Synergy™ Personal Peptide Synthesizer
Contents
1. eee Soft keys Figure 7 Synergy LCD and keyboard The LCD on the front of Synergy displays messages on two lines of 40 char acters each Usually the top line displays information or directions The bot tom line assigns names to the soft keys located directly under the LCD A cursor represented by a blinking horizontal line __ on the LCD appears under text that you can modify Five soft keys under the LCD correspond to choices displayed on the bottom line of the LCD The HOLD and PAUSE soft keys are like toggle switches When you press the HOLD or PAUSE soft key once an asterisk appears next to the key to indicate the key is operating or on Press the key again and the asterisk goes away to indicate the key is off Sixteen labeled keys to the right of the LCD let you interact with the Synergy software controller by way of the LCD e Use the alphanumeric keys to enter numbers on the LCD In some menus these keys can represent lower case letters a b c etc or upper case letters A B C etc e Use the arrow keys lt to move the cursor on the LCD to the left or to the right e Use the Previous and Next keys to increase or decrease the value cur rently selected by the cursor e Use the Delete key to erase the entry that is currently selected by the cursor e Press the Menu key to see the preceding LCD display and to return to the Main Menu Synergy Installation2. Figure 3 RS 232 cable terminals Plug the mini DIN terminal of the cable into the printer port on Synergy Figure 5 on page 6 Note The mini DIN terminal may be either round or D shaped The printer port on Synergy is D shaped If the mini DIN terminal is round line up the arrow on the terminal with the flat side of the D shaped port See Figure 4 Figure 4 Mini DIN terminal connection to D shaped port July 2002 Synergy Installation Guide 5 Applied Biosystems 4 Load Printer Paper Follow the instructions in the printer manual for feeding the paper through the printer 5 Attach the Printer To conserve workspace you may mount the printer on top of Synergy An optional printer mounting rack shown in Figure 5 may be purchased from Applied Biosystems If you prefer to place the printer directly on the adjacent work surface place it on the left side of Synergy Reserve space on the right side of the instrument for two external bottles in polyethylene safety carriers Printer Printer stand optional Printer mounting rack optional accessory Sg Ly Printer port Figure 5 Printer installation on the Synergy Peptide Synthesizer 6 Press the power switch on the rear of the printer The red light labeled PWR on top of the printer appears when the printer is on Note The Computer port above the Printer port currently has no user related functions It may be used occasionally by
3. IMPORTANT Place only one test fixture on the wheel for this wheel test July 2002 Synergy Installation Guide 25 Applied Biosystems Figure 13 Placing a wheel test fixture in position 1 one on the wheel 3 Place the wheel on top of the hub on the right side of Synergy Slowly rotate the wheel until the protruding pin on the hub slips into the corresponding groove in the bottom of the wheel Press the START soft key The wheel should now rotate so that position 1 moves into the jaw assembly Next a series of tests check the motor and the sensors that activate the jaws If a mechanical failure is detected during the Wheel Test an error message appears on the screen You may read about error messages on page 7 20 of the Troubleshooting section of the User s Manual Test passed This display appears if the autosampler jaw assembly and wheel are working Press the OK soft key to continue the installation If the LCD displays the message Test Failed press the OK soft key and repeat the wheel test If the test continues to fail call Applied Biosys tems Technical Support 26 Synergy Installation Guide July 2002 Applied Biosystems Internal Gas Delivery Leak Test This test confirms that all connections in the internal gas delivery system are tight and free of leaks Gas leak test 1 Leave the wheel with the calibration test fixture wheel in position one on Synergy Press the START key S x
4. November 1993 Applied Biosystems WWW address Applied Biosystems 12 Documents on Demand 13 November 1993 Index 3 Headquarters 850 Lincoln Centre Drive Foster City CA 94404 USA Phone 1 650 638 5800 Toll Free 1 800 345 5224 Fax 1 650 638 5884 Worldwide Sales Offices Applied Biosystems vast distribution and service network composed of highly trained support and applications personnel reaches into 150 countries on six continents For international office locations please call our local office or refer to our web site at www appliedbiosystems com www appliedbiosystems com AS Applied D Biosystems Applera Corporation is committed to providing the world s leading technology and information for life scientists Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses Printed in the USA 07 2002 Part Number 902169 Rev D an Applera business
5. click Ask Us RIGHT NOW blue button with yellow text 4 Enter the required information in the next form if you have not already done so then click Ask Us RIGHT NOW You will receive an e mail reply to your question from one of our technical experts within 24 to 48 hours Synergy Installation Guide July 2002 Applied Biosystems To Obtain Documents on Demand Free 24 hour access to Applied Biosystems technical documents including MSDSs is available by fax or e mail or by download from our Web site To order documents Then by index number a Access the Applied Biosystems Technical Support Web site at http Awww appliedbiosystems com techsupp b Click the Index link for the document type you want then find the document you want and record the index number c Use the index number when requesting documents following the procedures below by phone for fax a From the U S or Canada call 1 800 487 6809 or delivery from outside the U S and Canada call 1 858 712 0317 b Follow the voice instructions to order the documents you want Note There is a limit of five documents per request through the a Access the Applied Biosystems Technical Support Web site at Internet for fax http www appliedbiosystems com techsupp or e mail abi b Under Resource Libraries click the type of document you want ene c Enter or select the requested information in the displayed form then click Se
6. Test fails the LCD displays one of the following messages ROM memory error Valve continuity failure XXXXXXXXXXXXXXXXKXXX The zeroes and ones that appear in place of the X s shown here are a code that indicates which valve connections have caused the test failure If the Circuit Test fails make a note of the number code and call Applied Biosystems Technical Support In the installation program if the electrical circuits are properly con nected the following display appears after circuit testing Synergy Instrument Install Press OK key to continue 14 Synergy Installation Guide July 2002 Applied Biosystems 2 Press the soft key under the word OK Is the printer printing Printer Test If the printer was connected correctly and turned on before you pressed the Synergy power button it should now be printing the words The printer is working 3 If the printer is printing press the Yes soft key As you go through this installation procedure the printer records each step of the installation in a report Do not discard this report if you call Applied Biosystems Technical Support they may need information contained in this report in order to assist you If the printer is not working perform the following operations e Check that the power supply and the RS 232 cable have been prop erly connected e Check that the printer paper is properly loaded If the white light on the printer blinks
7. When the cursor is in the top line the soft key under the words Change Format toggles between 12 hour and 24 hour time displays Use the bottom line to enter the Date When the cursor is in the bottom line the soft key under the words Change Format toggles between two different date displays m d y month day year and d m y day month year Time 00 00 am 12 hr CHANGE Date 00 00 00 m d y AM PM FORMAT 1 Enter the time on the top line Press the appropriate alphanumeric keys to enter the correct time Use the arrow keys lt to move the cursor to the left or the right in the Set Time entry line To enter a two digit number place the cursor in the right most digit position Press the Change Format soft key to choose either a 12 hour or 24 hour time display If you choose a 12 hour time display press the AM PM soft key to choose either of these time suffixes 2 Enter the date on the bottom line Press the appropriate alphanumeric keys to enter the correct date Use the arrow keys lt to move the cursor from the top line to the bottom line Press the Change Format soft key to choose a date display format 3 After the time and date have been entered press the Menu key to continue the installation The printer should now print an Installation Report heading with the date and time values you just entered July 2002 Synergy Installation Guide 17 Applied Biosystems External Gas Connections
8. attached to the Synergy Peptide Synthesizer Now each bottle is individually primed before reagent deliveries are tested and calibrated One at a time the reagent bot tles are primed in the following order THF DMF HBTU DIEA PIP piperidine The LCD tells you which bottle is being primed After each priming routine a pressure test checks for leaks in the system Prime the THF bottle 1 At the beginning of each bottle prime press the START soft key A one minute pressure check follows Caution During the prime you should observe reagent flowing into the external waste bottle If you detect leaks around the waste port fitting tighten the compression nut at the fitting Test Passed 2 Press the OK soft key 3 Repeat Steps 1 and 2 for each reagent bottle After the PIP bottle prime is finished installation continues with flow tests If the pressure test fails during a priming procedure check the bottle seal and cap for that bottle Synergy Installation Guide July 2002 Applied Biosystems July 2002 WARNING CHEMICAL HAZARD Reagent bottles are pressurized With the exception of piperidine always switch the Pressure Vent switch to Vent before unscrewing a reagent bottle on the Synergy Peptide Synthesizer If a leak is detected during the piperidine prime routine Check that the piperidine bottle and bottle seal is free of cracks and is seated prop erly on the cap Replace a faulty b
9. set the top of the paper form e Ifnecessary prime the ink cartridge again e Check that the printer power switch is ON After you press the Yes soft key the following display appears The next test will check that all of the keys are working 4 Press the OK soft key July 2002 Synergy Installation Guide 15 Applied Biosystems 16 Keyboard Self Test The Keyboard Self Test verifies that all keys are working Press all keys MENU to exit 1S2S3S4S5 lt gt 0123456789 PREV NEXT DEL Press each of the 5 soft keys under the LCD As you press each key the program emits a beep and the name of the key S1 S2 etc disappears from the LCD Press the left and right arrow keys lt and each of the alphanumeric keys 0 9 Press the keys labelled Previous Next and Delete When all the key names have disappeared press the Menu key If the keyboard is working properly the next display should read Test passed Press the OK soft key Use the next menu to enter the date and time Press the OK soft key to continue the installation Synergy Installation Guide July 2002 Applied Biosystems Time and Date Entries Now you can enter the current time and date At the end of each peptide synthesis the printer prints the time and date the synthesis began and ended For this particular menu use both lines on the LCD to enter num bers Use the top line of the LCD to enter the Time
10. the LCD displays the Run Monitor The Run Monitor displays the step and function that is currently running Run ended 13 58 Run began 10 54 Cycles run 3 OK 7 This display appears when the synthesis is completed Press the OK soft key Synergy Installation Guide 57 Applied Biosystems 58 Note After the synthesis the AACs still contain white inert material but very little amino acid remains AACs contain only enough amino acid for one synthesis cycle They cannot be re used WARNING SOLID HAZARDOUS WASTE Used AACs and PSCs have been exposed to DMF N N dimethyl formamide THF tet rahydrofuran and other hazardous chemicals Dispose of used columns in accordance with local state and federal regulations regarding solid hazardous waste Read the Synergy Waste Profile in the Synergy User s Manual Synergy Installation Guide July 2002 Applied Biosystems Examine the Synthesis Trace Does the trace look like the example in the manual no ves Figure 24 on page 60 shows a typical conductivity trace generated during a synthesis of LAGV Compare the trace your instrument has generated to Fig ure 24 The text on page 61 describes the Trace Features of a conductivity trace July 2002 Synergy Installation Guide 59 Applied Biosystems synthesis End of Q knne magn nuna Cycle three ar Cycle one Initial resin solvation Figure 24 Seven features of a samp
11. trained Applied Biosystems Service personnel 6 Synergy Installation Guide July 2002 Applied Biosystems Prepare the Synergy Peptide Synthesizer for Installation Three fittings labelled P Pressure D Delivery and Hazardous Waste on the right side of Synergy allow fluids to move in and out of two external bottles Figure 6 Before shipping a plug is placed in the waste fit ting and a polyethylene loop is attached to the Pressure and Delivery fittings 1 Verify that a plug is in the Waste port and that a loop connects the P and D fittings WARNING ELECTRICAL FIRE HAZARD mproper voltage supply can damage the instrument wiring system and cause a fire Before proceeding with these instructions verify that the instrument voltage specified on the back of the instrument matches the voltage supply in your laboratory 2 Plug one end of the AC power cord into the rear of Synergy Plug the other end into a grounded wall socket Place a flow test calibra tion tube here for the installation procedure EIS g Sa Transfer vessels Power button Figure 6 The Synergy Peptide Synthesizer before installation July 2002 Synergy Installation Guide 7 Applied Biosystems LCD ontrast adjustment Menu key The LCD and Keyboard Read this page for a brief description of the LCD liquid crystal display and keyboard on the front of Synergy
12. wrench to remove the plug from the Waste port Save the waste plug for future Synergy Shutdowns described in Chapter 2 of the Synergy User s Manual 7 Place the plastic compression nut on the shorter tube from the waste bottle cap assembly Slip the tube into the Waste port and screw the plastic compression nut over the Waste port fitting Figure 14 Using a wrench gently tighten an additional 1 4 turn Be sure to recheck this fitting when running reagents p 32 waste port fitting compression nut Figure 14 Attaching the waste tubing at the waste port 8 Attach the longer tube from the cap assembly to the external ventilation system described in the Pre Installation Manual and in the Laboratory Ventilation Requirements on page 1 8 of the Synergy Safety Supplement Check that the waste line runs up to the external ventilation without any downward dips where waste can accumulate If necessary cut off excess line to allow proper flow 30 Synergy Installation Guide July 2002 Applied Biosystems Figure 15 External waste bottle assembly on Synergy 9 Place the waste bottle in a safety carrier Figure 15 Screw the cap assembly on to the waste bottle 10 Press the OK soft key A one minute pressure test checks for possible blockage in the waste delivery system Test passed If no blockages in the waste delivery system are found this display appears Press the OK soft key to continue installa
13. 1 478 0411 27 11 478 0349 Middle Eastern Countries and North Africa Monza Italia 39 0 39 8389 481 39 0 39 8389 493 Eastern As ia China Oceania Australia Scoresby Victoria 61 3 9730 8600 61 3 9730 8799 China Beijing 86 10 64106608 86 10 64106617 Hong Kong 852 2756 6928 852 2756 6968 Korea Seoul 82 2 593 6470 6471 82 2 593 6472 Malaysia Petaling Jaya 60 3 758 8268 60 3 754 9043 Singapore 65 896 2168 65 896 2147 Taiwan Taipei Hsien 886 2 22358 2838 886 2 2358 2839 Thailand Bangkok 66 2 719 6405 66 2 319 9788 Europe Austria Wien 43 0 1 867 35 75 0 43 0 1 867 35 75 11 Belgium 32 0 2 712 5555 32 0 2 712 5516 Czech Republic and Slovakia Praha 420 2 61 222 164 420 2 61 222 168 Denmark Naerum 45 45 58 60 00 45 45 58 60 01 Finland Espoo 358 0 9 251 24 250 358 0 9 251 24 243 France Paris 33 0 1 69 59 85 85 33 0 1 69 59 85 00 Germany Weiterstadt 49 0 6150 101 0 49 0 6150 101 101 Hungary Budapest 36 0 1 270 8398 36 0 1 270 8288 Italy Milano 39 0 39 83891 39 0 39 838 9492 Synergy Installation Guide 11 Applied Biosystems 12 Telephone Fax Region Dial Dial Norway Oslo 47 23 12 06 05 47 23 12 05 75 Poland Lithuania Latvia and Estonia 48 22 866 40 10 48 22 866 40 20 Warszawa Portugal Lisboa 351 0 22 605 3
14. 12 Turn the screw a quar ter turn clockwise in one direction only to raise the pressure 0 2 psi Wait 30 seconds for the pressure reading to stabilize IMPORTANT Turn the internal gas adjustment screw in one direction only and then wait 30 seconds for the pressure to stabilize 44 Synergy Installation Guide July 2002 Applied Biosystems July 2002 If the pressure is too high a Note the current internal gas pressure reading that appears after the words pressure on the LCD b Set the Pressure Vent switch to Vent to vent the excess pressure c Turn the pressure adjustment screw counterclockwise a quarter turn to lower the pressure by 0 2 psi d Set the Pressure Vent switch to Pressure and wait 30 seconds 3 After you have adjusted the internal gas pressure press the more soft key to return to the Run Monitor that displays the PAUSE soft key 4 Press the PAUSE soft key to continue Flow Test 1 As Flow Test 1 continues repeat the complete procedure to verify that all deliveries are within range If all delivery weights are within range continue with Flow Test 2 It is best to have a final delivery of 550 mg 10 mg although it is not required If any delivery weights are not in range repeat the internal gas pressure adjustment procedure Flow Test 2 Calibrate Flow Test Calibration Tube During this test two deliveries of DMF go into the flow test calibration tube placed in the peptide synt
15. 3 14 351 0 22 605 33 15 Russia Moskva 7 095 935 8888 7 095 564 8787 South East Europe Zagreb Croatia 38513491927 385 1 34 91 840 Spain Tres Cantos 34 0 91 806 1210 34 0 91 806 1206 Sweden Stockholm 46 0 8 619 4400 46 0 8 619 4401 Switzerland Rotkreuz 41 0 41 799 7777 41 0 41 790 0676 The Netherlands Nieuwerkerk a d 31 0 180 331400 31 0 180 331409 IJssel United Kingdom Warrington 44 0 1925 825650 44 0 1925 282502 Cheshire All other countries not listed 44 0 1925 282481 44 0 1925 282509 Warrington UK Japan Japan Hacchobori Chuo Ku Tokyo 81 3 5566 6230 81 3 5566 6507 Latin America Del A Obregon Mexico 305 670 4350 305 670 4349 To Reach Technical Support Through the Internet We strongly encourage you to visit our Web site for answers to frequently asked questions and for more information about our products You can also order technical documents or an index of available documents and have them faxed or e mailed to you through our site The Applied Biosystems Web site address is http www appliedbiosystems com techsupp To submit technical questions from North America or Europe Step Action 1 Access the Applied Biosystems Technical Support Web site 2 Under the Troubleshooting heading click Support Request Forms then select the relevant support region for the product area of interest 3 Enter the requested information and your question in the displayed form then
16. 4 turn more Avoid over tightening this connection Caution The application of excessive force to tighten the compres sion fitting connection to the Synergy gas entry port can strip the fitting threads This connection is tested for leaks during the installation process 20 Synergy Installation Guide July 2002 Applied Biosystems 5 Press the OK soft key Switch the Pressure Vent to Vent Turn on the gas and set to 55 psi OK 6 Set the Pressure Vent switch to Vent Figure 10 Vent position Figure 10 The pressure vent switch on the right side panel of Synergy 7 Open the main supply valve on the gas tank and the regulator needle valve if one exists Turn on the external gas regulator Adjust the external regulator pressure to 55 psi Turn off the regulator and wait 5 minutes 8 Perform an external gas delivery leak test by turning the regulator knob 3 5 complete turns counterclockwise As you turn the knob the lower pressure gauge needle immediately drops 1 5 psi and then stabilizes July 2002 Synergy Installation Guide 21 Applied Biosystems Note the reading on the lower gauge when it stops dropping Wait five minutes Press the OK soft key Is the gas still at about 55 psi NO YEs 9 If the lower gauge reading has remained stable after 5 minutes there are no leaks in the external gas delivery system Press the YES soft key and cont
17. F delivery to the peptide synthesis column PSC and should be 550 30 mg Test passed 7 The LCD displays this message at the end of each successful flow test Press the OK soft key to continue to the next test Directions for Flow Test 2 begin on page 45 If any one of the DMF delivery weights in Flow Test 1 is out of range the LCD displays the message Value is out of range When this display appears press the OK soft key The flow test continues to ask for weights until all three deliveries have been weighed At the end of the test the LCD displays the message Test failed If Flow Test 1 fails repeat the test one more time from the beginning Dur ing the repeat check the printer for the value of the third DMF delivery Synergy Installation Guide July 2002 Applied Biosystems weight If the repeat of Flow Test 1 fails you must adjust the internal gas pres sure to calibrate the third DMF delivery see page 43 IMPORTANT Always re tare the left transfer vessel at the beginning of Flow Test 1 Adjusting the internal gas pressure to calibrate DMF delivery If the repeat of Flow Test 1 fails adjust the internal pressure to calibrate the third DMF delivery Compare the value of the third DMF delivery weight to the acceptable range 550 30 mg Optimize this delivery to 550 10 mg if possible If the third DMF delivery weight was less than 500 mg increase the internal gas pressure If the third DMF de
18. Guide July 2002 Applied Biosystems Technical Support Contacting Technical Support You can contact Applied Biosystems for technical support by telephone or fax by e mail or through the Internet You can order Applied Biosystems user documents MSDSs certificates of analysis and other related docu ments 24 hours a day In addition you can download documents in PDF for mat from the Applied Biosystems Web site please see the section To Obtain Documents on Demand following the telephone information below To Contact Technical Support by E Mail Contact technical support by e mail for help in the following product areas Product Area E mail address Genetic Analysis DNA Sequencing galab appliedbiosystems com Sequence Detection Systems and PCR pcrlab appliedbiosystems com Protein Sequencing corelab appliedbiosystems com Peptide and DNA Synthesis Biochromatography PerSeptive DNA tsupport appliedbiosystems com PNA and Peptide Synthesis systems CytoFluor FMAT Voyager and Mariner Mass Spectrometers LC MS apisupport sciex com Applied Biosystems MDS Sciex or api3 support sciex com Chemiluminescence Tropix tropix appliedbiosystems com Hours for Telephone Technical Support In the United States and Canada technical support is available at the follow ing times Product Hours Chemiluminescence 8 30 a m to 5 30 p m Eastern Time Framingham su
19. Note Refer to the Synergy Pre Installation Manual for a description of the recommended external gas regulator configuration The first set of instructions in this section review how to attach the Parflex tubing to the gas regulator on the nitrogen gas tank These instructions pre sume that the low pressure port of the gas regulator has female threads If you have already completed this connection skip this page and continue at the top of page 19 To attach tubing to the external gas tank regulator l First wrap a short piece of 1 4 in Teflon tape counter clockwise around the threads of the male pipe fitting MPF The tape should not extend beyond the outside lip of the pipe Figure 8 Regulator adjustment knob Upper pressure gauge Lower pressure gauge Main gas tank shut off valve Teflon tape Ferrule Compression nut Male pipe fitting e fitting Figure 8 Attaching Parflex tubing to the gas regulator 2 Screw the taped fitting clockwise into the low pressure port of the gas regulator 3 Slide a brass ferrule and a compression nut on to the end of the tubing Figure 8 Insert the tubing into the MPF push the ferrule into the 18 Synergy Installation Guide July 2002 Applied Biosystems MPF and tighten the compression nut finger tight Use a 9 16 in wrench to turn the fitting 1 4 turn more WARNING GAS TANK EXPLOSION HAZARD Pressurized gas cylinders are explosive Attach pressuriz
20. Synergy Personal Peptide Synthesizer Installation Guide BS 28 Be Plied ms Copyright 2002 Applied Biosystems All rights reserved For Research Use Only Not for use in diagnostic procedures Synergy is a trademark of Applera Corporation or its subsidiaries in the U S and certain other countries Teflon is a trademark of E I duPont de Nemours amp Co ThinkJet is a registered trademark of Hewlett Packard Inc Applied Biosystems 1 Synergy Installation Guide This Installation Guide describes the steps necessary to prepare the Applied Biosystems Synergy Personal Peptide Synthesizer for its first run When you have completed all the procedures in this section Synergy should be oper ating and have synthesized a 4 residue test peptide The entire installation procedure usually takes from four to six hours You may walk away from the instrument for a break at any step of the installation Note Before proceeding with the installation procedure review the Synergy Pre Installation Manual The Pre Installation Manual con tains the MSDSs and Synergy Waste Profile and describes the recommended ventilation system space requirements and gas tank regulator for Synergy Contents Preparation for Installation 3 Printer Assembly 5 Prepare the Synergy Peptide Synthesizer for Installation 7 The LCD and Keyboard 8 Technical Support 9 Contacting Technical Support 9 To Contact Technical Support by E Mail 9 Hours for Teleph
21. The calibration test fixture wheel should be in position 1 one on the amino acid column wheel during this test Run Flow Test Pump AAC Press the START soft key to begin the flow test A one minute pressure test precedes the first reagent delivery Is there liquid in the left vessel only NO YES Look at both transfer vessels You should see liquid in only the left transfer vessel If you see liquid in the left vessel press the Yes soft key If there is no liquid in the left transfer vessel or if there is liquid in the right transfer vessel press the No soft key Watch the liquid as it drains out of the left vessel At the end of the liquid drain a few drops may flow back into the vessel Is there liquid in the right vessel NO YES Look at both transfer vessels You should see liquid in the right transfer vessel and no more than a drop of liquid in the left transfer vessel If you see liquid in the right vessel press the Yes soft key Synergy Installation Guide July 2002 Applied Biosystems July 2002 If there is no liquid in the right transfer vessel press the No soft key Again watch the liquid as it drains out of the right vessel At the end of the liquid drain a few drops may flow back into the vessel Is there liquid in the left vessel NO YEs 4 Again check that there is liquid only in the left vessel and no more than a drop of liquid in the right vessel If you see liquid i
22. V is the first amino acid in the sequence and goes in the PSC position As synthesis progresses G A and L are attached to V in that order Figure 23 The printer generates a trace that represents the deprotection and coupling reactions of the synthesis Compare the trace data from your synthesis with the trace shown in this manual The next menu will run the cycle test 1 Press the OK soft key to begin the cycle test Load the PSC V AACs 1 G 2 A 3 L 2 Remove the calibration column from the luer fittings at the peptide synthesis column PSC position Do not unscrew the black plastic bushing attached to the top luer fitting Replace the calibration column with the peptide synthesis column labelled V valine See Figure 22 Caution Leaks in the peptide synthesis column position can damage the conductivity cell To assure a leak proof connection between the peptide synthesis column and the luer fittings push the luer fittings onto both column ends with a slight twisting motion Synergy Installation Guide 55 Applied Biosystems 3 Push the top luer fitting into the PSC Figure 22 Pull out the PSC column clamp 4 Pull the top of the column clamp out toward you lift it up until it clears the top luer fitting and then release it Caution Do not attempt to push the column clamp onto the luer fitting without pulling out the clamp top as this may damage the bottom luer fitting Do not use the co
23. ace A flow test calibra tion tube should be in this position to begin installation Figure 1 The Synergy Peptide Synthesizer before installation 2 Check that you have the following tools to complete installation e a flat head screwdriver e open wrenches 1 4 in 1 2in 5 8 in 9 16 in or an adjustable wrench e an indelible ink marking pen or wax marker You also must have access to a scale that is accurate to 1 mg 3 Remove all the additional parts that have been shipped with Synergy and place them near the synthesizer You will need the following parts to install the Synergy Peptide Synthesizer e one amino acid column wheel e two calibration test fixtures PSC and a wheel test fixture Figure 2 A package with two more should be in the shipping container Synergy Installation Guide 3 Applied Biosystems e aone gallon plastic waste bottle with cap tubing and ferrule e reagent bottle seals 2 each for 40 mL and 8 oz bottles e one RS 232 electrical cable e an AC alternating current power cord e aprinter with power supply e Parflex tubing 1 4 in O D e Teflon tape 1 4 in Reagents and Amino Acids A package with six bottles of chemical reagents for Synergy and amino acids for the installation procedure are shipped separately This package contains e DMF N N dimethylformamide 4L e THF tetrahydrofuran 200 mL e 0 4 M DIEA DMSO NMP N N Diisopropylethylamine Dimethyl sulfoxi
24. ally if you must repeat the test Run Flow Test DMF gt L R PSC PRINT 1 Verify that a flow test calibration tube is in place in the synthesis posi tion Figure 18 Press the START soft key Remove the left vessel and put on scale Zero scale then replace the vessel 2 When this display appears remove the left transfer vessel on the front of Synergy Figure 18 Tare the scale by placing the vessel on a scale that is accurate to 1 mg and setting the scale to zero 3 Replace the left transfer vessel on Synergy Press the OK soft key A calibration test fixture should be in the peptide synthesis column position for Flow Test 1 Figure 18 Remove the left transfer vessel Remove the left vessel and weigh Synergy Installation Guide 41 Applied Biosystems 42 Note This message appears 3 times during Flow Test 1 When it appears the left transfer vessel contains DMF 4 Carefully remove the left transfer vessel on the front of Synergy without spilling the contents Figure 18 Immediately weigh the left vessel and use the alphanumeric keys to enter the weight on the LCD Do not discard the DMF Press the OK soft key Replace the vessel 5 Replace the left transfer vessel on Synergy Press the OK soft key 6 Repeat steps 4 and 5 two more times The first two weights both measure DMF deliveries from the valve blocks they both should be 600 140 mg The third value results from DM
25. arch d In the displayed search results select a check box for the method of delivery for each document that matches your criteria then click Deliver Selected Documents Now or click the PDF icon for the document to download it immediately e Fillin the information form if you have not previously done so then click Deliver Selected Documents Now to submit your order Note There is a limit of five documents per request for fax delivery but no limit on the number of documents you can order for e mail delivery July 2002 Synergy Installation Guide 13 Applied Biosystems Synergy Installation Program The first time you turn on the power to the Synergy Peptide Synthesizer an installation software program automatically begins This installation pro gram displays instructions on the LCD As you follow these instructions you prepare the synthesizer for the first test peptide synthesis l Turn on the power on the Synergy Peptide Synthesizer by pressing the power button on the front of the instrument Figure 7 on page 8 As the software program begins to operate you should hear a series of beeps and see a message on the LOD Ifyou hear a beep but cannot see a message move the contrast adjustment knob Figure 7 on page 8 at the left of the LCD until the letters become visible Initializing Synergy Please wait Circuit testing These messages always appear when you turn on Synergy If the Circuit
26. conductivity value is within range the LCD displays the conductivity Press the OK key to continue the installation after each display Test Passed 3 When this display appears press the OK soft key to complete the flow test Value is out of range This message appears when a conductivity value is not within specifica tions Press the OK key to see the value Press the OK key again to con tinue Flow Test 7 If the message Test failed appears repeat Flow Test 7 If Flow Test 7 con tinues to fail call Applied Biosystems Technical Support Flow Test 8 Calibrate HBTU WARNING CHEMICAL HAZARD HBTU can cause allergic reactions and skin irritations in sensitive persons Wear protective clothing and handle HBTU solution in a properly vented fume hood See the MSDS in the Synergy User s Manual This flow test measures delivery of HBTU Peptide Synthesis Reagent A to the left transfer vessel To perform this flow test you again tare the left trans fer vessel and weigh the contents of the left vessel after each of two reagent deliveries Then you re tare the left vessel and weigh one more delivery Synergy Installation Guide July 2002 Applied Biosystems July 2002 IMPORTANT Always tare the left vessel when prompted Run Flow Test CALIBRATE HBTU 1 Press the START soft key Remove left vessel and put on scale Zero scale then replace vessel 2 Remove the left transfer vessel on the front of Syn
27. de N Methylpyrrolidone 40 mL e HBTU 2 1 H Benzotriazol 1 yl 1 1 3 3 tetramethyluronium hexafluorophosphate 8 mmol e 0 2 M HOBt DMSO NMP 1 Hydroxybenzotriazole Dimethy sul foxide N Methylpyrrolidone 40 mL e Piperidine 200 mL e six amino acid columns AAC Figure 2 e two peptide synthesis columns PSC Figure 2 Wheel test fixture Pre loaded resin Flow test calibration tube Figure 2 Calibration Test Fixtures Amino Acid and Peptide Synthesis columns Synergy peptide synthesis columns PSCs each contain 25 pmol of either pre loaded resin or amide resin Synergy amino acid columns AACs each contain 75 pmol amino acid enough for a one time use only Calibration test fixtures contain two tubes and one wheel These are reusable and should be kept Synergy Installation Guide July 2002 Applied Biosystems Printer Assembly 1 Remove the printer from its packaging Follow the instructions in the printer manual for attaching the power supply cord and the printhead cartridge The power supply cord should plug into a grounded wall socket 2 Mode Select Switches The Mode Select Switches on the rear of the printer have been pre set by Applied Biosystems 3 Connect the RS 232 electrical cable Figure 3 Plug the DB 25 terminal into the RS 232 port on the printer By hand tighten the two screws on the DB 25 terminal Tighten these two screw DB 25 terminal q___ 4 mini DIN terminal
28. e between the two marks or right on the mark on the tube Run Flow Test DMF gt PSC 1 Press the START soft key to begin each flow test After two minutes reagent is delivered to the flow test calibration tube in the peptide syn thesis column PSC position Is the liquid between the marks NO YES 2 Ifthe level of reagent in the flow test calibration tube is between the two calibration marks or right on the mark press the YES soft key If the level of reagent in any flow test falls outside these two marks press the NO soft key After 2 more minutes the LCD reports if the test was successful Test passed 3 Press the OK soft key to continue to the next flow test Test failed July 2002 Synergy Installation Guide 47 Applied Biosystems 48 If a flow test fails check that the ends of the reagent lines in all the bot tles are submerged in fluid Press the OK soft key and repeat the flow test If one of these flow tests fails repeatedly call Applied Biosystems Technical Support Flow Test 6 Pump AAC This test first checks the flow of reagent from the left transfer vessel through the amino acid column AAC on the wheel to the right transfer vessel Then it checks the flow from the right transfer vessel back to the left transfer vessel The pump in the name of this flow test refers to the configuration of transfer vessels that assures continuous reagent delivery during synthesis
29. e OK soft key 34 Synergy Installation Guide July 2002 Applied Biosystems July 2002 Bottle Change Procedure Bottle Change procedure 1 Press the START soft key Switch the Pressure Vent to Vent 2 Verify that the Pressure Vent switch is set to Vent Press the OK soft key After 30 seconds the next display appears Replace empty reagent bottles with full reagent bottles 3 Remove the 4 empty reagent bottles and the bottle seal for each bottle on the front of the Synergy Peptide Synthesizer You may have to use tweezers to dislodge the bottle seal from inside the ratchet cap Discard the bottle seals 0 2 M HBTU Reagent Preparation You must combine the contents of two reagent bottles to prepare the HBTU 2 1 H benzotriazol 1 yl 1 1 3 3 tetramethyluronium hexafluorophos phate reagent Instructions for preparing the HBTU reagent follow WARNING CHEMICAL HAZARD HBTU can cause allergic reactions and skin irritations in sensitive persons Wear protective clothing and prepare the HBTU solution in a properly vented fume hood See the MSDS in the Synergy User s Manual a Pour the contents 40 mL of the bottle labelled HOBt DMSO NMP 0 2 M 1 hydroxybenzotriazole Dimethyl sulfoxide N Meth ylpyrrolidone into the bottle labelled Peptide Synthesis Reagent A HBTU 8 mmoles b Tightly cap the bottle and invert it several times to dissolve the HBTU Synergy Installation Guide 35 A
30. e second DIEA weight should be greater than the first Remove the left vessel and put on scale Zero scale then replace the vessel 7 Again remove the left pump vessel place it on a scale that is accurate to 1 mg and set the scale to zero 8 When prompted repeat steps 4 and 5 a third time The third weight should be between 380 and 460 mg Synergy records the time it took to deliver this third amount of DIEA and uses it as the default time for DIEA delivery during synthesis Test Passed 9 When this display appears the flow test has been successfully completed Press the OK soft key to continue to the Cycle Test If the LCD displays the message Test failed press the OK soft key and repeat the flow test If this flow test repeatedly fails call Applied Biosys tems Technical Support 54 Synergy Installation Guide July 2002 Applied Biosystems July 2002 Cycle Test During the last stage of the Installation Procedure you load a peptide syn thesis column and 3 amino acid columns on the Synergy Peptide Synthe sizer The instrument then performs a pre determined set of modules and synthesizes LAGV a 4 mer test peptide IMPORTANT Peptide sequences are written with the N terminal amino acid on the left and the C terminal amino acid on the right On Synergy however peptides are synthesized from the C terminal end towards the N terminal This means that with LAGV for example the C terminal amino acid
31. ed gas cylinders to a wall or bench by means of approved brackets or chains Always cap the gas cylinder when not in use If you have followed the instructions in the Pre Installation Manual you have already connected Parflex tubing to the gas regulator on the nitrogen gas tank Start with the following procedure To connect gas tubing to the Synergy Peptide Synthesizer Make sure all bottles are on tight and connect the gas to the 432A 1 Synergy is shipped with four empty reagent bottles and two transfer ves sels attached Check that these bottles and the two transfer vessels Fig ure 6 on page 7 are tightly screwed in place Caution Do not overtighten the bottles If you turn the bottle past the first point of resistance you may crack the bottle seal or dam age the ratchet cap assembly 2 Remove the compression nut and ferrule at the gas entry port They are covered by a protective plastic cap Slide them on to the end of the tubing opposite the gas tank regulator Figure 9 July 2002 Synergy Installation Guide 19 Applied Biosystems To regulator Compression nut Figure 9 Attaching the Parflex tubing to the Synergy gas entry port 3 Insert the tubing into the gas entry port on the back of Synergy labeled NITROGEN INPUT 4 Slide the ferrule and compression nut onto the protruding gas entry port Turn the fitting clockwise to tighten finger tight then use a 9 16 in wrench to turn the fitting 1
32. ergy Figure 18 Place the vessel on a scale that is accurate to 1 mg and set the scale to zero Figure 21 Remove the left transfer vessel 3 Replace the transfer vessel and press the OK soft key Remove the left vessel and weigh 4 When this display appears the left transfer vessel contains HBTU Without spilling the contents carefully remove the left vessel and weigh Synergy Installation Guide 51 Applied Biosystems 52 the HBTU delivered Use the alphanumeric keys to enter this value on the LCD Press the OK soft key Replace the vessel Replace the vessel on Synergy Press the OK soft key When prompted repeat Steps 4 and 5 The second HBTU weight should be greater than the first Remove left vessel and put on scale Zero scale then replace vessel OK Again remove the left transfer vessel Figure 18 place it on a scale that is accurate to 1 mg and set the scale to zero When prompted repeat Steps 4 and 5 a third time The third weight should be between 340 and 420 mg Synergy records the time it took to deliver this third amount of HBTU and uses it as the default time for HBTU delivery during synthesis Test Passed When this display appears the flow test has been successfully completed Press the OK soft key to continue to the next flow test If you see the message Test failed press the OK soft key and repeat the flow test If this flow test repeatedly fails call Applied Biosy
33. h means Synergy has automatically suspended operation The information in the top line identifies the Step and Function where the pressure failure occurred When a pressure failure occurs this line usually displays Function 89 PRS TEST You cannot continue the installation until the leak is eliminated You may call Applied Biosystems Technical Support for assistance Synergy Installation Guide July 2002 Applied Biosystems Index Numerics 1 hydroxybenzotriazole see HOBt 2 1 H benzotriazol 1 yl 1 1 3 3 tet ramethyluronium phosphate see HBTU A AAC 4 48 56 alphanumeric key 8 AM PM soft key 17 amino acid column wheel 3 test 25 26 amino acid column see AAC arrow key 8 autosampler jaw 25 B bottle change procedure 37 prime procedure 38 bottle seal 4 35 button power 14 C calibrate column calibration DIEA delivery 53 HBTU delivery 50 calibration column 46 Change Format soft key 17 circuit testing 14 conductivity FlowTest7 49 55 57 45 conductivity cell conductivity trace cursor 8 customer support See technical sup port 9 Cycle Test 55 to 60 November 1993 Index D date display 17 DB 25 see terminal Deletekey 8 delivery fitting 7 DIEA 36 bottle prime 38 Flow Test9 53 dimethyl sulfoxide see DMSO DMF 38 bottle prime 38 Flow Test1 40 Flow Test 3 47 reagent bottle DMSO 35 Documents on Demand 13 E electrical cable RS 232 4 5 e mail addressfortechn
34. hesis column position You need an indelible ink marker to mark the level of DMF in the column after each flow Run Flow Test CALIBRATE TUBE 1 Press the START soft key In the two minutes that follow Synergy per forms a brief pressure test and a DMF delivery Mark the calibration tube 2 Make a thin horizontal mark on the flow test calibration tube to indicate the level of the DMF in the column Figure 20 The mark should be level with the bottom of the meniscus Press the OK soft key Synergy Installation Guide 45 Applied Biosystems Figure 20 Marking the flow test calibration tube Mark the calibration tube 3 After a second DMF delivery the LCD directs you to make a second mark on the flow test calibration tube The second mark should be higher than the first mark and level with the bottom of the meniscus Press the OK soft key IMPORTANT Do not remove this marked flow test calibration tube you will use it again in the flow tests that follow Test passed 4 When this display appears press the OK soft key to complete the flow test 46 Synergy Installation Guide July 2002 Applied Biosystems Flow Tests 3 4 and 5 e DMF gt PSC e THF PSC PIP PSC The next three flow tests deliver reagent to the flow test calibration tube that you marked in Flow Test 2 During each flow test you observe the level of reagent delivered to the calibration tube This level should fall somewher
35. icalsupport 33 34 9 external gas connections 18 to 22 F ferrule brass 18 fitting D delivery 7 male pipe 18 P pressure 7 waste 7 Flow Test1 40 Flow Test 2 45 Flow Test3 47 Flow Test4 47 Flow Test5 47 Flow Test6 48 Flow Test7 49 Flow Test8 50 Flow Test9 53 flow tests 40 to 54 G gas entry port 20 external leak test gas regulator 18 gas tank 18 21 gas tank regulator 1 H HBTU bottle prime 38 Flow Test 8 50 preparation 35 help See technical support 9 HOBt 35 I initialization software 14 internal gas leak test 27 internal gas pressure adjustment 24 to 25 Internet address Documents on Demand 13 jaw autosampler K key 25 alphanumeric 8 arrow 8 Delete 8 Menu 8 Next 8 Previous 8 soft 8 Applied Biosystems L LCD 8 40 leak test external gas delivery 21 internal gas 27 liquid crystal display see LCD luer fittings 55 M male pipe fitting 18 Menu Run Monitor 27 28 57 Time amp Date 17 Menu key 8 mini DIN see terminal mode select switches 5 MPF see male pipe fitting N N N dimethyl formamide see DMF N N diisopropylethylamine see DIEA Nextkey 8 nitrogen input 20 N methylpyrrolidone see NMP NMP 35 P peptide synthesis column see PSC PIP see piperidine piperidine 37 bottle prime 38 Flow Test5 47 reagent bottle plug waste 7 port gas entry RS232 5 30 37 20 waste printer port 5 power but
36. inue with step 10 If the regulator needle moves down more than 1 psi in 5 minutes there is a leak in the external gas delivery line Press the NO soft key Check connections for leaks a Filla large syringe with soapy water and squirt the solution around the connections between the regulator Synergy and the gas deliv ery line to locate leaks b Tighten any leaky connections c Press the OK soft key and repeat the external gas delivery leak test that starts at step 8 of this procedure If you cannot eliminate the leak call Applied Biosystems Technical Sup port Do not continue with the installation procedure Set the gas to 65 psi 10 When the external gas delivery lines are free of leaks and the nitrogen tank regulator pressure set the external gas pressure to 60 75 psi Press the OK soft key to continue the installation procedure 22 Synergy Installation Guide July 2002 Applied Biosystems Adjust Internal Pressure Reagent delivery and flow throughout a synthesis depends on adequate internal gas pressure During this stage of the installation you adjust the internal gas pressure to 5 0 psi This internal pressure is fairly stable and should require little adjustment during normal operation Switch the Pressure Vent to Pressure 1 Set the Pressure Vent switch to Pressure Waste plug Switch to pressure A flow test cali bration tube in place Figu
37. ion 1 800 762 4001 then press 1 for PCR 2 for the 7700 or 5700 6 for the 6700 or dial 1 800 831 6844 then press 5 1 240 453 4613 Voyager MALDI TOF Biospectrometry and Mariner ESI TOF Mass Spectrometry Workstations 1 800 899 5858 then press 13 1 508 383 7855 Biochromatography BioCAD Workstations and Poros Perfusion Chromatography Products 1 800 899 5858 then press 14 1 508 383 7855 Expedite Nucleic acid Synthesis Systems 1 800 899 5858 then press 15 1 508 383 7855 Synergy Installation Guide July 2002 Applied Biosystems July 2002 Product or Product Area Telephone Dial Fax Dial Peptide Synthesis Pioneer and 9050 Plus Peptide Synthesizers 1 800 899 5858 then press 15 1 508 383 7855 PNA Custom and Synthesis 1 800 899 5858 then press 15 1 508 383 7855 FMAT 8100 HTS System and Cytofluor 4000 Fluorescence Plate Reader 1 800 899 5858 then press 16 1 508 383 7855 Chemiluminescence Tropix only or 1 781 271 0045 1 800 542 2369 U S 1 781 275 8581 Applied Biosystems MDS Sciex 1 800 952 4716 1 650 638 6223 Outside North America Region Telephone Dial Fax Dial Africa and the Middle East Africa English Speaking and West Asia Fairlands South Africa 27 11 478 0411 27 11 478 0349 South Africa Johannesburg 27 1
38. le conductivity trace of the synthesis of LAGV on Synergy scaled to fit page 60 Synergy Installation Guide July 2002 Applied Biosystems Conductivity Trace Features Note that there are actually two overlapping conductivity traces that reflect two conductivity ranges Trace Features 1 4 and Trace Feature 7 are in the low conductivity range Trace Features 5 and 6 are in the high conductivity range Typically at the beginning of every trace you should observe a series of upward spikes as the resin in the PSC solvates before the DMF baseline is established Following resin solvation the trace for the test peptide LAGV should have three deprotection peaks Trace Feature 1 each followed by a coupling plateau Trace Features 5 and 6 At the end of the synthesis the trace should show one more deprotection followed by a drop below the DMF baseline as THF washes through the instrument Seven Trace Features on the trace your instrument has generated should closely match the trace in Figure 24 on page 60 Each complete cycle should contain all seven features 1 Beginning deprotection a single sharp peak 2 Deprotection complete a level horizontal line slightly higher than the DMF baseline Piperidine washout a return to DMF baseline 3 4 Amino acid activation a level baseline consistent with point 3 5 Coupling begins a rapid rise followed by a steady high plateau 6 Pump AAC wash a level consistent with the plateau at
39. livery weight was greater than 600 mg decrease the inter nal pressure You can monitor the internal gas pressure when a flow test or synthesis is running by selecting the appropriate Run Monitor Menu on the LCD The acceptable internal gas pressure range is 3 5 5 5 psi Run Flow Test DMF gt L R PSC PRINT Current Step number S 02 48 00 F 84 PRS PSCT 09 10 HOLD PAUSE NEXTS jump S_ more Press pause to interrupt Flow Test 1 Press the START soft key to begin Flow Test 1 Immediately press the PAUSE soft key to temporarily interrupt the flow test When you press the PAUSE soft key the current step number should be either 02 or 03 An asterisk appears PAUSE to indicate the flow test has been temporarily interrupted July 2002 Synergy Installation Guide 43 Applied Biosystems S 02 48 00 F 84 PRS PSCT 09 10 HOLD PAUSE NEXTS jumpS_ more Press more two times Current 345 10 ave 1234 change 7 pressure 5 3 psi more Read pressure here 2 Press the more soft key twice until the Run Monitor displays the current pressure reading on the bottom line of the LCD Insert a screwdriver blade here to adjust the internal gas pressure Figure 19 Adjusting the internal gas pressure If the pressure is too low use a flat edged screwdriver to adjust the internal pressure Insert the screwdriver blade into the small hole located behind the reagent bottles Figure
40. lumn clamp with the flow test calibration tube 5 Remove the amino acid column wheel from Synergy and remove the calibration column from position one Place the amino acid column ACC labelled G in position 1 place the AAC labelled A in position 2 and place the AAC labelled L in position 3 Figure 23 IMPORTANT AACs and PSCs cannot be used interchangeably PSC labels are white AAC labels are light blue 56 Synergy Installation Guide July 2002 Applied Biosystems Run Monitor July 2002 Figure 23 Load the amino acid columns for the test peptide LAGV 6 Replace the amino acid column wheel on Synergy Press the START key to begin the cycle test As synthesis progresses check around the PSC luer fittings and the plastic compression nut at the waste port fitting for leaks Occasionally a drop of liquid may begin to form around the middle of the PSC not at the luer fit tings Wick this moisture away with a tissue and check frequently during syn thesis for any further moisture It takes approximately 3 hours to complete this cycle test During this phase of the installation pre programmed modules automatically direct the flow of reagents monitor pressure and generate a conductivity trace of the syn thesis You may walk away and leave the instrument unattended during this synthesis S xx yy z2 F F FUNCT NAME T XXX ZZZ HOLD PAUSE NEXTS jumpS more Throughout the cycle test
41. n position 2 Figure 17 5 When all the reagent bottles are in place press the OK soft key Switch Pressure Vent to Pressure 6 Switch the Pressure Vent switch to Pressure and press the OK soft key A three minute pressure test follows Test Passed 7 When this display appears all the bottle connections are tight and you can start the bottle priming procedures Press the OK soft key If this test fails one or more of the reagent bottles have not been prop erly attached to Synergy WARNING CHEMICAL HAZARD Reagent bottles are pressurized With the exception of piperidine always switch the Pressure Vent switch to Vent before unscrewing a reagent bottle on the Synergy Peptide Synthesizer Piperidine is the only reagent that is on its own pressure system sepa rate from the other bottles You may open the piperidine bottle without depressurizing the pressure system for the other reagents When you open the piperidine bottle you hear a small hiss as pressure is released If a pressure leak is detected during the bottle change procedure switch the Pressure Vent switch to Vent and check the bottle seal and cap on each reagent bottle including the DMF bottle If the pressure test continues to fail call Applied Biosystems Technical Support July 2002 Synergy Installation Guide 37 Applied Biosystems 38 Reagent Bottle Priming Procedure At this stage of the installation all the reagent bottles are
42. n the left vessel press the Yes soft key If there is no liquid in the left transfer vessel press the No soft key Test Passed 5 When this display appears press the OK soft key to continue to the next flow test If you have pressed the No soft key at any time during this flow test the LCD displays the message Test failed Press the OK soft key and repeat the flow test If this flow test continues to fail you may refer to page 4 26 in the Synergy User s Manual or call Applied Biosystems Technical Support Flow Test 7 Pump Cell The pump in the name of this flow test refers to the configuration of trans fer vessels that assures continuous liquid circulation during synthesis During this flow test two conductivity readings are taken The first one mea sures conductivity of DMF delivered to the calibration text fixture PSC in the peptide synthesis column position Next a small amount of HBTU is deliv ered into the DMF solution and a second reading is taken The first reading falls within the range of low conductivity readings the second reading falls within the range of high readings Run Flow Test Pump Cell Synergy Installation Guide 49 Applied Biosystems 50 1 Press the START key A two minute pressure test precedes the first con ductivity reading Conductivity 444 2 Two conductivity measurements are taken during this test with a two minute time lapse between each reading When the
43. one Technical Support 9 To Contact Technical Support by Telephone or Fax 10 To Reach Technical Support Through the Internet 12 To Obtain Documents on Demand 13 Synergy Installation Program 14 Keyboard Self Test 16 Time and Date Entries 17 External Gas Connections 18 Adjust Internal Pressure 23 Amino Acid Column Wheel Test 25 Internal Gas Delivery Leak Test 27 Vent Test and Waste Bottle Installation 28 Connect External DMF Reagent Bottle 33 Bottle Change Procedure 35 Reagent Bottle Priming Procedure 38 July 2002 Synergy Installation Guide 1 Applied Biosystems Flow Tests 40 Flow Test 1 DMF Delivery to Vessels and Peptide Synthesis Column 39 Flow Test 2 Calibrate Flow Test Calibration Tube 45 Flow Tests 3 4 and 5 47 Flow Test 6 Pump AAC 48 Flow Test 7 Pump Cell 49 Flow Test 8 Calibrate HBTU 50 Flow Test 9 Delivery and Calibration of DIEA 53 Cycle Test 55 Examine the Synthesis Trace 59 Conductivity Trace Features 61 Pressure Test Failures 62 Index 55 2 Synergy Installation Guide July 2002 Applied Biosystems July 2002 Preparation for Installation WARNING PHYSICAL INJURY HAZARD Use of improper lifting tech niques can cause painful and sometimes permanent back injury Use proper and safe lifting techniques to move the instrument 1 The Synergy Peptide Synthesizer weighs about 35 lb 16 kg moving the instrument may require two people Remove Synergy from the ship ping container and place it on its work surf
44. ottle seal and check that the bottle cap is tight If a leak is detected during any other reagent prime routine Switch the Pressure Vent switch to Vent and check the bottle s seal and cap If you cannot locate the source of the leak call Applied Biosystems Technical Support Synergy Installation Guide 39 Applied Biosystems 40 Flow Tests At this stage of the installation procedure you perform nine flow tests to test and calibrate chemical flow through the instrument For each test you must perform specific tasks which are described on the LCD The top line of LCD text tells which chemical flow is being tested The bottom line of LCD text shows soft key responses To perform these flow tests you must have access to a scale that is accurate to 1 mg All flow tests must be successfully performed to complete the installation procedure When a flow test fails Synergy automatically repeats the test If any of these flow tests repeatedly fail call Applied Biosystems Technical Support for assistance WARNING POTENTIAL CHEMCIAL HAZARD Regard all chemicals on the synthesizer including liquid in the lines as potentially hazardous Wear protective eye wear gloves and a laboratory coat when working with the chemicals used on the instru ment If a spill occurs clean it up in accordance with instruc tions in the MSDSs or Waste Profile found in the Pre Installation Manual and in the Synergy User s Manual Flow Test 1 DMF Deli
45. point 5 7 Coupling solution washout a drop that returns to DMF baseline If the conductivity trace matches the trace shown in Figure 24 press the Yes soft key to complete the Installation Procedure When you have completed this Installation Procedure the printer prints the words Install finished followed by the time and date Fill out the Warranty card and mail it to Applied Biosystems Save your installation trace in the front pocket of the Synergy User s Manual as a record of your successful installation If your conductivity trace does not have all seven features for each cycle call Applied Biosystems Technical Support Retain your trace and the installa tion printout for reference should you have a problem in the future July 2002 Synergy Installation Guide 61 Applied Biosystems 62 Pressure Test Failures The Synergy Peptide Synthesizer cannot operate properly with a leak in the pressure system The pressure system is tested several times during the instal lation procedure and before every cycle in a synthesis When a pressure leak is detected the following sequence of events occurs Pressure test failed initial 5 3 final 2 1 diff 3 2 1 When a leak is first detected the LCD displays a message similar to the one shown here Press the OK soft key S xx yy zz F F FUNCTNAME T xxx zzz HOLD PAUSE NEXTS jump S more 2 This next display features an asterisk after the word PAUSE whic
46. pplied Biosystems Ge u a au Write the date the HBTU reagent was prepared on the bottle label The prepared reagent can be used for up to six weeks d Locate the delivery line for the HBTU Press a reagent line filter onto the end of the delivery line Note One reagent line filter can be used for five consecutive bottles or approximately 200 mL of HBTU reagent 4 Place reagent bottles in position in the following manner a Open the reagent bottle and place a bottle seal on the rim With the reagent delivery line inside hold the bottle straight up and turn it carefully into the threads of the ratchet cap on Synergy Figure 17 The bottle should fit firmly in place Caution Do not overtighten the reagent bottles If you turn the bottle past the first point of resistance you may crack the bottle seal or damage the ratchet cap assembly ies Bottle seal Tetrahydrofuran Reagent line filter on Stabilized HBTU delivery line i h Figure 17 Reagent bottle positions on the front of the Synergy Peptide Synthesizer When all the reagent bottles are in place from left to right facing the front of the synthesizer the labeled reagent bottles should be HBTU in position A DIEA DMSO NMP 0 4M N N diisopropylethylamine 36 Synergy Installation Guide July 2002 Applied Biosystems dimethyl sulfoxide N methylpyrrolidone in position B Piperidine in position 1 and THF Tetrahydrofuran i
47. pport 8 00 a m to 6 00 p m Eastern Time All Other Products 5 30 a m to 5 00 p m Pacific Time July 2002 Synergy Installation Guide 9 Applied Biosystems 10 To Contact Technical Support by Telephone or Fax In North America To contact Applied Biosystems Technical Support use the telephone or fax numbers given below To open a service call for other support needs or in case of an emergency dial 1 800 831 6844 and press 1 Product or Product Area Telephone Dial Fax Dial ABI Prism 3700 DNA Analyzer 1 800 831 6844 then press 8 1 650 638 5981 DNA Synthesis 1 800 831 6844 then press 21 1 650 638 5981 Fluorescent DNA Sequencing 1 800 831 6844 then press 22 1 650 638 5981 Fluorescent Fragment Analysis includes GeneScan applications 1 800 831 6844 then press 23 1 650 638 5981 Integrated Thermal Cyclers ABI PRISM 877 and Catalyst 800 instruments 1 800 831 6844 then press 24 1 650 638 5981 ABI Prism 3100 Genetic Analyzer 1 800 831 6844 then press 26 1 650 638 5981 BioInformatics includes BioLIMS BioMerge and SQL GT applications 1 800 831 6844 then press 25 1 505 982 7690 Peptide Synthesis 433 and 43X Systems 1 800 831 6844 then press 31 1 650 638 5981 Protein Sequencing Procise Protein Sequencing Systems 1 800 831 6844 then press 32 1 650 638 5981 PCR and Sequence Detect
48. re 11 The Pressure Vent Switch on the right side panel of Synergy 2 Press the OK soft key 3 Check that a flow test calibration tube is in place on the front of Synergy Figure 11 Press the OK soft key July 2002 Synergy Installation Guide 23 Applied Biosystems ON NEXT MENU SEE USER S MANUAL IF PRESSURE NOT BETWEEN 3 5 5 5 psi OK 4 Read the internal pressure reading that appears after the words Current pressure The internal pressure should be 3 5 5 5 psi Insert a screwdriver blade here to adjust the internal gas pressure Figure 12 Adjusting the internal gas pressure If the pressure is below 3 8 psi use a flat edged screwdriver to adjust the internal pressure to 5 0 0 5 psi Insert the screwdriver blade into the small hole located behind the reagent bottles Figure 12 A quar ter turn clockwise raises the pressure reading by about 0 2 psi Turn the screw clockwise in one direction only and wait 30 seconds for the pres sure reading to stabilize IMPORTANT Turn the internal gas adjustment screw in one direction only and then wait 30 seconds for the pressure to stabilize If the pressure is above 5 4 psi a Note the current internal gas pressure reading that appears after the words Current pressure on the LCD The internal gas pressure should initially be set at 5 0 0 5 psi Ifa quarter turn counterclock wise lowers the pressure reading by about 0 2 psi estimate how far you will need
49. ry line first 1 Switch the Pressure Vent switch to Vent 2 Usea l 4 in wrench to remove the loop in the side port labeled D Save this loop for use in the Synergy Shutdown Procedure described in Chapter 2 of the Synergy User s Manual 3 Locate the cap assembly for the DMF N N dimethyl formamide bottle Two lines of tubing run out of the cap assembly for the DMF bottle July 2002 Synergy Installation Guide 33 Applied Biosystems Attach Delivery line first Figure 16 Switch to Vent and attach the DMF bottle 4 First attach the tubing line labeled D to the D port Turn the fitting until it is finger tight then use a 1 4 in wrench to turn the fitting an additional quarter turn 5 Next remove the loop in the port labeled P Attach the tubing line labeled P to the P port Turn the fitting until it is finger tight then use a 1 4in wrench to turn the fitting an additional quarter turn WARNING CHEMICAL HAZARD DMF is flammable and an irritant to skin and eyes Avoid all skin contact with and inhalation of DMF The MSDS can be found in the Synergy User s Manual 6 Feed the cap through the top piece of the safety carrier The top piece can be fitted onto the bottom piece after the cap is in place 7 Place the DMF bottle in a safety carrier in front of the waste bottle Figure 16 Screw the cap assembly tightly on the DMF reagent bottle and press th
50. s Switch the Pressure Vent to Pressure 5 Switch the Pressure Vent switch to Pressure and press the OK soft key The pressure test continues for two more minutes When the pressure test is completed the display gives more instructions If the LCD has not displayed Pressure test failed go on to step 6 If the LCD displays the message Pressure test failed before step 6 of this procedure there is a leak that you must locate before installing the 28 Synergy Installation Guide July 2002 Applied Biosystems waste bottle Instead of performing steps 6 10 of this written proce dure follow these troubleshooting steps a Press the OK soft key after the Pressure test failed message ap pears b Verify that the waste port is tightly plugged The waste line should not be attached S xx yy zz F F FUNCT NAME T XXX ZZZ HOLD PAUSE NEXTS jump S more c Press the more soft key S 14 20 C 00 01 M A LOCK set int end run more d Press the end run soft key Are you sure you want to end the run cancel END RUN e Press the END RUN soft key Test failed f Press the OK soft key The Vent Test LCD shown at the top of page 28 returns Restart the Vent test If the pressure test fails again call Applied Biosystems Technical Support Remove the waste plug and attach waste container July 2002 Synergy Installation Guide 29 Applied Biosystems 6 Usea5 8 in
51. stems Tech nical Support Synergy Installation Guide July 2002 Applied Biosystems Flow Test 9 Delivery and Calibration of DIEA This flow test measures delivery of DIEA Peptide Synthesis Reagent B to the left vessel As with the previous flow test you tare the left transfer vessel and then weigh the contents of the left vessel after each reagent delivery WARNING CHEMICAL HAZARD DIEA N N Diisopropylethylamine can irritate skin eyes and mucous membranes Wear protective clothing and gloves when handling DIEA See the MSDS in the Synergy User s Manual Run Flow Test CALIBRATE DIEA 1 Press the START soft key to begin the flow test Remove the left vessel and put on scale Zero scale then replace the vessel 2 When this display appears remove the left pump vessel on the front of Synergy Figure 18 Place the vessel on a scale that is accurate to 1 mg and set the scale to zero 3 Replace the left transfer vessel on Synergy Press the OK soft key Remove the left vessel and weigh 4 When this display appears the left transfer vessel contains DIEA Without spilling the contents carefully remove and weigh the left vessel of DIEA Use the alphanumeric keys to enter this value on the LCD Press the OK soft key Replace the vessel 5 Replace the left transfer vessel Press the OK soft key July 2002 Synergy Installation Guide 53 Applied Biosystems 6 When prompted repeat steps 4 and 5 Th
52. tion Waste line is clogged If this message appears an obstruction in the waste delivery system has been detected Press the OK soft key The LCD then displays the mes sage Test failed July 2002 Synergy Installation Guide 31 Applied Biosystems Verify that the waste plug a hexagonal nut has been removed from the waste port Visually check the lines attached to the waste cap for blockage If you can see a crimp or blockage in either of the two waste lines a Detach the waste line from Synergy and clear the obstacle from the line When you remove the waste line you can hear a soft hiss of es caping pressurized air b Replace the hexagonal nut that plugged the Waste port c Set the Pressure Vent switch to Pressure d Press the OK soft key and repeat the Vent test If you cannot see an obstacle in either of the two waste lines or if the vent test fails repeatedly call Applied BiosystemsTechnical Support for assistance 32 Synergy Installation Guide July 2002 Applied Biosystems Connect External DMF Reagent Bottle WARNING POTENTIAL CHEMICAL HAZARD Regard all chemicals on the synthesizer including liquid in the lines as hazardous Wear protective eyeglasses gloves and a laboratory coat when working with these chemicals If a spill occurs clean it up in accordance with instructions in the MSDSs or Waste Profile found in the Synergy User s Manual Switch to vent and connect DMF Connect the delive
53. to turn the internal gas adjustment screw Do not make this adjustment until you have completed steps b and c of this procedure Synergy Installation Guide July 2002 Applied Biosystems b Usea5 8 in wrench to remove the plug in the Waste fitting Figure 11 c Set the Pressure Vent switch to Vent to vent the excess pressure d Turn the pressure adjustment screw counterclockwise to lower the pressure e Use a5 8 in wrench to replace the plug in the Waste fitting f Set the Pressure Vent switch to Pressure and wait 30 seconds Observe the value displayed after the words Current pressure on the LCD If the pressure is still too high repeat steps a f 5 Press the OK soft key when the internal pressure is set Amino Acid Column Wheel Test This test confirms that the autosampler jaws and the wheel that holds amino acid columns are working properly During this test the wheel rotates until a wheel test fixture in position one moves into the jaw assembly and the jaws close down on the test fixture WARNING PERSONAL INJURY HAZARD The autosampler jaw is oper ated by a pneumatic valve under high pressure Keep your fingers away from the jaws during this wheel test The next menu will test the wheel and jaw assembly 1 Press the OK soft key Put a wheel test fixture in position one on the wheel 2 Place a wheel test fixture Figure 13 in position 1 one on the amino acid column wheel
54. ton power switch 14 printer 6 2 Index pressure fitting 7 pressure test failure 62 Pressure Vent switch 21 Previous key 8 prime procedure DIEA 38 DMF 38 HBTU 38 piperidine THF 38 power switch 23 38 38 printer 6 printer port 5 printer assembly 5 to 6 procedure bottle change 35 bottle prime 38 flow tests 40 to 54 PSC 4 42 55 calibration 45 Pump AAG see Flow Test6 48 Pump Cell see Flow Test 7 49 R ratchet cap 19 reagent bottle positions HBTU 35 reagent bottle DMF 33 to 34 piperidine 37 reagent change 35 to 37 RS 232 see electrical cable Run Monitor Menu 27 28 57 S safety carriers 6 softkey 8 AM PM 17 Change Format soft keys 8 software 36 36 17 14 initialization switch mode select 5 power 14 Pressure Vent 21 23 T technical support 9 to 13 e mail address 9 Internet address 12 regional sales offices 11 to 12 telephone fax North America 10 terminal DB25 5 mini DIN 5 test external gas leak 21 flow 40 to 54 leak internal gas 27 pressure failure 62 28 wheel 25 26 test peptide 55 THF 37 38 bottle prime 38 Flow Test 4 47 Time amp Date Menu 16 time display 17 transfer vessel 7 Flow Test6 48 y vent test vent 17 time and date 19 28 ventilation system W waste 28 bottle installation 28 to 30 installation 1 28 external ventilation fiting 7 plug 7 wheel test 25 to 26
55. very to Vessels and Peptide Synthesis Column This flow test checks three deliveries of DMF first through the top valve block second through the bottom valve block and third through the syn thesis column During this test you are prompted to tare the left transfer ves sel and then weigh the contents of the left vessel after each of three reagent deliveries and enter the values If the reagent delivery weights do not fall within the acceptable ranges Flow Test 1 fails and you must repeat it before you can continue installation Since the success of this flow test depends on accurate weights take these special precautions to insure accuracy and precision e Use ascale that is accurate to Img e Always tare the left transfer vessel at the beginning of the flow test e Weigh the contents of the vessel immediately after reagent delivery to avoid reagent weight loss due to evaporation or spillage If you have taken all these precautions and Flow Test 1 fails repeat it once more If Flow Test 1 fails the second time you must adjust the internal gas pressure to calibrate the DMF flow For this adjustment the gas pressure range is expanded to 4 5 1 0 psi After you adjust the gas pressure repeat Flow Test 1 one final time to assure the delivery weights are within range Synergy Installation Guide July 2002 Applied Biosystems July 2002 IMPORTANT Always tare the left transfer vessel at the beginning of Flow Test 1 especi
56. x yy zz F F FUNCT NAME T XXX ZZZ HOLD PAUSE NEXTS jumpS more This LCD display is called the Run Monitor Menu When it appears a test for leaks in the internal gas system automatically follows This par ticular pressure leak test takes 6 minutes if no pressure test failures occur To read about pressure test failures see page 62 of this Installation Guide Test passed 2 When this display appears press the OK soft key to continue installation July 2002 Synergy Installation Guide 27 Applied Biosystems Vent Test and Waste Bottle Installation This particular vent test is only performed during the installation proce dure while the waste port is plugged It is never performed during routine operation of Synergy The vent test checks the internal ventilation system for leaks and the exter nal waste system for blockages It conducts a series of five pressure tests on the valve blocks both transfer vessels and the waste lines Vent Test 1 Verify that the plug is still inserted in the Waste port before beginning this test and then press the START soft key Switch the Pressure Vent to Vent 2 Switch the Pressure Vent switch above the Waste port to Vent 3 Press the OK soft key S xx yy zz F F FUNCT NAME T XXX zzz HOLD PAUSE NEXTS jumpS_ more 4 The Run Monitor Menu appears and a pressure test automatically begins After a minute the following display appear
Download Pdf Manuals
Related Search