in the sample immediately after the dispense step for equalizing air pressure and liquid movement inside the pipette
59. d to be driven out This can affect accuracy To avoid this use the mix option prior to a programmed aspiration to equalize the air in the tips before pipetting the liquid Proper vapor pressure will be maintained even if the device is left idle with filled tips for a prolonged period The Mix command should also be used to aspirate dispense liquid in a vessel to re suspend material in the vessel so that a homogenous solution can be created prior to aspiration This command requires a preceding Move command to ensure that the vessel is positioned at the tips 2 Mix ad Cycles li Volume 15 000 Sul Blow out i Height Us well top Volurne 5 O00 z ul Fields Cycles This field is used for defining the number of mix cycles required Volume The liquid volume to be aspirated and dispensed during each mix cycle The increment and decrement buttons will change the volume value accordingly The increment for these actions can be set via the Change Pipettor or Tips Add In Blowout This field will if checked ensure that a blowout is performed after the last mix cycle The height at which the blowout is to be performed and also the volume to blowout can be set Home Axes Command Occasionally it may be necessary to reset an axis to its home position during file execution It is possible to reset individual axes or by selecting one option to reset all axes User Manual 55 Chapter 3 ControlMate Software iia Ho
60. e tubing e Inspect the tubing in the peristaltic pump periodically during a pipetting run If the tubing appears to be slipping in either direction adjust the tension levers on both sides of the peristaltic pump Ensure that the tubing is not stretched over the pipettor hood or being pulled out of the sensor bracket 7 1 3 Cleaning WARNING Never plug unplug or otherwise touch the power cord when your hands are wet Contact with the cord can cause severe shock hazard CAUTION Always turn off the power and unplug the power transformer before cleaning the instrument Fluid seepage can damage internal components e Clean the exterior of the instrument as needed with a mild detergent CAUTION Do not clean the instrument with abrasive cleansers flammable or caustic solutions or solvents such as paint thinners or acetone Use of such cleansers will damage the instrument housing keyboard and display e If aliquid is spilled during use wipe it up immediately If the instrument is operating stop the operation turn off and unplug the instrument then wipe the liquid before continuing 7 1 4 Storage 116 If the instrument will not be used for a period of time do the following e Remove any remaining liquid from the tubing e Remove used tips e Unplug and clean the instrument After storage and prior to using the instrument do the following e Inspect the power cord for frayed or worn spots or tears and clean off any
61. eMate 2x3 is configured to set this value to 1 000 8 Click Add to create another liquid type User Manual 113 Chapter 6 Pipetting Techniques 9 Name the liquid type and calibration temperature Addin Yolumetric Calculation Liquid type Plasma Temperature C 20 to E Calibration olume ul Conversion factor mg to ul Sample Weight mg Volurne ul 1 10 Enter the correct conversion factor for the liquid e g 1 123 The conversion factor will be used to convert the weight to volume 11 Enter the five gravimetric weights obtained in step 5 a Addin Yolumetric Calculation Liquid type Plasma Temperature C 20 to 23 Calibration wolume jo ul Conversion factor 1 123 rg to ul Yolume ul 12 69 12 355 12 51 12 47 12 69 12 62 Update Cancel Edt OF Cancel Help The volume calculation average values and motor steps factor are automatically generated Motor steps factor 0 752 12 Click Update The motor steps factor for the liquid iti Aspirate type is saved in ControlMate and used when you select this liquid type for an Yolumetric all liquid types 20 25 Celsius aspiration or dispense step E Cverstroke fi 114 Thermo Scientific Matrix PlateMate 2x3 7 Maintenance and Service WARNING Do not disassemble or modify the components of the Thermo Scientific Matrix PlateMate 2x3 except as specified in this manual Only Thermo F
62. eading fail therefore transmit the read error ID 6 Ifthe X axis slips transmit E01 and wait for A or R When receiving A the X axis returns to home position again and continues 132 Thermo Scientific Matrix PlateMate 2x3 B 1 133 ControlMate Rules Definitions Introduction Contro Mate uses external configurable rules architecture to provide field bounds and sequential sequence checking This method provides the maximum flexibility by which field and program sequencing validation can be achieved and facilitates the building of a good degree of accuracy and device resilience The rule parameters are totally configurable and can be increased or reduced for each installation The rules engine is generic and is therefore not dependent to a specific device module However it is possible to create specific rules for a particular device Note This architecture allows the minimum amount of support in rule creation by applying a generic architecture yet allows the maximum flexibility in device control The rules parameters are contained within the module INI file e g PlateMate 2x3 ini Rules are declared as one of two types e Field Bounds Checking These are created to validate the minimum and maximum values of specific fields e Sequential Sequence Checking These exist to validate the relationship between commands within a programmed sequence Note Once a file has passed validation it can
63. ensure that the piston motor is primed and improves volumetric accuracy throughout all subsequent dispense aliquots Volume The liquid volume to be aspirated The increment and decrement buttons will change the volume value accordingly The increment for these actions can be set via the Change Pipettor or Tips Add In Dwell Time The dwell time is used to specify a period of time over which to leave the tips in the sample immediately after the aspirate step for equalizing air pressure and liquid movement inside the pipette tips Tip touch This action causes the tips to be touched against the top of the well after aspiration to remove liquid which may have adhered to the side or bottom of the tips Note Tip touch is executed near to the chosen vessels well top the height of which can be adjusted via the Tip Touch Z offset value in Tools Options Plates Post air gap This introduces an air gap at the end of the tip to ensure that sample does not leak during stage movement Dispense Command Dispenses a measured volume or all of the liquid in the tips The command will cause the piston motor to dispense the given volume The action is immediate and therefore requires the use of a preceding Move command to ensure that a vessel is positioned at the tips An option exists within the command to factorize the volume required based on volumetric calculation settings for different liquid types at different temperatures 50 Thermo S
64. ent Reservoir Fluid Lines or allow for sufficient slack for the right sensor bracket to prevent pulling or straining of the tubing during pump operation 5 Thread the new tubing through the peristaltic pump pressing it firmly between the rollers in the pump then turn the pump lever to the right to secure the tubing Pump Lever Tension Levers Figure 7 3 Installing Tubing in Upper Peristaltic Pump 6 Adjust the tension levers on both sides of the pump to prevent the tubing from slipping while the pump is in operation You may need to observe the tubing during pump operation to ensure that the tubing is secure User Manual 119 Chapter 7 Maintenance and Service 7 Insert the free end of the tubing into the reagent reservoir 8 Repeat this procedure to replace the second reagent tubing if it is needed The new reagent tubing is ready to use 120 Thermo Scientific Matrix PlateMate 2x3 7 2 Service Tip Wash Tubing When the Tip Wash Station is used it occupies stage position 2 see following diagram and requires the lower peristaltic pump therefore only one reagent solution can be used in stage position 1 Waste Tubing _ Tip Wash Tubing i Waste Bottle Wash Solution be B iin i Tip Wash Tubing ee attached to Supply Inlet Waste Tubing Figure 7 4 Tip Wash Fluid Lines attached to Drain Outlet The Tip Wash Station uses two external tubing that connect the wash solut
65. escribes each instrument action as it is performed Action lana the tip magazine clamp Step Selection Action show steps to change 1 Remove the tip magazine 2 elect the Done button when finished C Pipettor and tips Tips only i Remove tip magazine T Loosen pipettor head clamps l Replace pipettor head Tighten pipettor head clamps W Inserttip magazine h Home pipettor 7 Remove the old tip magazine from the Thermo instrument 8 Click Done User Manual 83 Chapter 4 System Operation 9 Read and follow the steps on the screen Select Pipettor and Tips Replace Pipettor or Tipe Step Selection Acton Show steps to change 1 Insert the new tip magazine Pipettor and tips Tipe onl 2 Select the Done button when i j ily finished this will cause the motor to M Remove tip magazine Done more Loosen pipettor head clamps Replace pipettor head P Tighten pipettor head clamps Insert tip magazine J Home pipettor eane 10 Insert the new tip magazine 11 Click Done The system resets the pistons to the home position clamping the tips The Thermo Scientific Matrix PlateMate 2x3 is ready to run your pipetting program 84 Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 4 2 3 Onboard Reagent Filling The Thermo Scientific Matrix PlateMate 2x3 provides onboard reagent filling and level sensing Stationary senso
66. etes the currently highlighted command Add Command Adds a new command below the current command node Brae A Views print preview Validates the current sequence file Executes the current sequence file Views configuration and default options Views help page Toolbox The Toolbox provides easy access to intrinsic or module commands such as creating or calling procedures aspirating or dispensing fluids moving stage positions and mixing The Toolbox is a floating palette and can be positioned anywhere on the screen The commands in the Toolbox can also be selected from the Add Command drop down menu in the Menu bar Toolbox icons Intrinsic Commands User Manual Call Procedure Calls a procedure from within the current sequence file or from another sequence file Saves time by reusing an existing procedure Notepad Creates a note in the sequence file Useful for documenting the steps in the sequence and for reminders during the pipetting procedure Group Commands Groups together commands for a common purpose For example the commands used to perform a common mix procedure can be grouped together Procedure Executes a series of commands whenever the procedure is called from the main sequence For example a simple pipetting procedure would consist of a move to position aspirate second move to position and dispense commands Global Define the name and format of a register called a Global Value tha
67. first priority This model features an integrated light curtain safety shield as standard An operator s hand activates an interrupt system that temporarily pauses all movement ensuring unparalleled operator safety Once the obstruction is removed the device is allowed to resume processing Figure 2 1 Thermo Scientific Matrix PlateMate 2x3Standard Base Unit Cat No 801 10007 The Robotic Friendly Base Unit The robotic friendly base unit has been designed for the purpose of robotic integration and access This base unit configuration is not equipped with a light curtain interrupt system and has been modified for easy front or side access by a robotic arm Figure 2 2 Thermo Scientific Matrix PlateMate 2x3 Robotic Friendly Base Unit Cat No 801 10005 6 Thermo Scientific Matrix PlateMate 2x3 2 2 Instrumentation 2 2 2 2 2 3 System Components f l rY 10 Peristaltic A Pumps 1 Pipettor Hood 9 Liquid Level Sensors 2 Safety Shields 8 Light Curtain _ Safety Shield 3 I O Connector ri 4 Stepper Motors _ inside base unit 5 Vacuum Pump inside base unit 6 Power Switch Figure 2 3 Thermo Scientific Matrix PlateMate 2x3 Components Main System Components Base Unit Contains two stepper motors that provide X and Y motion of the 6 position microplate stage The motors are software controlled through the PC or manual keyboard This component also contains all of
68. for example an incorrect height value may have been entered e Last Run Information The duration and date of the last run if applicable for the respective file is displayed in this panel Determining run time is useful for workload planning User Manual 47 Chapter 3 ControlMate Software Toolbox The command toolbox contains all of the intrinsic and module specific commands that can be used to create sequence files for the current device installation To add a command from this toolbox highlight the command in the command tree after which the new command is to be added and then click on the icon of the command required If the command is added at the incorrect position it can be moved to the required location within the command tree The command toolbox can be dragged and positioned anywhere within the Contro Mate window environment It can also be docked by positioning it against the side of the application window left right top or bottom If the toolbox is not docked then it will float over the top of other window dialogues to ensure that the command icons are always visible The size of the command icons can be set to either small default or large Use the View menu to do this From this menu it is also possible to choose to display text captions associated with each command icon using the Toolbox Text option Clipboard Viewer The clipboard viewer displays the current contents of the command clipboard T
69. g programs you must first configure Contro Mate to work with your Thermo Scientific Matrix PlateMate 2x3 system The next section describes the Contro Mate configuration settings 3 3 2 Configuring Device Options 26 After installing and starting Contro Mate configure the software for your Matrix PlateMate 2x3 system by selecting the Tools gt Options command on the menu bar or by pressing the Options icon on the main application toolbar Matrin Technologies Corp ControlMate File Edit View Run Tools Add Ins Window Help D a Options x Add Pai The Options screen displays tabs for the device configuration screens The first screen displays computer connection settings BF Options E E L_ o Connection Commends Liras Positions Pilotes Motors Beccodes Serial par i Baud Sali Panty Even Data tes asap bits Sand dolay fit 18 seconds Test Figure 8 Connection Screen The configuration screens are described below e Connection To set default parameters for serial communication with the device e Command Defaults To set the default field values for module specific commands e Limits To set the range limit values for the fields within the module specific commands e Positions To set the location entries for each deck position and to set the device minimum and maximum limits for each axis at each stage position e Plates To edit and add informatio
70. g sequence files and speeds up the process of reusing commands rather than deleting them and recreating them manually If the current command is a group command such as main sequence command group or procedure then all child commands will follow the same action as their parent e 4 Cut To cut a command highlight it and then click this button on the toolbar Copy TO copy a command to the clipboard highlight it and then click this button on the toolbar e Paste To paste a command from the clipboard highlight the command after which the new command is to be pasted then click this button on the toolbar Command Settings The command settings frame is used to change specific command field values Q Main Sequence This i the main command sequence The commands In this section will be executed sequentially from the first command Set Undo lest mode Help Command Buttons e Set This refreshes the screen and updates the tree structure with the changes made The changes are not saved to file until a save file option has been selected Values are checked for validation against the rules which can be set via the Tools Options dialogue before they are written to the tree structure Any validation errors are displayed in a frame below the command setting frame and the icon in the tree structure is displayed overlaid with a red cross to indicate invalidity e Undo This will change the settings back to the origi
71. ghout a series of incremental dispense Aspirating with overstroke is required when smaller aliquots are to be dispensed after a large volume aspiration Aspiration with overstroke Remaining volume in tips will provide the required volume atter compensating for piston motor lf dry tips are used more time is required to saturate the dry air with moisture while vapor pressure increases above the liquid inside the tips As a result dry tips may cause liquid to be driven out This can affect accuracy To avoid this use the Mix command prior to a programmed aspiration to equalize the air in the tips before pipetting the liquid Proper vapor pressure will be maintained even if the device is left idle with filled tips for a prolonged period Ty Aspirate Volumetric Jal liquid types all temperatures Overstroke M volume i 0 ul Volume 5 O00 d ul Ea Dwell time lo A 1 100 seconds Tiptouch 7 Action Side lett Alr gap M Yolume 5 000 ul User Manual 49 Chapter 3 ControlMate Software Fields Volumetric lf greater volumetric accuracy is required then select an entry from this drop down list which best represents the liquid sample type and temperature range This will factorize the volume used by increasing or decreasing the motor steps accordingly If no volumetric correction is required then use the default setting Overstroke Check this box if the aspirate is the first aspirate prior to multiple dispenses This will
72. gue Wash Tips Command The wash tips command facilitates the washing of both the inside and outside of each tip loaded in the tip magazine The command uses the wash reservoir which can be positioned at any stage position that allows access to the wash T liquid and waste pump connectors Tip washing sequence Step1 Step2 Step3 Step4 StepS Step Blowout Aspirate Dispense Aspirate Dispense Blowout KR Repeat steps 4 and 5 Depths Step 1 3 and 5 at dispense depth Step 2 at aspirate depth Step 4 and 6 at wash depth Aspirate and Dispense depths can be set in Tools Options Plates Wash depth set in Add In Change Pipettor or Tips User Manual 57 Chapter 3 ControlMate Software The command may require a preceding Move and Reservoir Pump Control command to optionally pre fill the reservoir and also to position the wash station at the tips lt q Wash Tips Cycles li Volume 5 000 ul Pump speed Slow 4 k Fast 1050 Dispense f nto chimneys Cf Into waste bath Blow out E Volume 19500 ul Fields Cycles This field is used for defining the number of wash cycles required Pump speed The wash pump speed can be controlled by using this field Volume The liquid volume to be aspirated and dispensed during each wash cycle The increment and decrement buttons will change the volume value accordingly The increment for these actions can be set via the Change Pipettor or Tips Add In Dispense Into chimneys This f
73. h Space around instrument Bench space on left side for computer and monitor 6 5 ft serial cable is provided Bench space on right side for reagent supplies approx 1 ft 3 ft tubing provided Grounded wall outlet supporting 110 220 VAC standard outlet for instrument plus outlets for PC system PC system for ControlMate software User Manual 11 Chapter 2 System Overview 2 3 Software Interface Contro lMate 2 3 1 Overview Control Mate is a Windows based PC application that provides a graphical programming interface for creating and executing device and module control programs The commands can be logically structured according to the control requirements The application provides a standard method by which control programs are created the configuration defines the device module in use Note See Chapter 3 Control Mate Software for installation and operating instructions 2 3 2 Creating a Program 12 Pipetting programs are created in Contro Mate by clicking the icons in the Toolbox Each icon represents either a software command or pipetting command When you click an icon the command it represents is added to the sequence of commands called the Command Tree While the command is highlighted you can enter the Command settings that are specific to that command Matrix Technologies Corp Contr alate ol X Fip Edit View Bun Tools Add Ink Window Help De Ha eame Kft Command AA ee oolbox aS
74. h the exception that it is used for determining a pre set height for dispensing liquids Tip Touch Z offset Use this field to set a value which will be used when positioning the vessel for tip touch off The value is used to determine how near to the top of the well the tips are positioned for example a value of 200 1 100mm will position the vessel so that the tips are approximately 2mm inside the top of the well Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate Quadrant Centers The quadrant grid can be used to enter values which represent the well centers for each quadrant The X and Y axis offset values are measured from the tip center position when no offsets are applied for example the dead center for a 96 well plate To determine the offset values applied the direction that the stage has to travel is the opposite of the location of the quadrant i e to position tips to the left and back of the plate the stage has to move to the right and towards the front of the device The Note frame in the dialogue windows and the diagram below show how to apply the offset values A different grid with different quadrants is available for each plate the total number of quadrant groups i e 1 4 and 16 depends on the total number of wells contained in the vessel and the current selection of the tip radio buttons The radio buttons are used to redraw the grid based on whether a 96 384 or 1536 tip set is loaded For examp
75. he height at which the tips will be positioned after the deck movement This is useful for when gauging the tip location If a new position is selected in the Position field then the tips will ignore this height and move to the safe travel height first X offset This allows the amount of movement the selected stage can move from left to right and right to left and is represented by two fields the first being the minimum value the second being the maximum value Any value which is negative causes the stage to move to the right therefore moving the tips to the left of a well for example Y offset This is similar to the X Offset fields except that the values represent movement of the selected stage position from back to front and front to back Z offset These fields similar to the previous two groups represent movement of the selected stage position in the vertical axis Allow column row incremental movements These fields are used to define whether the position is capable of allowing incremental movements in the specified direction Command Buttons Mowe Perform movement Clicking on this button will communicate with the device to test the associated position Reset from test height This will reset the device axes and is used to reset the device after testing Move the deck to the back Move the deck to the front User Manual 31 Chapter 3 ControlMate Software 32 Move the deck to the left
76. his is useful when using the Cut Copy and Paste features of the command tree within the sequence file editor window Module Specific Commands The module specific commands for the Thermo Scientific Matrix PlateMate 2x3 device relate to the control of the pipetting head and the liquid handling parameters The following commands are available E Aspirate Dispense Move Mix Home Pause Wash Tips Change Tip Magazine Speed Control Reservoir Pump Control I O Switch DUOOUOUOUOD The following Add In modules are also available a Change Pipettor or Tips a Volumetric Calibration a Calibrate Device 48 Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Aspirate Command Aspirates a specified volume The command will cause the piston motor to aspirate the given volume The aspiration is immediate and therefore requires the use of a preceding Move command to ensure that a vessel is correctly positioned at the tips Checks exist to ensure that the piston does not over aspirate and therefore stays within the maximum volume limit defined for the current piston head An option exists within the command to factorize the volume required based on volumetric calculation settings for different liquid types at different temperatures Aspirating with overstroke on the first volume ensures that the piston motor is primed this is especially useful at lower volumes and works to ensure consistency and accuracy throu
77. ield will if checked cause the dispensing within the tip wash vessel chimneys Dispense Into waste bath This field will if checked cause each dispense in the wash cycle to occur in between wash station chimneys and directly into the waste bath The tips will be positioned diagonally behind and to the right of the chimneys prior to each dispense step in a wash cycle Note This wash step must be preceded by a Move command for Vessel Type Tip wash 96 well into waste bath or Tip wash 384 well into waste bath Blowout This field will if checked ensure that a blowout is performed after the last wash cycle 58 Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Change Tip Magazine Command This command is used to pause a sequence file execution in order for the tip magazine to be replaced The command has the ability to check and issue the instruction to pause and replace tips each time it is called within a program sequence or by an incremental counter to check the usage To use the incremental counter the command must exist in a command Group that uses iterations ca 1 7 Please remove the tip magazine ca 1 7 Please insert a new tip magazine Changing the tip magazine will either display a series of window dialogue prompts on the screen see above or simply wait for the magazine change sequence to complete Either way the routine is based on the tip magazine sensor limit switch status at diffe
78. ification then continue with the rest of the procedure to calculate the motor steps factor Thermo Scientific Matrix PlateMate 2x3 6 2 Calibrating for Different Liquids 6 2 2 Calibration Procedure Use the following procedure to calibrate Thermo Scientific Matrix PlateMate 2x3tor different liquids 1 Create a ControlMate dispense program for 96 well or 384 well microplate 2 Weigh a dry microplate using a gravimetric balance 3 Use the distilled water setting motor factor 1 000 to dispense a specified volume of the target liquid e g 10 uL Note Since Thermo Scientific Matrix PlateMate 2x3 is calibrated to distilled water it uses a motor factor setting of 1 000 4 Dispense the liquid into the microplate 5 Weigh the filled microplate and calculate the final weight of the liquid in a single microwell 6 Repeat the weighing and dispensing steps to obtain five weights 7 Start ControlMate to use the Volumetric Calculation program From Add Ins Window Help the Tools Menu click Add Ins then Volumetric Calculation Change Pipettor or Tips Volumetric Calculatian The following window opens Addin olumetric Calculation Liquid Type Temperature Range All liquid types 20 C 25 C 1 000 Add Delete Edit UE Cancel Help ze The first liquid type which was used in Step 2 is the calibration value for distilled water at room temperature Thermo Scientific Matrix Plat
79. ii ve Fields e Sequence File Name of the file in the current Sequence File Editor dialogue e Last Run Date Date the file was last executed on the device e Last Run Duration The duration of the last execution for this file User Manual 71 Chapter 3 ControlMate Software e Estimated time remaining An estimation of the amount of running time left for the current sequence file execution This is based on the current duration with reference to the Last Run Duration Command Buttons e Start Start processing the sequence file e Stop Pause or Abort File Execution e Help This help dialogue Pause or Abort File Execution When Stop button is clicked on the File Execution the following dialogue will be shown Pause or Abort run execution AN Press OK to resume or Cancel to Sbork the run execution Cancel Command Buttons e OK Continues with the file execution e Cancel Aborts the file execution 72 Thermo Scientific Matrix PlateMate 2x3 4 1 System Operation The Thermo Scientific Matrix PlateMate 2x3 instrument and Contro Mate software are tightly integrated to provide an efficient system of transferring diluting and mixing fluids This section covers both instrument and software tasks that are required to set up and run the Matrix PlateMate 2x3 Introduction This chapter consists of the following sections Setting up Thermo Scientific Matrix PlateMate 2x3 Running Pipett
80. ile execution is cancelled Note Once a file has passed validation it can be used to control a device unless a command is changed added deleted moved or a field amended it does not need further validation This reduces the startup time when issuing the sequence to the device 138 Thermo Scientific Matrix PlateMate 2x3 C Precision Data C 1 Precision at 0 5yl into a dry 384 well plate 1362 1317 1372 1305 1451 1371 1426 1478 1344 1375 1442 1444 1381 1427 1433 1389 1329 1323 1371 1312 1228 1361 1303 1414 1285 1410 1294 1402 1277 1412 1228 1325 TOD 3 x TQ m7 QA0 TTD 0 5ul incr plate1 no blow tip touch Plate average 1303 5 Plate SD 95 543 Plate CV 7 3 Stats calculated from Control Wells Only Column Column Column Column Row Plate or Row average SD CV Average Row SD average Value 1345 38 72 19 5 37 1300 70 99 47 1303 53 High Control 1292 81 3xSD 253 17174 1379 06 51 96 3 77 1271 85 107 78 1303 53 High Control SD 84 39 mean 3SD 1545 98 1331 44 70 14 5 27 1301 40 85 77 1303 53 Low Control 1348 41 Mean 3SD 1039 64 1301 25 54 68 4 20 1327 20 91 54 1303 53 Low Control SD 67 69 1321 75 68 48 5 18 1340 70 54 46 1303 53 Signal window 6 69 To find values outside 3 SD 1266 63 170 22 13 44 1330 95 68 65 1303 53 z 9 21 of control wells press 1253 75 91 58 7 30 1263 80 173 90 1303 53 Signal Noise 0 51 1258 69 86 86 6 90 1353 30 66 19 1303 53 Signal Background 0 96 1294 81 113 16 8 74 1253 65 120 29 1303 53 Whole
81. iles for the Thermo Scientific Matrix PlateMate 2x3 device To achieve successful liquid transfer the following rules must be observed e A Move command must precede not necessarily directly each Aspirate Dispense Mix and Wash Tips commands e f dispensing specific volumes then the total volume dispensed cannot exceed the total volume aspirated except for when dispensing all with blow out e The start column and end column fields in the Move command can be used to set the pipetting head position at different columns within a plate This requires the installation of a tip magazine that has single tip columns This facilitates tasks such as serial dilution or an incremental dispense to multiple columns If this incremental row movement is required then remember to place the Move command or a call to a Procedure containing a Move command within a Command Group that has a loop value greater than 1 e Typically aspiration must precede a dispense action The rules above are checked whenever the File Validation or File Execution options are selected User Manual 63 Chapter 3 ControlMate Software 64 Add In Commands Change Pipettor or Tips This option assists in the installation of a new piston head and tip magazine or tip magazine only Tip magazines can also be changed by including the Change Tip Magazine as part of a sequence file program a Change pipettor and tips a Replace pipettor or tips Change Pipettor and Tips
82. information relating to the sequence file that is currently open File Header The file header contains the fields that are specific to the whole sequence file Title Copy plate using procedures F Editlack f Run lack Fields Title A text entry used to label the file for captions and reports Edit Lock Used to set a password on the file to control access for editing Checking this field will display the Edit Lock dialogue window Run Lock Used to set a password on the file to control access for execution Checking this field will display the Run Lock dialogue window User Manual 43 Chapter 3 ControlMate Software 44 Edit and Run Locks Title Copy plate uzing procedures Editlock Run lock File Locked This file has an active edit lock IF you wish to cae edit it then pou must provide the correct password Select Cancel if you want to view the file in Read Only mode Password Cancel Help The edit and run lock dialogues are used to control access to sequence file editing and execution on a file level basis Once a lock has been set the correct password is required to enable access to all file functions This means that it is possible to create sequence files and then set an edit lock to prevent a file from being changed This is useful for example in creating file templates where the new files are created based on existing ones When setting a run lock the lock dialogue will prompt for a pas
83. ing Program Shutting Down Setting up Thermo Scientific Matrix PlateMate 2x3 Proper setup of Thermo Scientific Matrix PlateMate 2x3 is critical to the accuracy and precision of the pipetting run therefore most of this chapter is devoted to instrument setup Section 4 2 contains all instrument setup procedures Running Pipetting Program After the Thermo Scientific Matrix PlateMate 2x3 is set up it is ready to run a pipetting program Section 4 3 describes a sample pipetting program Shutting Down Section 4 4 contains a checklist of tasks to shut down the instrument Note To avoid instrument damage and ensure optimal performance of your pipetting program use the pipettor head and D A R T s tips that are appropriate for the program and accessories to be used All instrument setup procedures are described in this chapter User Manual 73 Chapter 4 System Operation 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 Before the Thermo Scientific Matrix PlateMate 2x3 can be used to runa pipetting program it must be set up with the correct pipetting head D A R T tips reservoirs and tip wash The setup procedures are listed below Change pipettor head see Section 4 2 1 Change D A R T tips See Section 4 2 2 Attach Reagent Reservoir see Section 4 2 3 Attach Tip Wash Station see Section 4 2 4 Attach fluid lines for reagents buffers wash solution and waste container see Section 4 2 5 Not all of the setu
84. ion and waste bottle to the instrument through the Supply Inlet and Drain outlet as shown in the previous diagram The Tip Wash Station also uses internal tubing located in the platform stage see following photo The internal tubing is located on the underside of the tip wash station and can be replaced with a new Tip Wash Station Any other internal tubing should be replaced by authorized Thermo Fisher Scientific service personnel Internal tubing outlets on Input Outlet ports on tip platform staae wash station Figure 7 5 Tip Wash Fluid Lines on platform and tip wash station User Manual 121 Chapter 7 Maintenance and Service To replace external tubing 1 Remove used tubing a Flush remaining fluid from the tubing back into the Tip Wash reservoir Use the Reservoir Pump Control command and select Empty for approximately 20 seconds to remove all residual fluid from the system b Turn the pump lever to the left to release the tubing for the Wash Solution c Remove and properly dispose of the used tubing 2 Select replacement tubing that is approved for use with the Thermo Scientific Matrix PlateMate 2x3 system 3 Insert the new tubing into the Supply Inlet on the side of the instrument Supply Inlet n p i 4 Allow for sufficient slack to prevent pulling or straining of the tubing during pump operation 5 Thread the new tubing through the lower peristaltic pump pressing it firmly between the roller
85. ips radio button has been selected Piston remove height Used to set the distance the piston motor has to move in order to release the piston head Piston lock height Used to set the height at which the head is lowered to reveal the piston head lock clamp knobs situated on either side of the head unit Piston speed This slider sets the value by which the piston motor moves during head and tip replacement User Manual 65 Chapter 3 ControlMate Software 66 Command Buttons Test height Clicking on this button will communicate with the device to test the associated height This will reset the device axes and is used to reset the device after testing heights All axes will return to their home positions Reset To Factory Default Settings Selecting this button will reset all field values for the current piston tip configuration to those originally set as the factory default values Any changes that have been made via this dialogue will be overwritten Replace Pipettor or Tips This dialogue is used to physically control the device to either replace the piston head and tip magazine or simply the tip magazine by itself The pipettor head and tip magazine must be the same as the ones selected in the Change Pipettor and Tips Caution Failure to select the proper piston head and tip combination will cause the tips to crash into plates and stages and will result in improper volume accuracy Action Select the s
86. isher Scientific service personnel are authorized to perform any additional service to the instrument 7 1 Maintenance 7 1 1 Regular Inspections Perform the following tasks before running the Thermo Scientific Matrix PlateMate 2x3 as indicated below em Joe en Container Before start Confirm proper containers are set on correct position type areas Setting Before start Ensure proper reagent and amounts are in correct containers reservoirs Warm up At start Perform operation without containers in position areas Verify Once weekly Operate with empty containers and confirm that the movement tip enters properly into the mouth of each container If accuracy not factory values need to be reset or adjusted Contact Thermo Fisher Scientific Service Department Leak test Once weekly After aspirating liquid pause the instrument and confirm the liquid level in the tips Allow the Thermo Scientific Matrix PlateMate 2x3 to sit paused for approximately 5 minutes then observe the level in the tips again to ensure that there is no leak Problems are caused by wear on the nozzle piston O rings and seal rings Contact Thermo Fisher Scientific Service Department if a leak is observed User Manual 115 Chapter 7 Maintenance and Service 7 1 2 Periodic Inspections e Inspect tubing and power cord periodically for frayed or worn spots or tears Replace damaged tubing or power cord before using the instrument See Section 7 2 1 to replac
87. ispenseAll 1 MAXVOL 0 optDispenseAll 1 DISPENSEVOL 0 optBlowOut 1 MINVOL 0O optBlowOut 1 MAXVOL 0O optBlowOut 1 DISPENSEVOL 0O optVolume 1 MINVOL txtVolume optVolume 1 MAXVOL txtVolume optVolume 1 DISPENSEVOL txtVolume In this example the following is done e The MINVOL register is set to zero if the field optDispenseAll has a value of 1 Command field names a prefixed with an symbol Logic checks are defined with a symbol e The MAXVOL register is set to zero if the field optDispenseAll has a value of A e The DISPENSEVOL register is set to zero if the field optDispenseAll has a value of 1 The MINVOL register is set to zero if the field optBlowOut has a value of 1 The MAXVOL register is set to zero if the field optBlowOut has a value of 1 The DISPENSEVOL register is set to zero if the field optBlowOut has a value of 1 e The MINVOL register is decremented by the value of the txtVolume field if the field optVolume has a value of 1 e The MAXVOL register is decremented by the value of the txtVolume field if the field optVolume has a value of 1 Thermo Scientific Matrix PlateMate 2x3 B 3 Sequential Sequence Checking e The DISPENSEVOL register is decremented by the value of the txtVolume field if the field optVolume has a value of 1 The Thermo Scientific Matrix PlateMate 2x3 Aspirate command will apply the
88. late deep well block tube rack manually filled reservoir or sepraseal piercing manifold Stage 5 microplate deep well block tube rack manually filled reservoir or sepraseal piercing manifold Stage 6 microplate deep well block tube rack manually filled reservoir or sepraseal piercing manifold 8 Light curtain safety shield Safety sensors cover the front entry to the instrument If an operator attempts to access the pipetting area during an operation the instrument automatically stops to prevent possible injury 9 Liquid level sensors Two non contact liquid level sensors monitor liquid levels in the reagent reservoir during reagent filling 10 Peristaltic pumps Two pumps mounted on the side of the base unit supply fluid to the reagent reservoir or tip wash station on the microplate deck Quick release handles allow for quick and easy tube replacement 11 Keypad Manual keypad provides direct control en of the microplate deck for basic microplate cere positioning or troubleshooting Se 12 Control Mate Software not shown Windows based PC interface software for sequence based program creation and editing plus OLE option for robotic integration Other System Components a Pipettor Head Air and positive displacement AA interchangeable pipetting heads that can be easily inserted into or removed from the base unit Air displacement ET _ pipetting heads contain a silicone gasket that forms an airtight se
89. le setting the radio button to 96 tips for a 384 well plate would display a grid containing 4 quadrants Command Buttons Add Select this button to add a new vessel type see further information later in this topic Delete Select this button to remove the currently selected vessel type A dialogue box will be displayed to confirm or cancel the deletion action Adding new vessel types To add new vessel types select the Add button This will change the plate type frame to show additional fields to allow the creation of a plate caption and also allow the copying of existing vessel type parameters expediting new vessel creation User Manual 35 Chapter 3 ControlMate Software 36 Hew Plate Type Description New plate type Ano Cancel ppl ANCE Similar bo Nore o 1536 Square well Wlatris 45115 45175 1536 Square well Hunc 384 Round well flat 36000777711727711112 364 Round well flat large 37000111 384 Round well YW 360042711 350042112 Well spacing 394 Square deep well 4925 4326 5 Depth Well CEJ TO F se ETIU T Pehse LH fo 1 100 mm Detail for Vessel type mi well count eter lo 1 100 mm AL column movements Fields Description This allows for the entry of descriptive text that would represent the new vessel type in the selection list Similar to If the new vessel type is similar to one already defined in the library then use this field The vessel parameter
90. le from executing if this is omitted Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Reservoir Pump Control Pump f Upper f Lower Control Speed Slow 4 r Fast Direction cf Fill 1050 f Untiltull Overtill timeout T eooo E 1 100 seconds f Lett sensor f Right sensor f Duration E 1 100 seconds c Empty Duration fo 1 100 seconds Fields Pump Upper Lower Selects the outlet and associated pump to use Speed Specifies the pump speed The faster the speed the less time taken to fill a reservoir Slower speeds will give more volume control Direction Fill Empty Specifies the pump motor direction used to either fill a reservoir vessel or to empty residual liquid in the tube connected to the pump Until Full Select this option if the vessel is to be filled until the liquid level sensor is activated This is useful for filling empty vessels and can reduce operating time when reusing vessels that already contain liquid Overfill timeout Checking this field will guard against overfilling a vessel by switching off the respective pump if the associated sensor does not detect the liquid within the time specified These fields are only available if until full is selected Left sensor Right sensor This field is used for defining which sensor to check when filling Until full Duration Fill Empty This setting is provided to allow reservoir vessels to
91. lows for movement to different quadrants within a vessel then this field will be made available Quadrant offset values are entered via the Options Plates window dialogue for the respective vessel Tip well offset It may be necessary to position the tips away from the center of each well for example when using 384 well plates with low volumes it may provide more accuracy by positioning the tips in one of the well corners Checking this field will allow the setting of tip positioning by one of the pre set positions or by specifically entering X and Y axis offset values See Options Positions and Options Plates window dialogues for more information on entering offset values Column If the vessel type specified and the currently load tip magazine allows for incremental column movements within a plate then this field will be made available An example would be in the process of serial dilution in rows across a plate Once checked the column start end and increment fields will be made available Start column Specifies the first column on the vessel to be positioned under the tips End column Specifies the last column on the vessel from to be positioned under the tips If this value is set to one that is greater than the start column and the command exists in a command group which has a loop counter greater than 1 then the device will process the columns by incrementally increasing the column number in each loop pass Row If the ve
92. lue is 7 Stop Bits Default value is 1 Send Delay Use this to change the delay between commands issued to the Thermo Scientific Matrix PlateMate 2x3 device The lower the value the faster the response to query type commands for example when querying for tip magazine loading status However too low a value may cause the response sent from the device to be lost If the device is situated in a noisy environment or in a location that is not close to the PC then increasing this value would provide a better means of eliminating noise and interference that may exist on the serial interface cable Transaction Log Checking this box will cause all commands issued via the serial port to be logged into a file PortLog txt which can be found in the application program file directory To clear the file click the remove button User Manual 27 Chapter 3 ControlMate Software Command Buttons Test Test connection Clicking on this button will communicate with the device by issuing a reset command You must ensure that a The device is connected to the serial communication port on this computer a The fields described above have been correctly set up a The device is switched on Cea Clear the port log file This action will remove all actions form the port log file Commands The command defaults tab sets the default field values for the module specific commands This means that any values entered against command fields he
93. me Axes al C Piston Yanda Axes Fields All If checked will reset all axes including the piston Caution This will cause any liquid in the tips at the time to be dispensed over stage position 2 It is therefore advisable to position a vessel such as a wash station or reservoir under the tips before executing this command Piston Resets the piston motor X Y and Z Axes Checking this field will reset the X Y and Z axis respectively for each stage position Pause Command Inserting a pause command into a program causes the device to stop processing according to the pause parameters Once the continue condition has been reached the program continues at the next step within the sequence There are two types of pauses These are a Time based a Infinite requiring a user to specify when to resume A Pause f Duration z Seconds QOUMNO AAM nen pade Comp ele Sound al h Wait for user Fields Duration This causes the device to pause for a set timed interval 56 Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Seconds duration This specifies the time interval over which to pause if the Duration checkbox has been checked Sound alarm when pause complete This will sound the internal speaker on the PC 5 times once the pause period has been reached Wait for user This pauses the device indefinitely and requires the user to select when to continue via a window dialo
94. mna z4 24 i Aspirate Tiu t i eater a a te eran ka p n r alae d ml Dinpende All with Blowout cai wash ove i k d Ppeti Stage f i howe Pigetor Slage Wash Tips 2 Cycles Gire oul U Freeda Lisrery T Edil D 07 Notepad Setup JA Seal diyon Tiu Jiul 354 plate mene bps Atte beled aige Solan 1b tps DJi standard tp inthe ageing hala Figure 4 8 Control Mate Program for Serial Dilution For this example use the following guidelines Stage 1 Reagent Plate Stage 3 Select pipettor configuration for single row tips Change tips to single row or two row SD tip magazine Specify start and end column in Move command Place Reagent plate in stage position 1 Place Tip Wash in stage position 2 Place Dilution plate in stage position 3 Place 384 channel Reservoir in stage position 4 Stage 2 Tip Wash Stage 4 Dilution Plate 384 ch Reservoir Stage 5 Dilution Plate User Manual Stage 6 Dilution Plate 105 Chapter 4 System Operation 4 4 Shutting Down When you are ready to shut down the Thermo Scientific Matrix PlateMate 2x3 refer to the following checklist a Change pipettor head or pipet tips Change the pipettor head if you will be using different sized pipet tips next time Remove used tips and insert new tips for use next time a Remove buffers or reagents Remove the buffers or reagents that you have used Use the Pump procedure to empty buffer or reagents from
95. n relating to plate and vessel types that are to be used on the device e Motors To set device axis home positions e Barcodes To set the parameters used for retrieving and storing barcode data Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate Connection The Thermo Scientific Matrix PlateMate 2x3 device is connected and controlled by a PC via a serial communication port The parameters that enable communication with the device can be set on this dialogue It is possible to test the serial connection by clicking the test connection button L te This will communicate with the device by issuing a reset command A warning message will be displayed if the parameters have not been correctly defined or if the device is not connected and switched on Fields Name The device name EPROM This field will display the current EPROM version number returned after successfully pressing the Test connection button Serial Port Use this field to set the serial communication port number available on the controlling PC Range values are from 1 to 256 however the most common value for most systems is 1 Baud Use this field to set the communication speed this must match the DIP switch setting on the device motherboard The Thermo Scientific Matrix PlateMate 2x3 uses a baud rate of 9600 Parity Use this field to specify the parity used for serial communication Default value is Even Data Bits Default va
96. n the Contro Mate software the pipetting program is called a sequence file Separate sequence files can be created for serial dilutions plate to plate transfers and simple dispensing operations Once created and saved the sequence files can be quickly retrieved for use Contro Mate software includes a number of sequence file examples which can help you design your own programs All commands are supported by online Help See the remarks in the following section Using Online Help Moreover every command menu item has a Help button for calling context sensitive Help Creation of a sequence file begins with opening a new file window by selecting New in the File menu or pressing the key combination CTRL N or clicking the New Sequence button You can view and select the list of program commands by clicking the Add Command drop down menu add Command Refer to Help for special notes and explanations After you complete the program test it for possible errors by clicking the Validate button k before executing it with the Run button NOTE When testing the program set the main loop s of the program to a low number to keep the testing time short Once the program has passed the test the loop counts can be restored to the desired number Remember to save the program before starting a new program Before executing the program on valid samples perform a dummy run using water to check ea
97. nable position deep or shallow well plates any of the standard interchangeable pipetting heads and a host of other system accessories User Manual 1 Chapter 1 Introduction Figure 1 Thermo Scientific Matrix PlateMate 2x3 System A base unit includes these following standard features A variable position portrait or landscape microplate deck for easy plate or reservoir placement onto the device High resolution linear plate movement allows accurate 0 05mm microplate positioning of 96 384 864 and 1536 well plates Two power interrupt safety sensors guard access to the pipetting area a Sliding door that stops vertical pipettor movement if it is opened during an operation Q Front light curtain that stops vertical pipettor movement if it detects motion e g an Operator s hand entering the pipetting area during an operation Stepper motors provide operator safety and prevent instrument damage Two peristaltic pumps with integrated liquid level detection enable onboard reagent or wash fluid replenishment One vacuum pump provides waste fluid removal from the tip wash station which reduces cycle time and sample carryover 8 Interchangeable pipetting heads are a powerful feature that provides optimal performance and flexibility for either 96 or 384 channel pipetting applications Pipetting heads can be easily replaced as needed depending on the plate format or volume range requirements One switched 24 volt DC s
98. nal values prior to the current edit Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs e Jest mode This allows the values for the command to be tested on the device by restricting the editor to the current command only Any changes made are then sent directly to the device This is useful for example for the testing of heights and positions To return from this mode select the button again it will now show Edit Mode as a caption e Help Displays help for the respective command Status Bar The status bar provides information relating to the sequence file currently open Serial ate Changed Sequence unchecked iw Commands OK Last min 23 Feb 2000 A Panels e Module This panel displays the respective device module name to which the commands relate New Screen shot e Changed Status This shows the current edit status of the file and displays whether or not any changes have been made e Sequence Validation This panel indicates whether the entire sequence has been checked for validation and whether the validation has passed or failed The sequence validation looks at the command relationships rather than the individual limit values of commands This is useful for determining total volume levels etc throughout the sequence Sequence validation is carried out via either File Validation or File Execution e Command Validation This provides status on the validation of individual commands
99. ned for Thermo Scientific PlateMate out 2X3 Contact Thermo Fisher Scientific Service Department for repair or replacement of the pump motor Tips crash into Pistons need to be Recalibrate pistons See Section microplate calibrated 4 2 7 Platform Calibration Procedure Mismatch of tips to Redefine plate type See Section plate type 4 2 6 Defining New Plate Types Mismatch of D A R T Correct settings for pipetting head tips to pipetting head or tips in AddIn gt Select Pipettor or Tips command Thermo Scientific Power cable loose or Check connection to the wall outlet Matrix PlateMate disconnected 2x3 does not power Contact Thermo Fisher Scientific on Blown fuse Service Department User Manual 123 Chapter 8 Troubleshooting 8 2 Error Messages X axis error Y axis error Stage 1 Z axis error Stage 2 Z axis error Stage 3 Z axis error Stage 4 Z axis error Stage 5 Z axis error Stage 6 Z axis error Platform stage movement impeded by obstruction Axis address value for stage configuration is too large Pipettor head movement impeded by obstruction Pipettor tips crash into vessel Check for obstruction to vessels on platform stages Check for obstruction to platform stage tracks Check platform stage settings Check for obstructions to pipettor head or vertical track Check for the correct combination of pipettor head tips and vessel type Syringe motor error Pistons in
100. ng on the cord can damage the cord exposing the electrical wires and cause a shock hazard Use replacement fuses that conform to the current rating and specification Use of improper fuses or short circuiting the fuse holders can cause fire hazard or damage the instrument Do not exert undue pressure on the slide rails Do not restrict movement of microplate carriage Never load an empty tips magazine as this may damage the pistons Use only accessories and replacement parts provided by or recommended by Thermo Fisher Scientific Use of improper accessories and parts can damage the instrument Do not clean the instrument with abrasive cleansers flammable or caustic solutions or solvents such as paint thinners or acetone Use of such cleansers will damage the instrument housing keyboard and display The following components contact liquid directly therefore use only liquids that are compatible with these components Polypropylene tips PMMA or PTFE vessels Silicone hoses User Manual 23 Chapter 2 System Overview e Avoid using acids bases and organic solvents in the instrument they will reduce the life of the piston gasket system and can damage other critical components Also note that indirect contact can occur between the liquid and the piston gasket system through aerosols Pistons are stainless steel and gaskets are polyethylene Tips and the tip magazine can be placed in the tip rack and be steam autoclaved at 121
101. nt 2 flows through the lower peristaltic pump and filling nozzle in the right sensor bracket to stage position 2 L Reagent Tubing B i Bp LA Reagent 2 Right sensor bracket ___ we d with filling nozzle Reagent 1 Figure 7 1 Reagent Reservoir Fluid Lines Both reagent tubing and filling nozzle can be replaced with the tubing kit included with the Thermo Scientific Matrix PlateMate 2x3 system If additional tubing kits are needed contact Thermo Fisher Scientific Service Department to order Part No 301 30030 Tubing set includes tubing filling nozzle and weight To replace Reagent tubing 1 Remove used tubing a Flush remaining fluid from the tubing back into the reagent reservoir by reversing the pump flow see Reservoir Pump Control in Help b Turn the pump lever to the left to release the tubing 118 Thermo Scientific Matrix PlateMate 2x3 7 2 Service c Loosen the adjustment screw to release the filling nozzle and tubing Filling Nozzle and Tubing Adjustment Screw Figure 7 2 Replacing Filling Nozzle and Tubing d Remove and properly dispose of the used tubing 2 Select replacement tubing that is approved for use with the Thermo Scientific Matrix PlateMate 2x3 system 3 Insert the new filling nozzle into the sensor bracket and tighten the adjustment screw to secure the filling nozzle 4 Drape the tubing over the pipettor hood for the left sensor bracket See Figure 7 1 Reag
102. ntions References to other sections inthe See Chapter 3 Contro Mate Software manual are shown in italic text for software installation and operation Software buttons and menu Select Pipettor and tips Click Start selections are shown in bold text Notes provide additional information Note P d ti and are chown mehaded DOxes ote Passwords are case sensitive Important notes provide essential information and are shown in shaded IMPORTANT Use Zan SD OOU N a piston reset is required boxes Cautions alert you to conditions that can cause equipment damage and are shown in shaded boxes CAUTION Do not restrict movement of the microplate carriage Warnings alert you to conditions that can cause personal injury and are shown in shaded boxes next to the warning icon WARNING Do not use a power cord that is frayed or cut 4 Thermo Scientific PlateMate 2x3 2 2 2 2 1 User Manual System Overview General Description The Thermo Scientific Matrix PlateMate 2x3 Automated Microplate Pipetting System is a flexible multichannel automated pipetting workstation capable of performing various routine liquid manipulations In either the 96 channel or 384 channel mode operations such as reagent addition serial dilution microplate replication and sample dilution can be easily accommodated Using air displacement technology and Matrix s filtered or non filtered disposable automation research tips D A
103. ode types Code39 ITF Industrial 2 of 5 Codabar EAN UPC A E CDOE 128 COOP 2 of 5 Read Error CODE93 ee amp Oe OOO Oo DO Vacuum Manifold An optional accessory that can be used on stage position 3 to perform filtration procedures on the Thermo Scientific Matrix PlateMate 2x3 deck The manifold accessory kit includes 5 plate lifters to accommodate for the height restrictions when using short 96 or 384 format D A R T s The manifold is compatible with 96 and 384 filtration labware User Manual 9 Chapter 2 System Overview 10 Sepraseal Piercing Manifold An optional deck accessory that allows for the simultaneous piercing of 96 seprasealed storage tubes The piercing manifold is compatible with 1 4mL 0 7mL and 0 5mL Tubes Separate piercing head is required for sepraseal piercing applications Thermo Scientific Matrix PlateMate 2x3 2 2 Instrumentation 2 2 4 Pre installation Requirements The Thermo Scientific Matrix PlateMate 2x3 with its compact size and small footprint requires little bench space However additional bench space is needed for reagents buffers waste container and computer system 23 584 mm Figure 2 4 Selecting the Proper Location Consider the following requirements when selecting a place for your system Flat surface capable of holding 110 Ibs 50 kg plus weight of computer Ventilation space 23 in 584 mm height 29 5in 749 mm depth 25 in 635 mm widt
104. odes Flate Type Description 1536 square well Matrix 45116 4517 7B Add Delete Detail for 1536 Square well Matrix 451 1B 451 7B Wesseltype Plate Height 1200 1 100mm Well count fisa Shape Square Width po 1 100 mm Well spacing Ea 100mm M Allow incremental movements Depths 1 100 mm Well u faso AspirateL 350 Tip touch Z offset CJ 200 Dispense LJ 250 quadrant centres 1 100 mm Note Applicabale to tip 7 magazine that has eehed Jes GBS ee f 96 tips ees The detail and number of entries depends on how accurate the stage positioning is required either by defining a vessel plate type for each specific type or by a generic group For example a single vessel type group can be defined to represent all 96 well plates that are likely to be used However a specific vessel type may be required to ensure a higher degree of accuracy for a 1536 well plate Note The parameters entered in the Plates option are critical for correct positioning and filling of reagent reservoirs and tip wash stations as well as for specific microplate types User Manual 95 Chapter 4 System Operation 96 Use the following procedure to enter a new vessel type or to amend an existing vessel type Defining a new plate Note Ensure that the instrument is on and connected to the PC Also ensure that the correct pipetting head is installed 1 Inthe ControlMate software select T
105. on for high viscosity liquids Further to this it is also possible to select which scale of piston speed movement to apply Selecting to use a slow piston speed is useful when dispensing small volumes A speed setting used in a sequence file is used for that motor until another speed control command is encountered in the sequence during file execution The default speeds for all motor axes are set at their respective maximum settings Speed commands must appear before a Move Aspirate or Dispense commands in order to use this feature Reservoir Pump Control The reservoir pumps can be used to fill reservoir vessels and can also provide finite control over the speed at which the liquid flows in either direction fill or empty Typically there are two pumps and their respective outlets available these are positioned on either side of the pipetting head The pumps can be controlled by either filling until a reservoir liquid level sensor is activated or by filling or emptying for a fixed length of time Using a sensor rather than a fixed duration to control pump motor activation will reduce the operating time of a process if the reservoir is to be used many times during a run Note A Move command must be added to the sequence prior to a Reservoir Pump Control command to ensure that a reservoir vessel is positioned at the dispensing location The Move command must have a Reservoir position specified The software will prevent the fi
106. on the Command Toolbox dialogue or by selecting the required command from the drop down menu on the main application toolbar Commands are added directly underneath the highlighted command e Deleting an existing command Existing commands can be deleted from the command structure by highlighting the required command and then either pressing the Delete key on the keyboard or by clicking on the delete icon on the main application toolbar e Moving a command Commands can be moved to a new position in the sequence structure using the drag and drop method To move a command highlight it then while keeping the left mouse button pressed drag it to the new position and then release the mouse button Commands are moved below the one indicated as the new position An alternative to dragging commands to new positions would be to use the Cut Copy and Paste buttons which uses the clipboard to move or copy commands e Execution selection of commands Commands can be selectively included or excluded from execution To prevent a command from executing check the box beside the icon of the required command in the tree structure Checking or unchecking a group command will cause the child commands of that command to be checked or unchecked User Manual 45 Chapter 3 ControlMate Software 46 Cut Copy and Paste Commands in the command tree can be cut copied to or pasted from the clipboard This is useful when creating or editin
107. ontrol SD 83 19 1985 06 84 28 4 25 2030 70 4 48 1996 46 Signal window 5 81 To find values outside 2006 50 93 16 4 64 2025 00 4 06 1996 46 Z 32 18 3 SD of control wells 1911 06 127 25 666 2031 45 4 30 1996 46 Signal Noise 0 13 1950 75 118 68 6 08 2047 50 4 00 1996 46 Signal Background 1 01 2026 38 84 30 4 16 2014 70 5 58 1996 46 Whole Plate Max value 2287 2023 44 78 97 3 90 1972 05 3 66 1996 46 Whole Plate Min value 1641 1995 75 95 23 4 77 1938 50 5 85 1996 46 1983 00 101 50 5 12 1936 10 6 14 1996 46 2018 56 96 25 4 77 2015 75 4 44 1996 46 2008 00 122 96 6 12 2009 45 3 94 1996 46 1988 94 74 66 3 75 2000 95 5 32 1996 46 1985 44 104 70 5 27 1999 50 4 70 1996 46 2085 50 91 55 4 39 1996 46 2043 94 111 55 5 46 1996 46 1986 69 116 48 5 86 1996 46 2002 19 96 84 4 84 1996 46 2049 88 517 72 25 26 1996 46 2043 31 533 80 26 12 1996 46 2045 69 533 14 26 06 1996 46 1983 63 559 37 28 20 1996 46 Blank Plate QC 2500 00 2000 00 y 1500 00 Plate Average E Column Average 1000 00 A Row Average 500 00 0 00 01234567 8 9 101112131415161718 192021 Row or Column Number 140 Thermo Scientific Matrix PlateMate 2x3 C 3 Precision at 2 5ul into a wet 384 well plate C 3 Precision at 2 5ul into a wet 384 well plate 4784 4575 4825 4765 4629 4720 4913 4675 4651 4806 4860 4836 4711 4923 4773 4683 VPOZSBrFAC LTAONAMIVOIOWDYD Volume 2 5ul Plate a
108. ontrolMate software In ControlMate select Add Ins gt Change Pipettor or Tips from the Toolbar Click Replace Pipettor or Tips tab Select Tips only Only the steps associated with changing tips are checked in the Step Selection box The steps are shown in the Step Selection box in the order they should be performed Note Ensure that the pipettor head housing door is closed before proceeding to the next step Click Start to begin the instrument process The screen will remain displayed as the instructions in the Action box shown in blue text guide you through each F Matrix Technologies Corp ControMate Ele Edt yew fun Took addins Window biip je ge Change Pipettor or TPS j Womumetne Cake Latin Tia i Calor abe Device Seen neeeeneneemenmeeeeeeenae een aenenaeesemeemeeeemneueeeensemenmeeeemeeeae eens Action select the steps required il Selection lef then use th to start the process The pr be stopped at any time via button Step Selection show steps to change Pipettor and tips Tips only V Remove tip magazine T Loosen pipettor head clamps l Replace pipettor head Tighten pipettor head clamps M Inserttip magazine lh Home pipettor Start Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 step The piston motor loosens the tip magazine clamp The software screen briefly d
109. ools gt Options Select the Plates tab to display the following screen Plate Type Description 1536 Square well Matris 45116 45176 Add Delete Detail for 1536 Square well Matix 4511B 45178 Vessel type Plate Height 774 17100 mm well count 1538 Shape Square Width 70 1700 mm Well spacing 225 17100 mm M Allow incremental column movements Depths 11 00mm Well ES faso Aspirate Le 350 Tip touch offset Cj 200 Dispense L4 250 Well quadrant centres 1 100 mm Applicable to tip magazine that has Hote Quadrant sy Quadrant gt axis positions e 96 tips 8 z C 384 tips f 1536 tips See Y y Note Refer to the ControlMate help file for information on each field entry and command button 2 Select the Add button The software will display a blank plate type to allow you to create a new vessel type This screen also allows you to copy the plate parameters of an existing vessel type to expedite the creation of the new vessel type Click in the Similar to window to select an existing plate type from the drop down menu New Plate Type Description Apply Cancel Simil r ta 1 53K Sci are well Matrix 451 TEJE 7B i j _ 3 Enter the description of the new plate type and make any modifications needed to match the new plate type Refer to the help file for details on each parame
110. p procedures are needed for each pipetting run The following procedures are included for special situations that require undefined microplates not in the plate library or stage adjustments 0D 0 O0 UO O a Define new plate types see Section 4 2 6 a Calibrate stage positions see Section 4 2 7 Each procedure is described in more detail in the sections that follow Refer to the section that applies to the pipetting program you will be using Note If this is your first time running the Thermo Scientific Matrix PlateMate 2x3 review all of the sections to better understand when you would use each procedure The indicated procedures are software controlled and require both the Thermo Scientific Matrix PlateMate 2x3 and ControlMate software to be running 74 Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 4 2 1 Changing Pipettor Head and Tips The Thermo Scientific Matrix PlateMate 2x3 can accommodate various pipettor heads providing different volume ranges for either 96 channel or 384 channel formats The ControlMate Software contains step by step instructions to change the pipettor head and tips The steps are also documented below Each step is described in the left column and illustrated with picture or screen in the right column For details on each option or field shown in the screens refer to Chapter 4 ControlMate Software 1 Start the Thermo Scientific Matrix PlateM
111. r 3 ControlMate Software Barcodes The Barcodes options dialogue is used to set the parameters associated with the barcode reader attached to the device All output from a successfully read barcode is written to a file Each field is comma separated with each record being carriage return and linefeed CRLF terminated The format for each record is Date DD MM YY time HH MM SS barcode data text CRLF Barcode reader connected r Manual entry for barcode read failures fw Export file Filename Ic Program Files Contral ate B arcodes txt Date stamp Time stamp M Fields Manual entry for barcode read failures Check this box to enable the input of barcode text should the barcode reader fail to read a barcode during the execution of a Move command Filename All barcode data that is successfully read will be output to a file This field will allow the entry of the filename If this field is left empty then the default filename will be used Date stamp lf checked then the current system date will be written along with the barcode data for each successful barcode read Time stamp lf checked then the current system time will be written along with the barcode data for each successful barcode read 38 Thermo Scientific Matrix PlateMate 2x3 3 4 3 4 1 3 4 Creating Pipetting Programs Creating Pipetting Programs A pipetting program is a sequence of pipetting actions that accomplishes a pipetting task I
112. r brackets on each side of the pipettor head hold the filling nozzles and liquid level sensors over the reagent reservoirs for automated filling and noncontact liquid level sensing see figure below Right Sensor bracket Lower Peristaltic Pump Tubing Non contact Liquid Level Sensor Filling Nozzle Reagent Reservoir on Stage 2 k B Figure 4 1 Right Sensor Bracket and Reagent Reservoir The Reagent Reservoir can be placed on Stage 1 and automatically filled by a filling nozzle inserted in the left sensor bracket and attached to the upper peristaltic pump A second Reagent Reservoir can be placed on Stage 2 and automatically filled by a filling nozzle in the right sensor bracket and attached to the lower peristaltic pump The non contact liquid level sensor in each bracket ensures that each reservoir is filled to a predefined volume every filling cycle Tubing From Lower Peristaltic Left Sensor i Pump if Reagent Reservoir Used Bracket A o Right Sensor Bracket Reagent Reservoir on Stage 1 Reagent Reservoir or Tip Wash Station on Stage 2 Figure 4 2 Reagent Filling Components User Manual 85 Chapter 4 System Operation Reagent reservoirs for 96 well and 384 well pipetting are available see following table The Thermo Scientific Matrix PlateMate 2x3 can also use the following disposable reagent reservoirs Catalog Capacity No 1064 05 8 96 channel 125mL Non Sterile Polypropylene 1064 15
113. re will be used as initial values when the respective command is added to a sequence file in the Sequence File Editor dialogue Command Aspirate ha Default Yalues Lif Volumetric fai liquid types 3 all temperatures Overstroake M volume f T ul d Volume 5 000 E ul Dwell time la 1 100 seconds Tip touch E Action Side left A gap 7 Yolume 75 000 ET ul Fields Command This drop down box allows the selection of available module specific commands 28 Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate Limits The fields within the module specific command set have to be validated against a minimum and maximum value for the respective field This options tab allows the setting of those values The values are used whenever commands are changed in the Sequence File Editor dialogue or during File Validation Only minimum and maximum values can be changed using this dialogue Some values cannot be changed and are displayed for information purposes only To change a value use the mouse pointer to click on the required value and enter the required change To set the value press the Enter key or click on another field value in the list Value Hin HM ax Unit Aspirate or Dispense volume 0 5 30 ul Delay atter aspirating 0 1000 17100th seco Delay after dispensing 0 1000 17100th seco Pause duration 100 Seconds Mix cycles 1 10 lterations Wash cycles 10 Iterations 2 asis height 0 13000 1700 mm Rese
114. re or Round Width The well width is especially important for determining well centers and quadrant offsets and tip touching The field value represents the physical width of the well measured at the top of the well Well spacing The well spacing field is used when determining the distance in 1 100mm between well centers and also when incremental column movements are required within a vessel for example when serial dilution is required The field value is measured from the center of one well to the next and is also known as the well to well spacing Allow incremental column movements This checkbox determines whether the vessel can be used in conjunction with the correct tips for incremental column movements within a vessel for example when serial dilution is required If this checkbox is unchecked then the vessel does not support incremental movements regardless of tip usage Well Depth The well depth value is used to define a preset height which defines the bottom of the well The value entered must be measured from the well top to the well bottom at the well center Aspirate Depth This field is used to represent a pre set height available within the Move command This height is useful for setting a default height at which liquid is aspirated The larger the value the higher the stage movement and therefore the further down into the well the tips are positioned Dispense Depth This is similar to the Aspirate Depth wit
115. rent steps within the change sequence to indicate when a step has completed i i Change Tip Magazine Track usage Change after fo LISES Manual ff User is prompted to contin each step Automatic 7 Action is based on tip sensor activity Fields Track usage This sets an internal counter that determines when tips should be changed within a loop Change after n uses This determines the internal tip change counter This field is only displayed if the Track usage check box has been checked Manual Automatic The setting of these radio buttons determines whether the window dialogue prompts are shown above or not Either way the process waits for changes in the magazine tip sensor status to determine the current step before continuing Speed Control Piston horizontal and vertical soeeds can be adjusted using the Speed Control command User Manual 59 Chapter 3 ControlMate Software 60 H Speed Control Control Normal Piston D Z vertical Slow r Fast 1030 Slow 4 F Fast 1030 amp Horizontal left right E Bj t Horizontal front back Slow a F Fast 1030 To change a motor speed click the check box for respective motor and then use the slider to set the required speed The number under the slider indicates the current numerical value of the speed setting The lower the number the faster the motor action Reducing piston speed is recommended for improving accuracy and precisi
116. rolMate OLE component is the ability to dynamically change and set command field values within a sequence file This allows the external integration of information such as source values for example aspiration volumes to be extrapolated from databases 5 3 2 Build and Distribution The Control Mate OLE component can be distributed as a required component within the client application Any component dependencies will be included as part of the application build 5 3 3 Development Environment 108 The ControlMate OLE component has been developed for use with Microsoft Visual Basic versions 5 and 6 For more information about how to use this option refer to the Contro Mate OLE User Manual PlateMate 2x2 6 1 Pipetting Techniques This chapter discusses pipetting techniques that can be used to optimize pipetting precision for small volumes and to calibrate for different liquid densities Optimizing Pipetting Performance Precision and accuracy can be difficult to obtain when pipetting small liquid volumes such as 1 0 uL or 0 5 pL This section describes the dispense procedure that was used to test the Thermo Scientific Matrix PlateMate 2x3 for small volumes and discusses the critical parameters that affect pipetting performance 6 1 1 Dry Plate Dispense Procedure This procedure documents the techniques that were used to optimize Thermo Scientific Matrix PlateMate 2x3 dispense capabilities for dry plate dispensing of 0 5 to
117. rvoir wash fill time 0 BOOU 1 100th seco a ul cm Blow out volurnie BOO 1 100th seco IO switch momentary duration 100 Seconds blasimum amp asis movement 0 15770 1 1 00th mn Auto corect invalid values during command edit D Reservoir overtill timeout Z Fields Value This represents the field type Min This is used to set the minimum value allowed Max This is used to set the maximum value allowed Unit This represents the field unit of measurement if applicable Auto correct values during command edit When checked this box enables the auto correction of values which fail command validation in the Sequence File Editor dialogue The values used will be from the respective setting in the list above The following rules apply If a field value is below the limit minimum value then the limit minimum value is used If a field value is above the limit maximum limit value then the limit maximum value is used User Manual 29 Chapter 3 ControlMate Software 30 The main application window displays the current status of this field on the status bar at the foot of the window Positions Each position on the device has been mapped to a specific stage location for example Stage 1 positioned at the pipetting head Each stage allows for the positioning along 3 axes which allow for the two X and Y associated with the deck positioning and for the tip position Z axis These are shown in the following
118. s in the pump then turn the pump lever to the right to secure the tubing 6 Adjust the tension levers on both sides of the pump to prevent the tubing from slipping while the pump is in operation You may need to observe the tubing during pump operation to ensure that the tubing is secure F Pump Lever Figure 7 6 Installing Tubing in Lower Peristaltic Pump 122 Thermo Scientific Matrix PlateMate 2x3 7 2 Service 7 Insert the free end of the tubing into the Tip Wash solution 8 Insert the new tubing for the Waste liquid into the Drain on the side of the instrument Drain Outlet 9 Insert the free end of the tubing into the Waste Bottle The new Tip Wash tubing is ready to use User Manual 123 8 1 Mechanical 8 Troubleshooting 8 1 Mechanical Reagent reservoir Liquid level sensor is not Adjust liquid level sensor see overfills functioning Section 4 2 3 Onboard Reagent Filling Contact Thermo Fisher Scientific Service Department Tip wash station Liquid level sensor is not Reconnect the sensor wire overfills plugged into the connector Tubing in peristaltic e Peristaltic pump not Adjust side forks on peristaltic pump slips adjusted for tubing pump See Section 7 2 1 Replacing Fluid Lines Incorrect tubing was Replace with tubing recommended used for Thermo Scientific PlateMate 2x3 Peristaltic pump is Wrong tubing was used Replace with tubing recommended stalled or bur
119. s will be copied and used as a default value for the new type which can then be changed This is ideal for adding new entries which a similar to but not the same as existing entries Command Buttons Apply Select this button to add the newly defined vessel type to the library Cancel Select this button to cancel the entry of the newly defined vessel type Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate Motors The Motors options dialogue is useful for defining the home positions for each axis motor The home position is the reference position from which all movements are made Normally this information is set at the factory and does not require any further changes Changes made to this dialogue will affect the movement of motors and are not recommended It is advisable to seek vendor assistance before making any changes Y Axis Home position lo 1 100 mm mm per step 0 05 A AXIS Home postion fo 17100 mm mm per step n 06 Piston Home position lo 17100 mm Z AXIS Home position fo 17100 mm Steps per mm 250 d mm per step n 005 d ES The default settings are shown above Fields Home position This is used to set the home position for the respective axis from which all movements will be made for the axis Mm per step Steps permm This is used to define the translation of motor stepper movements to mm for the respective axis User Manual 37 Chapte
120. ssel type specified and the currently load tip magazine allows for incremental row movements within a plate then this field will be made available An example would be in the process of serial dilution in columns down a plate Once checked the row start end and increment fields will be made available User Manual 53 Chapter 3 ControlMate Software 54 Start row Specifies the first row on the vessel to be positioned under the tips End row Specifies the last row on the vessel from to be positioned under the tips If this value is set to one that is greater than the start row and the command exists in a command group which has a loop counter greater than 1 then the device will process the rows by incrementally increasing the row number in each loop pass Increment This is used to set the row increment value A value of 1 will cause the stage to move to each well of the selected vessel Read barcode If the vessel type is one of PLATE and the preset height is Barcode Height then this field will be made available During execution a dialogue box may be displayed if the barcode reader fails to read a barcode Use Tools Options Barcodes to set whether or not to display the manual barcode entry dialogue window Movements for vessel placement jet Move to Position Position Place R emove Yessel Stage 1 Vessel type 384 Square well flat 4310 4324 f Place vessel Remove vessel Note Selecting a position which is b
121. status 2 At any time during the pipetting sequence you can click Stop to interrupt the program User Manual 13 Chapter 2 System Overview 2 3 4 Changing Thermo Scientific MatrixPlateMate 2x3 Components ControlMate software also provides step by step instructions to change Thermo Scientific PlateMate 2x3 components such as pipetting tips or pipetting heads Addin Change Pipettor or Tips Select Fipettor or Tips Replace Pipettor or Tips step Selection Action show steps to change select the steps required in Step selection left then use the Start button to start the process The process can be stopped at any time via the Stop button Pipettorandtips Tips only M Remove tip magazine W Loosen pipettor head clamps M Replace pipettor head iM Tighten pipettor head clamps M Inserttip magazine hf Home pipettor Done Continue 2 3 0 Calibrating Liquids For liquids that require an accuracy adjustment during volume dispensing you can determine the calibration factor that adjusts to the specific gravity of the liquid The Volumetric Calculation option in Contro Mate adjusts the movement of the piston motor to improve pipetting accuracy for specified liquids Liquid Type Temperature Range All quid types All temperatures Distilled water 20 C 22 5 C Distilled water fol 23 C Add Mejete Eat 14 Thermo Scientific Matrix PlateMate 2x3 2 3 Software Interface ControlMate
122. sword and then prompt for confirmation of the password If the two password entries do not match then the lock is not set Note Passwords are case sensitive Password Validation Sequence files that have an edit or run lock set will cause this dialogue box to be displayed whenever the file is opened within the sequence file editor if edit lock set or file execution if run lock set The dialogue will prompt for a password If an incorrect password is entered file access via the lock is not granted This means that in the case of an edit lock the file cannot be edited or in the case of a run lock cannot be executed on the device Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Command Tree The command tree represents the program sequence Sequence files are executed from the top to the bottom of this tree structure Commands can be manipulated in the tree structure in a number of different ways Main Sequence 3 I Edi i Group commands Copy plate 8 iterations elfe Collect tips coon ales Mover position 3 col 1 to 8 settee Cte Call procedure Aspirate 10ul ssc wife Move position 4 col 1 to 8 senenn Cte Call procedure Dispense 10ul Be are Procedures sne mai Procedure Aspirate 10l Geol j Aspirate 10 ul go mg Procedure Dispense 10ul ow Dispense 10 ul e Adding a new command Commands are added to the tree or command structure by either clicking the required command icon
123. t is designed to hold a value A global value command can be added anywhere to the sequence file tree structure Assign Change or define field or other Global Value command values The field value change can be made either before a command executes for example to change the current quadrant or after a command executes for example to capture a plate barcode Export Extract information held in global values into external text based files Aspirate Aspirates a measured volume Should be preceded by a move command 41 Chapter 3 ControlMate Software Toolbox icons Dispense Dispenses a measured volume or all of the liquid in the tips Should be preceded by a move command E Move to Position Position a stage to a specific location on the instrument For example a stage must be moved under the pipet tips prior to the Aspirate or Dispense command rp Home Axes Resets a piston or stage to its home position oe Pause Inserts a pause into a program to stop processing according to the pause parameters Once the continue condition has been reached the program continues to the next step within the sequence Speed Control Adjusts piston speed aspiration or dispensing speed horizontal and vertical stage speeds Wash Tips Washes inside and outside of pipet tips Requires automated wash reservoir Mix Aspirates and dispenses a measured volume in specified cycles to mix the microwell content Also equali
124. t menu click Run b Type D setup if the D drive is not correct change the drive letter to match your CD ROM drive If you install Contro Mate from a server or common directory enter the complete path name then setup c Press Enter to start installation 2 Follow the setup instructions on the screen 24 Thermo Scientific Matrix PlateMate 2x3 3 3 Configuring ControlMate 3 3 Configuring Contro Mate 3 3 1 Starting Contro Mate Start Contro lMate by clicking Start in the Windows Taskbar and selecting ControlMate from the Programs menu The following window appears r Matrix l echa rokgies Corp CG wilro bale Ea Bu se iB Tec Tes aH e Tie E jorentinem eenaa S Figure 6 ControlMate Main Screen When you create a new pipetting sequence a new window called child dialog window opens in the ControlMate software Maris Techrala waji Orp Loninoviats af toe S64 crs Def t Hain Sequence This is the main comm end seq in e erm bo enuhrd Ende Agural form deppa Mork gji Manat fo Pigaetlor Stage 1 F f Aspralt Miad h cay deep into 33401 P miT disp imio 334 02 ot capa disp imo 33403 cat disp into 19404 cae Procedure Library OET Ea DOO Amo Corrente 9 doup wel to Bema Figure 7 Main Screen with Child Dialog Window User Manual 25 Chapter 3 ControlMate Software Before you begin creating pipettin
125. teps required in Step Selection left then use the Start button to start the process The process can be stopped at any time via the Stop button Step Selection Show steps to change Pipettor and tips f Tips only If Remove tip magazine M Loosen pipettor head clamps W Replace pipettor head I Tighten pipettor head clamps M Insert tip magazine I Home pipettor Dorne onthe Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs To start the process select which option is required change pipettor and or tips to change tip magazine only then follow the prompts in the Action frame If any errors occur or a step is not successful completed then the status or follow on action will also be displayed in the Action frame It is possible to stop the process at any time and also possible to process any particular step at any time by checking the check boxes of the steps required Typically though all actions will be defined by the selection of one of the two radio buttons to define the full set of actions required Volumetric Calculation It is possible to set a volumetric factor to use within the Aspirate and Dispense commands The factor can be used to cause the piston motor to increase or decrease the number of steps required in order to achieve an accurate volume movement based on liquid sample type and also by environment operating temperature This will assist in achieving
126. ter 4 Click Apply to save the new vessel type Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 You can test the new vessel type by inserting a Move command in a ControlMate program then selecting Test Mode The new vessel type is ready to use If the vessel type requires different stage positions then continue to the next section 4 2 7 Calibrating Stage Positions The Thermo Scientific Matrix PlateMate 2x3 comes with a six position microplate deck that can accommodate different container types that are used in the pipetting operations such as deep well or shallow well microplates Figure 4 5 Platform Stages You can use all six stages to transfer microplates or reserve stages 1 and 2 for the reagent reservoir and tip wash station respectively Stages are assigned as follows Stage 1 Microplate deep well block tube rack or reagent reservoir Stage 2 Microplate deep well block tube rack reagent reservoir or tip wash station Stage 2 only Stage 3 Microplate deep well block tube rack vacuum manifold or manually filled reservoir SepraSeal piercing station Stage 4 Microplate deep well block tube rack or manually filled reservoir SepraSeal piercing station Stage 5 Microplate deep well block tube rack or manually filled reservoir SepraSeal piercing station Stage 6 Microplate deep well block tube rack or manually filled reservoir
127. the tubing to their source containers Flush the tubing with distilled water if necessary a Remove microplates Remove any coated microplates or v bottom reservoirs if necessary a Shut down ControlMate Save any programs if you made changes and shut down the Contro Mate software Shut down the PC if you will not be using it a Shut down Thermo Scientific Matrix PlateMate 2x3 instrument After all necessary plates and ancillaries have been removed press the on off switch to power down the instrument and shut it off a Clean any liquid spills as needed 106 Thermo Scientific Matrix PlateMate 2x3 5 1 External Keypad 5 Alternate Computer Options 5 1 External Keypad The external keypad provides basic functionality to the Thermo Scientific Matrix PlateMate 2x3 It is used primarily for troubleshooting 1 2 Turn on the Keypad MN Die Sie we Figure 21 External Keypad Connect the Keypad cable to the Controller port on the side of the instrument PlateMate 2x3 READY The READY screen appears MANUAL NEXT KEY Press the NEXT key to enable manual movement of the Thermo Scientific Matrix PlateMate 2x3 The screen shows the current axis positions of the moveable components of the Thermo Scientific Matrix PlateMate 2x3 Pipettor Stage Syringe Head Up Back MANUAL X 46 Y 93 Z P A 71 R P amp W P O Staae Left X Staae Right X EXC or RESET Key
128. the activation of the DC supply to the connectors This supply can be switched on or off and also constant or momentarily 1 0 Switch Connection i Left Fight Action f On f Constant f Momentary i secands Off 16 Thermo Scientific Matrix PlateMate 2x3 2 4 Overview of Operation 2 4 Overview of Operation 2 4 1 Laboratory Application Some of the possible laboratory applications for the Thermo Scientific Matrix PlateMate 2x3 are outlined below e Preparation for enzyme immunoassays EIA Enzyme immunoassays in the ultra micro liter volume range Rotavirus antigen antibodies against toxoplasma gondii antibodies against adenoviruses Double antibody sandwich assay for determining AFP TSH HGH IgE Lipid A antibodies DNA antibodies potato viruses antibodies against bovine leucosis viruses e Preparation for agglutination reactions with subsequent quantitative photometric analyses Blood group determinations in the ABO and Rh systems Coombs reactive antibodies Latex agglutination tests e Application in cell cultivation Hybridoma screening for working with cell cultures Cell seeds cell cloning Changing the nutrient medium of cell cultures e Dosing the scintillation solution in microplate LSC e Dosing and transfer steps in PCR e Simple reagent liquid addition e Serial dilution across 8 12 or 16 24 columns for sensitivity analysis e Plate to plate replica
129. the manual warnings will be marked with the Warning icon in the left margin e Ensure that the power plug is connected to a power receptacle that provides voltage and current specified for the device Use of incompatible line power can cause shock and fire hazard e Never use a two prong adapter or connect the device into a two prong receptacle Use of a two prong receptacle disables the electrical grounding and creates a severe shock hazard Always plug the device directly into a three prong receptacle with a functional ground e Do not use a power cord that is frayed or cut Do not kink or strain the power cord Use of a damaged power cord can cause shock and fire hazard e Never plug unplug or otherwise touch the power cord when your hands are wet Contact with the cord can cause severe shock hazard e f you notice smoke or unusual odor or noise coming from the instrument turn it off immediately then unplug the power cord Do not use the instrument until it has been serviced and inspected by Thermo Fisher Scientific or authorized service representative e Always turn off the power switch and unplug the power cord when servicing the device Contact with internal components or other components connected to the line power can cause severe shock hazard Perform only service procedures that are described in the manual or authorized by Thermo Fisher Scientific service personnel e Do not allow tools objects or liquids to enter the instr
130. the well Dwell Time During the dispense step for a small volume it is important to use a Dwell Time to allow the volume droplet to form on the end of the pipet tip As a general rule dwell times are dependant on the dispense volume and liquid type Smaller dispense volumes require longer dwell times e g 0 5 1 0 uL dwell times should be 1 5 2 0 seconds User Manual 111 Chapter 6 Pipetting Techniques 6 2 Blowout Do not use Dispense All with a Blowout Use a specific dispense volume Instead of using the blowout command aspirate a small volume of air before aspirating the desired quantity of liquid Using this aspirated air as the blowout allows the Dwell Time to be executed near the bottom of the well not above the well where a pause after a blowout takes place usually a pause after a blowout is not required The extra air volume should be great enough to overcome any capillary action in the small tip orifice The air volume should be sufficient to assist the separation of the droplet from the tip to the well bottom but not so great that air bubbles become a problem The air blowout is another parameter that is often optimized by trial and error Calibrating for Different Liquids Improving pipetting accuracy Thermo Scientific Matrix PlateMate 2x3 is factory calibrated for distilled water at room temperature however you can add calibration values to improve pipetting accuracy of liquids with specific gravity that is
131. tion e Automating IC 50 assays User Manual 17 Chapter 2 System Overview 2 4 2 General Operation The following outline summarizes the tasks you would perform for a pipetting operation Not all of the tasks may be needed depending on the instrument setup and the pipetting program you use 1 Start ControlMate 2 Start Thermo Scientific Matrix PlateMate 2x3 3 Setup Thermo Scientific Matrix PlateMate 2x3 a Change pipettor head Change tips Attach Reagent Reservoir Attach Tip Wash Station OoU 4 Run pipetting program 5 Shut down Thermo Scientific Matrix PlateMate 2x3 Each task is described in more detail in Section 4 System Operation 2 4 3 Device Precision 18 The Thermo Scientific Matrix PlateMate 2x3 was tested for precision at volumes ranging from 0 5 pl to 5 0 ul The results are summarized below To review the raw data go to Appendix C Precision Data Table 2 1 Device Precision Volume Plate average Plate SD Plate C V 0 5 into a dry 384 well plate 1303 5 95 54 1 0ul into a dry 384 well plate 1996 5 105 06 5 26 2 5ul into a wet 384 well plate 4877 8 208 78 4 28 5 0ul into a wet 384 well plate 10073 253 67 2 52 Thermo Scientific Matrix PlateMate 2x3 2 5 Specifications 2 5 Specifications 2 5 1 System Specifications Instrument Dimensions Base unit weight Dimensions Liquid Capacity Pipetting Volume Plate Access Reagent Reservoirs Tip Wash Station System Control Ke
132. ts Your Thermo Scientific Matrix PlateMate 2x3 and pipetting heads are covered by a one year factory warranty Your comments and suggestions for improving the performance and versatility of the Thermo Scientific Matrix PlateMate 2x3 system are always welcome and appreciated We also appreciate your comments and suggestions for improving this manual If you have any questions or comments about your Thermo Scientific Matrix PlateMate 2x3 system contact your equipment provider Some of those contacts are listed on this page if your instrument was provided by a distributor not listed here contact that distributor Thermo Fisher Scientific Matrix Liquid Handling Solutions 22 Friars Drive Hudson NH 03051 USA Toll free 800 345 0206 Tel 603 595 0505 Fax 603 595 0106 European Headquarters Lower Meadow Road Brooke Park Handforth Wilmslow Cheshire SK9 3LP UK Tel 44 161 486 2110 Fax 44 161 488 4560 Freefone 0800 389 4431 French Office 30 Quai de la Bataille 54000 Nancy France Tel Fax 33 383 542 975 German Office Vogelsangstrasse 12 D 61273 Wehrheim Germany Tel 49 6081 981878 Fax 49 6081 981959 Swiss Office Seedammstrasse 3 Postfach CH 8808 Pfaffikon SZ Tel 41 55 417 4546 Fax 41 55 417 4647 Thermo Scientific Matrix PlateMate 2x3
133. ttempts to run sequence file before completing pipettor or tip configuration Device does not respond when user presses Start to begin sequence file User presses Stop button during sequence file run Tip magazine is not detected during the initialization of a sequence file Close housing door to resume action Remove hand or other obstruction from the pipetting area before resuming action Configure pipettor and tips in Add in gt Change Pipettor or Tips screen Verify that the tip magazine is in place and properly seated behind the stop tabs in the clamping frame Contro Mate will not allow a program to run unless the tip magazine is in place Check that the cables are correctly connected and that the power is switched on and available Check communication port in Tools gt Options gt Connection screen Follow directions in the error message Insert a tip magazine lf a tip magazine is present ensure that it is properly seated behind the stop tabs in the clamping frame Check the limit switch that detects the tip magazine replace if it is defective 125 Chapter 8 Troubleshooting 126 Thermo Scientific Matrix PlateMate 2x3 A Host PC Communication A 1 Hardware Specifications 1 2 9600 bps STOP 1 PARITY EVEN X NONE BITS 7 ALL ASCII G G TXD TXD RXD gt RXD DTR DTR DSR gt lt DSR CTS CTS RTS RTS Essential Message Format SXT
134. ument through ventilation slots or other openings Contact with electrical or other internal components can cause severe shock hazard fire hazard or instrument malfunction If a hazardous condition occurs disconnect the instrument from the line power immediately e Keep hands away from moving parts e g tips magazine mechanism and the peristaltic pump Personal injury may result Warning symbols on the device indicate areas of potential personal injury 22 Thermo Scientific Matrix PlateMate 2x3 2 6 Hazards and Precautions 2 6 2 Cautions The following cautions describe conditions or situations that can cause damage to the instrument Do not install or operate unit in extreme environmental conditions e g direct sunlight extreme temperature or humidity or restricted ventilation Refer to installation instructions for proper environmental conditions When unpacking or transporting the Thermo Scientific Matrix PlateMate 2x3 always support the base to prevent damage to the instrument The Thermo Scientific Matrix PlateMate 2x3 is designed for use on a bench top Set up the instrument on a sturdy bench or table that is capable of holding its weight and remains stable during its operation Always turn off the power and unplug the power transformer before cleaning the instrument Fluid seepage can damage internal components When disconnecting the power plug from the power receptacle grip the plug itself not the cord Pulli
135. upply outlets for additional externally controlled devices Thermo Scientific PlateWate 2x3 1 2 User Manual 1 2 About this Manual Efficient pipette tip replacement Matrix D A R Ts Disposable Automated Research Tips are compatible with the Thermo Scientific Matrix PlateMate 2x3 pipetting heads Tips held in the disposable magazine are placed on the device and seal directly against a silicone pad This forms a definitive seal without the use of conventional tip fittings or O rings In addition to providing a cleaner seal that presents less opportunity for contamination this method provides the added benefit of ensuring uniform tip height across all 96 384 pipette tips which facilitates consistent drop delivery onto fiat bottom microplate surfaces Filter tip options are available for disposable tips Serial dilution feature To further expand the versatility of the Thermo Scientific Matrix PlateMate 2x3 Matrix has designed the system to support 8 12 16 or 24 channel serial dilution applications This is accomplished by using a dedicated 8 12 16 or 24 channel tip magazine The instrument s discrete x y advancement design allows for incremental plate movement needed to accomplish row by row or column by column dilutions directly on the Thermo Scientific Matrix PlateMate 2x3 Volumetric calibration Thermo Scientific Matrix PlateMate 2x3 systems are factory calibrated using distilled water at room temperature 20 C
136. values in a program to be checked prior to running the sequence on the device This ensures that the maximum liquid handling accuracy and device protection is achieved The process of applying the rules allows the creation of external registers or variables against which the rules are compared These registers can be incremented decremented or set with literal values by each individual command The setting of the value can also be determined by either setting it literally or by logic selection conditional processing The rules can only be entered into the configuration file by a text editor there is no rules editor available at this time The rules are very flexible and allow the creation of parameter strings by which individual commands or entire sequences can be checked They are created as a Rule Declaration and then by applying a rule to a specific command The format of each is shown below B 3 1 Rule Declaration A rule has to first be declared before it can be used The basic principal of a rule declaration is to ensure that the rule is added to a library of available rules and consists of creating a rule identifier comparator operand and failure text message The comparator value can be either a literal value or a field bounds rule element minimum or maximum value Comparison with a Field Bounds Rule element Example Sequence_01 MINVOL lt LIMIT_01 MIN Total volume too low This example creates a rule MIN
137. vements to position for pipetting a Movements for vessel placement Movements to position for pipetting jet Move to Position Position Pipettor Stage 1 Vessel type 384 Square well flat 4310 4324 Height 0 Preset T Well top Specific 3460 gt 1 100 mm Quadrant FH 1 Tip well offset Precelicnd side top left C Specific X D H 1400mm if fo 17100 mm Column Start li End li Increment f H owy Stat li End li Increment li Read barcode P Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs Fields Position Sets the stage position Other field parameter availability is dependent on the position selected for example selecting a Plate Remove vessel position will only show fields applicable for vessel placement Vessel type Specifies the vessel type which is situated at the target location Different vessel types have different settings for the other fields within this command The values for this drop down list a created via the Options Plates window dialogue Height This specifies the height at which the tips should be lowered Heights can either be set by choosing one of the preset heights as determined by the vessel type parameters or by setting a specific height value Movement is measured from the position when the tips are at their home location to at the base of the stage downwards Quadrant If the combination of vessel well count and tip count al
138. verage 4877 8 Plate SD Plate C V 4 28 Stats calculated from Control Wells Only Column Column Column Column Row Plate or Row average SD CV Average Row CV average Value 4758 06 101 07 2 12 4847 90 2 97 4877 84 High Control 5027 42 3xSD 574 471386 1 2 4908 06 153 30 3 12 4728 90 4 26 4877 84 High Control SD 191 49 meant 3SD 5601 89 3 4905 81 158 17 3 22 4829 30 4 24 4877 84 Low Control 5086 91 Mean 3SD 4452 95 4 4868 63 129 53 2 66 4731 65 4 38 4877 84 Low Control SD 156 79 5 4783 50 208 05 4 35 4775 55 3 80 4877 84 Signal window 6 31 To find values outside 3 SD 6 4799 94 172 99 3 60 4698 05 3 85 4877 84 zZ 18 56 of control wells press 7 4765 00 213 24 4 48 4914 70 3 65 4877 84 Signal Noise 0 24 8 4847 13 169 21 3 49 4848 95 4 14 4877 84 Signal Background 0 99 9 4872 38 144 09 2 96 4897 40 2 62 4877 84 Whole Plate Max value 5606 10 4821 13 217 46 4 51 4825 40 2 72 4877 84 Whole Plate Min value 4332 11 4771 88 205 84 4 31 4861 40 4 41 4877 84 12 4800 69 189 00 3 94 4828 45 3 35 4877 84 13 4968 88 94 83 1 91 4802 05 3 69 4877 84 14 4875 38 223 22 4 58 4940 90 3 41 4877 84 15 4826 69 178 69 3 70 5078 80 4 19 4877 84 16 4945 19 137 10 2 77 4957 45 3 16 4877 84 17 4965 00 294 47 5 93 4877 84 18 4806 69 307 72 6 40 4877 84 19 4770 69 245 67 5 15 4877 84 20 4897 88 176 12 3 60 4877 84 21 4954 31 1308 85 26 42 4877 84 4981 56 1347 78 27 06 4877 84 5153 81 1348 01 26 16 4877 84 5020 00 1413 70 28 16 4877 84
139. very accurate volume dispensing The factors are generated by using a standard volumetric correction factor for the specific liquid type at the temperature range required and to use this applied to the gravimetric measurement taken for the required volume The net result will be the factor that will be used to correct the piston motor to achieve the required accuracy for the specific liquid temperature range Liquid Type Temperature Range All liquid types All temperatures Distilled water ZC 22 9 C Distilled water 290 25 C Add Delete Edit This dialogue is used to create the table in which these volumetric setting are held To add a new entry select the add button To delete an existing entry select the delete buttons to amend an entry either double click or highlight it and select the edit button User Manual 67 Chapter 3 ControlMate Software Measurements Whether adding or amending an entry the following dialogue will be displayed Liquid type Distilled water Temperature C 20 to 22 5 Calibration volurnie 25 ul Conversion factor j 003 rig to ul Weight rig Y olume ful Motor steps factor i 100 Update Cancel Edt Fields Liquid type A descriptive text field to identify the liquid type Temperature A descriptive text field to identify the liquid type Temperature Minimum and maximum temperatures in Celsius for the current entry Calibration volume The required volume to achieve
140. y dispensing into 384 and 1536 well plates 3 Fig Edit View Fun Tool Addie Window Hep u An eee yi Dis cheered l D in eri i Ej zr EL hn Fia cer ra Erga De Sea pere orld Peg dea Ay Al dhe Penn Pan Corks bp Peel ole l m Rinseeer Purp Covel Use Fi loop Program for 10 miera ai Diaria m hgt daniy piaia ragi J Z Hl u Ape See A Aapamig Hh El ole Mit ip Apion Soe all Chipeta oad a Co peru mim high by ple ringa A l T Wow i hapsi Stee A Aeris T ai hire W pann Se 4 zl if awa pir A Rima Api cai Replenish Resgeni Reservoir 7 Notepad El wta howe to Reservoir Stage a CHANNEL JOUL HEAD ack aa i ill DWSEEMSE INTO 334 WELL PLATE ary 404 PLATE REAGENT ADDITION STAGE 3000 iterations ay Chuacieari 1 Irainestior E elt Minat io Fupotlor Stsqe 1 cap nl Agpireala Mul a ey Move to Pipettor Sage 3 cal i Dispense All 4h ary Quadrant 2 transfer E aii Quadrant J transfer E ary Quadrant 4 transfer ary WASH TIPS t Kore 0 Pipette Sage 3 VWieh Tps 3 Coches py CHANGE PLATES Figure 6 2 Dry Dispense using 1 0 mL 110 Thermo Scientific Matrix PlateMate 2x3 6 1 Optimizing Pipetting Performance Pipetting Techniques for Small Volumes The dispense procedure resulted in the following techniques to optimize pipetting precision for small dispense volumes of fluorescence into dry 384 and 1536 well plates Critical parameters affecting performance included
141. y the Vacuum Pump and flows to the Tip Wash Station stage 2 only Waste fluid is removed from the Tip Wash Station by the Vacuum Pump exits via the Drain Outlet into the Waste Container Thermo Scientific Matrix PlateMate 2x3 4 2 Setting Up Thermo Scientific Matrix PlateMate 2x3 4 2 6 Defining New Plate Types The Thermo Scientific Matrix PlateMate 2x3 comes with a library of commonly used microplate types and vessel types for example reservoirs and tip wash stations When you select a microplate in the library the Thermo Scientific Matrix PlateMate 2x3 uses the stored parameters to properly position that microplate under the pipetting tips If you use a microplate type that is not in the library then the instrument may need to be retaught to ensure optimal pipetting position and performance Caution Improper definition of the microplates can cause the pipet tips to crash into the microplate Be sure to follow the procedure in this section for the microplate type that will be used in pipetting operations To ensure accurate pipetting the vessel type whether it is a microplate tip wash or even a reagent reservoir must be defined in the plates library The Plates option in the Tools menu is used to set the dimensions and well positions for each vessel type Matrix Technologies Corp ControlMate File Edit view Pun Tools Add Ins Window Help LS Ee Connection Commands Limits Positions Flates Motors Barc
142. ypad control PC control I O Switch User Manual 190 pounds 85 5 kilograms Height 23 inches 584 millimeters Depth 29 5 inches 749 millimeters Width 25 inches 635 millimeters 96 Channel Head 384 Channel Head Tip 1 0 5 ul 30 0 pl Tip 3 0 5 pl 30 0 pl Tip 2 5 0 pl 300 0 pl Tip 4 1 0 pl 100 pl 96 384 864 1536 384 amp 1536 shallow wells shallow wells 96 deep well 384 deep well 96 channel 100 mL 384 channel 50 mL with automatic fluid replenishment and level detection 96 channel tall and 384 channel tall and standard height standard height Liquid crystal touch panel Dialog type input for programming mode operations PC 64 MB RAM 400 MHz processor Windows platform with a serial port Software Contro Mate Software version 1 06 or later Input Output Switch for External Devices 19 Chapter 2 System Overview 24 VDC 0 4 amp switch 0 7 amp total 20 Thermo Scientific Matrix PlateMate 2x3 Environmental requirements Operational environment Temperature Relative Humidity Altitude Supply voltage fluctuations Installation category Pollution degree Power requirements Fuse Indoor use only 15 C 40 C for operation lt 85 at 30 C 2 5 Specifications Up to 2 000 meters or 1 5 miles AC 100 240 V 10 II 2 AC 100 240 V 10 50 60Hz 100VA Time lag type Voltage 250V 2A 2 5 2 Accuracy and Precision
143. ypes Plate Type Description 1536 Square well Matrie 45718 4571 7B Add Delete Detail for 1536 Square well Matrix 45118 45176 Vessel type Plate Height 774 17100 mm Well count 1536 shape Square Width 70 1 100 mm Well spacing 225 1100 mmf Allow incremental column movements Depths 1 7 00rrn wel La 450 Aspirate Lj faso TiptouchZoffset Cy eo Dispense LJ 250 Well quadrant centres 1 100 mm Applicable to tip magazine that has e 96 tips 384 tips 1536 tips Hote F uadrant aT positions 8 E ZRI F H E ie oe Quadrant axis Fields Description The required vessel type for which parameters are to be changed User Manual 33 Chapter 3 ControlMate Software 34 Vessel type The collective name for the vessel for example a Plate or Reservoir Height The physical height of the vessel This is measured from the bottom of the plate to the top of the plate The height is important as this is used for all movement commands when calculating the height at which the stage can be safely presented to the tips and also for tip touch positioning etc Well count The physical number of wells contained within the vessel The value can be one of either 96 384 or 1536 The field is used for determining positional parameters for quadrants etc Shape This represents the physical top shape of the well and can either be Squa
144. zes vapor pressure within the pipet tips to ensure accurate volume delivery Should be preceded by a move command 6 e amp Module Commands Change Tip Magazine Pauses sequence file execution for tip magazine change Provides step by step instructions to change tip magazine Reservoir Pump Specifies upper or lower reservoir pump left or right liquid level sensor speed direction duration and overfill timeout E I O Switch Controls on and off switch for one and two I O input output connections a Child Dialog Windows The Child Dialog Window opens whenever you click a ControlMate function or open a sequence file Status Bars The Status Bars provide information relating to the save status open file and auto correction 42 Thermo Scientific Matrix PlateMate 2x3 3 4 Creating Pipetting Programs 3 4 3 Creating Sequence Files Sequence File Editor The sequence file editor dialogue window is used to create or amend sequence file programs The dialogue contains a number of frames File Header The file header contains the field s specific to the whole sequence file Command Tree The command tree represents the program sequence Sequence files are executed from the top to the bottom of this tree structure The tree structure is used to add delete and select commands Command Settings The command settings frame is used to change specific command field values Status Bar The status bar provides

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