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1. 149 Michaelis Menten nennen nemen nennen eeeeennneanenecaices 149 Sigmoid Equation essei eene LOL Curve 4404000 153 AXIS 11 155 Semi Log Fit LOS Log Log 199 Index bbb terti a a h h h h l a A a l a a a h a a a A a a ah h AR 1 57 Endpoint Program User Manual 87125 About This Manual About This Manual This manual has been written for assay developers and describes the features and concepts of the Endpoint Program With the information in this manual vou can Create edit and run assay test procedures Manipulate the results of tests using standard thresholding and curve fitting methods This manual assumes that The Reader has been installed according to the instructions the Microplate Reader User Manual You familiar with using the Reader user interface You have some degree of numerical aptitude You have a basic understanding of how to write assays and a basic knowledge of Enzyme Linked Immuno Sorbent Assay ELISA techniques This manual does not attempt to teach you how to write meaningful assays as it confines itself to a description of the program features For t
2. 0 C NC3 0 0 0 D 0 0 1 F COZ G PCI 0 H PCZ 0 Endpoint Program User Manual 87125 127 Appendix Sample Printouts Curve Fit Data Test Printout 1 0 EQUATION DMPL Lab JF Printed at 14 45 on 22 06 94 Page 8 TEST NO G2 TEST 2 PASSWORD WAVELENGTH MODE DUAL TEST FILTER 405nm REF FILTER 630nm PLATE ID PROMPT YES O D MATRIX YES NO ELANK MODE AVERAGE 1 2 3 4 5 6 8 9 10 11 12 54 TI B Bi 54 T1 51 55 T2 D 51 55 TZ E 52 56 52 56 T3 53 57 T4 H 53 S7 T4 EQUATIONS AREA STATISTICS NO CURVE FIT CONC OF 51 1 000 ug mi CONC OF S2 2 000 ug ml CONC OF 53 3 000 ug mi CONC OF S4 4 000 ug ml CONC OF S5 5 000 ug ml CONC OF S6 6 000 ug mi CONC OF S7 7 000 ug ml CURVE FIT TYPE LINEAR POWER FIT WITHOUT TAILS LINEAR AXIS FITTING CURVE FIT Q C NO SCALE GRAPH NO SAMPLE I T2 1 1 T3 1 1 DILUTIONS T4 1 1 Endpoint Program User Manual 87125 Appendix B Sample Printouts Curve Fit Data Results Printout DMPL Lab amp JF Printed at 14 45 on 22 06 94 Page 9 TEST NO 02 W L MODE SINGLE DATE 18 03 94 TEST NAME MRX2 TEST FILT
3. 55 2 088110000 590000 i i cadda ri 89 Versi 90 ERR ET RAE Backup gaupa s ehkqephbhh babeogme hhkbhkamhkdphdhhhhpkqamuaa Ru hb hh EEEE 90 V Ea RhdhchdRhhhhgmmdhdhhbuuthbd4ddlhd amp 5dhkdGdhggkhbhhhEc 91 Stats PADO Rb hh uuu nun 91 Batch REE 92 Spectrum SPREE ae RE 92 Chapter 7 Computer Control 95 7 1 Hardware Specification eese eese nennen nnne 97 Linking with an IBM Compatible 98 Linking with an Apple Macintosh 21 2 2 1 99 7 2 Software Specification 1 11 1 1 anten 100 7 3 4 2 22 2 4 11 6 100 7 4 Checksum REM 102 2 Read Mode essen nera re erem ene nemen esas venn rene eeeee iara sessions LOG 3 Filter Select
4. eese eene enenatis 24 Defining the Yorni Wavelength Mode Blanking ARR 33 Results Matrix staat nennen 26 Area Statistics NEMINEM Quality Control Equations NEMINEM Inserting Output Options into the Test NER Threshold Matrix Output Option 49 Ratio Matrix Output nasa natns instans 92 Curve Fitting Output 36 Difference Matrix Output Option esee eene tnter nenne OF 4 2 Editing a Test 0 2 2112 66 Editing Tests Options Od 4 3 Printing Tests LIST HR 68 4 4 Printing Directories 69 Endpoint Program User Manual 87125 17 Chapter 4 Creating and Editing Tests This page 15 intentionally left blank 18 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Once the instrument is switched on and the self test routines are successfully completed the Main menu appears This shows the choice of programs The appearance of this menu will depend upon the application programs installed If the Endpoint Program is the only software program installed the Main menu will show only the Endpoint and Setup options READY 4 45P 30 06 94 ENDPOINT SETUP Select END
5. HERE 102 7 5 Computer Control Commands NER 102 Step X Y LOS 1 2 Read Mode LOG 3 Filter LOG 4 Blank 2 5 Print 4 0 4 0 6 Display Control 2 teinte nate testata sentar 110 7 Computer Control 10 9 Reduced eese LEO 7 6 Data tata da sata 111 Response with Response without Data Uncontrolled 5 11 Endpoint Program User Manual 87125 95 Chapter 7 Computer Control This page is intentionally left blank 96 Endpoint Program User Manual 87125 Chapter 7 Computer Control This chapter contains information on how to interface the Reader to an external PC for data retrieval and control Example programs are available to assist with computer interfacing Input Output Routines The information provided in this section 1s intended for those users who want to write their own applications software If you are a capable
6. 2 2 2 2 222 139 Area Statistics Results esee nene near nn anh earns 139 Endpoint Program User Manual 87125 121 Appendix Sample Printouts This page is intentionally left blank 122 Endpoint Program User Manual 87125 Appendix B Sample Printouts Directory of Tests DMPL Lab JF Printed at 14 45 on 22 06 94 Page 1 TEST DIRECTORY TEST NAME TEST NAME 00 READ 50 01 READI 51 02 HEPATITUS 52 03 HIV 1 53 04 HIV 2 54 05 SINGLE 55 06 READ3 55 07 THRESH 57 08 DIFF 58 09 RATIO 59 10 CURVEI 60 11 CURVE2 6i 12 CURVE3 62 13 CURVE4 63 14 CURVES 64 15 CURVE6 65 16 CURVE7 66 17 CURVES 67 18 CURVES 68 19 CURVELO 69 20 DUAL 70 21 71 22 72 23 73 24 74 25 75 26 76 27 77 28 78 29 79 30 80 31 81 32 82 33 83 34 84 35 85 36 86 37 87 38 88 39 89 40 90 41 91 42 92 43 93 44 94 45 95 46 96 47 97 48 98 49 99 Endpoint Program User Manual 87125 123 Appendix Sample Printouts Directory of Plates 124 DMPL Lab Printed at 14 45 22 06 94 Page 2 PLATE DIRECTORY PLATE ID TIME DATE PLATE ID TIME DATE 00 0000 16 14 18 08 94 50 15 03 04 08 94 01 0001 22 54 11 09 94 5l A 15 08 04 08 94 02 52 15 12 04 08 94 03 53 15 15 04 08 94 04 54 15 16 04 08 94 05 55 0055 15 19 04 08 94 06 56 0056 15 25 04 08 94 Q7 57 0057 15 34 04 08 94 08 58 0058 15 37 31 08 34 09 59 0
7. HHHH HHHH 9 Note If a five filter read value is over range the value 9 999 is transmitted Endpoint Program User Manual 87125 Chapter 7 Computer Control Response without Data In all instances where a command requires no data from the Reader the microplate will issue one of the following data streams STX ACK ETX indicating it has complied and is ready for further commands STX ETX indicating that it cannot comply with A as one of the codes 5 ERROR DESCRIPTION 1 Taree ou aro o NM UTI A 5 Filter command out of range E Blank argument out of range Uncontrolled Transmission The Reader can send a results matrix to the parallel printer port and seria RS232C port simultaneously Data is sent to the RS232C port provided that the Reader detects the presence of the computer the above condition is met the RS232C port will transmit data uncontrolled without the normal handshake The data format 1s identical to that described earlier You can readily copy the input from the computer s 5232 port to a data file and examine or edit the file when transmission 15 complete To prevent the computer s input buffer becoming overloaded and data being lost software handshaking using XON XOFF should be used When an character 13H controi code 15 transmitted the Reader stops transmitting data and wa
8. eee OD Plate ID RENE enr Barcode 78 Reading neta anne eet 78 Variables RR 79 Editing EN Co RR Curve Fit 0 212 79 Read 1 censere 83 5 2 Recalling 83 Endpoint Program User Manual 87125 71 Chapter 5 Running Tests and Recalling Plates This page is intentionally left blank 72 Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Plates Once the instrument 1s switched on and the self test routines are successfully completed the Main menu is displayed This shows the choice of programs The appearance of this menu will depend upon the application programs installed If the Endpoint Program 1s the only software program installed the Main menu will show only the Endpoint and the Setup options READY 4 45P 30 06 94 ENDPOINT SETUP Select ENDPOINT to view the Endpoint menu ENDPOINT READY 4 45P 30 06 94 START RECALL UTIL PROGRAM CE START Lets you run assay test procedures which have been created using the Program menu RECALL Lets you recall data obtained from a previous assay test procedure for further processing UTIL Lets you carry out a manu
9. l Note This equation is also known as 5 Four Parameter equation the four parameters are a minimum response b shape factor determines the gradient of the curve the response midway between maximum d and the minimum a responses d maximum response Note This definition assumes a positive value for b Where b is negative the definitions for parameters a and d are reversed Endpoint Program User Manual 87125 151 Appendix C Curve Fitting 152 The Reader contains an efficient algorithm for estimating the four parameters and determining the best fit for the sigmoid curve The curve requires at least four Standards data points one for each of the four parameters It is recommended that at least eight Standards are defined o ensure satisfactory statistical significance The Reader will allow a maximum of 24 Standards The sigmoid curve algorithm is iterative requiring many complex calculations and the Reader may take some time to process the results If the Keader has difficulty fitting the data to the curve processing will continue either until the Reader has processed the data or until you select ABORT you have aborted the data processing examine the data carefully to see if the number of Standards could be altered to better define the curve Endpoint Program User Manual 87125 Appendix Curve Fitting Akima Curve Fit The Akima option constructs a smooth curve throu
10. 44 Ln Cok 9 2 RR 45 79 iw 67 1 45 Physical Environmental Conditions eese eese eerte nna tanta 45 Index 4 Microplate Reader User Manual 87125 About This Manual About This Manual This manual has been wntten for the laboratory technician and describes how to use the Microplate Reader With the information this manual you can Install the Reader Configure the Reader using the Setup menu to suit your particular needs Connect the Reader to a printer Perform basic maintenance procedures This manual also describes all the features and specifications of the Reader hardware and software For information on how to use any software you have installed such as Endpoint or Barcode software refer to the individual user manuals For information on how to connect the Reader to an external computer refer to the Endpoint Program User Manual For explanations of error messages and possible solutions refer to the Troubleshooting Guide Micropiate Reader User Manual 87125 1 About This Manual This page is intentionally left blank 2 Microplate Reader User Manual 87125 Safety Information Safety Information there is any doubt or concern about the safety of the instrum
11. esee rennen nenne enema enne eee 106 4 Blank Modification eese nene nennen ennemis 5 Print 2 trenes a esa an eterna tens 108 6 Display 7 Computer 2 42 2 4 2 119 9 Reduced Matrix cc ccccscscecenssnncesscsusccsuenasseeuravenaeeuarencenccaassacssescaseaeeeenees 119 7 6 Data 2 22 2222 00 0 000 Response with 1 1 2 2 1 1 1 0 41 41 6 atosteciee Response without Data 22 113 Uncontrolled Tramsimission 1 cccsssssssssessseeecssnsnsesusesecusacecusaeeseuareeeeseueeeeserenss 113 Endpoint Prograrn User Manual 87125 Table Contents Appendix A Examples of Plate Formats 115 Single Well Standards in sees 00 antreten ata 117 Single Well Standards in Columns 2 2 00 40000 117 Double Weil Standards in Rows Replicates m Columns 118 Double Well Standards in Columns Replicates in Rows 118 Triple Well Standards in Rows Replicates in Columns 119 Triple Well Standards Columns Replicates in 5
12. rena a e aba antra eund nt 132 Cubic LOD Polygon 132 Curve Fit 221 1 4 06 06 08000000 133 Sigmoid Fit Michaelis Menten Fit Curve Fit Data NEMINEM 134 Ratio Data Test Printout 135 Ratio Data Results 2 2 1 11111 136 Difference Data Test Printout 2 2 44 nen 137 Difference Data Results Printout eese eere 138 Area Statistics Test shit 139 Area Statistics Results eere enean nnn 139 Endpoint Program User Manual 87125 iii Table of Contents Appendix C Curve Fitting eene ener er eooaeesseee 141 Linear 4 144 Polygon 145 Non Linear Curve 2 1 1 6 ene nent reser nena rns 146 Quadratic Cubic and Quartic 147 Cubic Spline Curve 2 2 21 1 400 0 0 1 6000 eene 148 Other
13. Microplate Reader User Manual Manual code 87362 Lot number lot 9710 9904 Revision of the manual October 1997 Software versions End Point 2 0 SBY1 3 MB Main Menu 2 02 SB 1 33 English 87360 67364 sanofi PASTEUR Se 55522255523 DECLARATION OF CONFORMITY according to ISO IEC Guide 22 and EN 45014 Manufacturer s Name DYNEX TECHNOLOGIES Manufacturer s Address DYNEX TECHNOLOGIES Inc 14340 Sullyfield Circle Chantilly VA 20151 1683 USA declares that the product Microtiter Plate Reader Model MRX MRX MRX aus B Product Options All B conforms to the following Product Generic Specifications Safety EN 61010 1 1993 IEC 1010 I 1990 plus AMD 1992 BS EN 61010 1 1993 EMC EN 50081 1 1992 EN 50082 1 1992 Supplementary Information The product referred to above was tested in a typical configuration and complies with the requirements of Low Voltage Directive 73 23 EEC and Directive 89 336 EEC Note If changes are made to this product including the use of unapproved material or peripheral equipment then this declaration of conformity is invalid Chantilly Vir ginia 4 eL 7 E ohn L Eccles USA April 17 1998 Director of Quality and Regulatory Affairs European Contact Wolfgang Trautwein Managing Director DYNEX Technologies GmbH Justinus Kerner Strasse
14. Test Curve Test wells must be arranged in the same number of replicates as the Standard wells Sets of Test curves The number of Test wells must be a multiple of the number of Standards For example a test sequence with eight Standards can have 9 16 24 etc Test wells If these three conditions have been met the PARALLEL option can be selected from the OTHER Curve Fit Types menu CURVE FIT TYPE 4 45P 30 06 94 SIGMOID MICHAEL AKIMA PARALLEL CE Parallel statistical technique Analysis of Variance ANOVA is used to determine if the test data for the parallel line bioassay is valid curves must be parallel for the test to be valid not the worst cases are rejected until the remaining curves are parallel or all the data has been rejected Select PARALLEL to specify a parallel line bioassay The Reader will ask you to enter the units for the curve Use the left and right cursor keys to scroll through the characters Press the function key to enter a character or CE to delete a character Use the alphanumenc keypad to enter numbers When the units label is complete select ENTER to accept it Endpoint Program User Manual 87125 59 Chapter 4 Creating and Editing Tests If more than 12 curves are entered or all of test curves are rejected then a PARALLEL LINE ERROR message will be displayed and the calculations will be aborted dq Note Parallel line bioassay data cannot be passed to a threshol
15. 0 5 1 3 10 30 100 200 CONCENTRATION Figure C2 Using Tails 146 Endpoint Program User Manual 87125 Appendix C Curve Fitting Quadratic Cubic and Quartic Regression Polynomial quadratic cubic and quartic regression is best explained in parallel with linear regression where the function to fit to experimental data be written as bx where b the slope corresponding to m in straight line equation the y intercept of the line corresponding to c in the equation for a straight line quadratic equation is defined as A cubic equation as dx And quartic equation as dx The procedures to fit such functions to experimental data are closely related to linear regression and have a similar mathematical derivation Polynomial regression minimises the deviations of the data points from the polynomial equation the square of the data point deviations are minimised since positive and negative deviations would otherwise cancel each other out There is an analogous regression coefficient which when R 1 indicates that all the data points have been fitted to the curve when R 0 the data points are highly scattered Endpoint Program User Manual 87125 147 Appendix C Curve Fitting Cubic Spline Curve Fitting Cubic spline curve fitting passes a curve through all the data points This is not a best fit
16. 11 Section 1 Error Messag Timing overflow error TLOSS Error Token error in an equation Too few Standards Unable to allocate queues Underflow Error Unsupported baud rate Warning Fit aborted after 20 iterations Warning Invalid blank mode selected Blank mode has been modified Warning Limits are out of sequence 12 You have not allowed a sufficient time interval between kinetic readings or you have interrupted the kinetic assay Increase the time interval or try running the assay again without performing any mouse or keyboard operations Contact an approved service center The Reader has found an error equation Check ail equations to make sure that they are valid and edit them if necessary The curve fit type you have specified requires more standards than you have entered Edit the test template 10 contain more Standards or use a stored curve Check the communication settings and cables Contact the service center if the error persists Contact an approved service center Check the communication settings and cables Contact the service center if the error persists Data was poor match for the defined sigmoid 4PLC curve Edit the plate to remove ODs which are a poor match using the Outlier Removal option The blank mode you chose was not appropriate for the template Change the blank mode or change the template The positive positive or posi
17. Character ASCII code sum1 sum2 0 0 STX 2 2 2 5 53 55 57 0 48 103 169 Checksum 160 x 255 103 40903 The command therefore becomes STX 5 9 Note The Reader data format includes a checksum whether this command is Sent or not 7 5 Computer Control Commands The COMMAND data string has the following format SIX A ARGUMENTS Checksum ETX where STX 1s the ASCH Start of Text character ASCI character 0 1 2 3 4 5 6 7 9 ARGUMENTS are alphanumerics needed by the particular command ETX is the ASCH End of Text character Checksum optional see above Endpoint Program User Manual 87125 Chapter 7 Computer Control qe Note Make sure that the computer only sends the above codes Some computers automatically send CR and LF these must be suppressed There are 10 basic commands which are described by the ASCII numbers 0 to 9 These have been supplemented by additional commands which are denoted by two ASCII numbers as subsets of the core command The basic commands are 0 Step X Y 1 Start Stop 2 Read Mode 3 Filter Select 4 Blank Modification 5 Printer Control 6 Display Control 7 Computer Control 9 Reduced Matrix Step X Y STX 0 A ETX 15 ASCH number 0 1 or 2 0 Step only in the X direction 1 Step only in the direction 2 Step both X and B is the number of steps in the fir
18. Multiple Wavelength Mode Using multiple wavelength mode can help you to examine results which would normally be outside the range of the Reader It lets you take two readings of each sample using different filters The first reading 15 run 1n Primary mode using standard filter wavelengths this can be run in single or dual wavelength mode The second reading 15 run in Secondary mode using slightly higher or lower wavelengths this can also be run in single or dual wavelength mode The Reader automatically uses the primary readings when it calculates its results If however any of these ODs are above the Over limit of the Reader it then examines the secondary readings of the wells in question The secondary ODs will be in a different range from the primary readings because they were obtained using different filters so they must be converted into the same range as the primary readings To achieve this the Reader offers three different calculation modes 1 Linear Regression calculates a line of best fit between the two sets of data This line 1s used to convert secondary ODs into the correct range 2 Well Location uses a well specified by the user to convert the readings The ratio between the primary and secondary ODs from this well is applied to the other secondary ODs 3 Constant Value uses a constant specified by the user The secondary ODs are multiplied by this value to convert them to the correct range Endpoint Program Us
19. non linear curve fitting 146 Number of samples 75 77 0 Optical path 9 10 Output options editing the 68 inserting into a test 44 66 44 66 Endpoint Program User Manual 87125 Paired blanking mode 35 Password adding to a test 45 Pathlength 10 Photometry theory of 7 Plate bianking 34 Plate ID prompt 22 77 Plate identification 3 polygon fitting 145 polynomial regression 147 Printing directories 69 tests 68 69 Q QC equation components 43 44 quadratic cubic and quartic regression 147 Quality control equations 38 44 R Ratio matrix output option 52 55 ratio and IU equation components 53 Reading a plate 89 Recalling plates 83 84 Restore option 91 Results matrix 36 Row blanking mode 35 Running test 73 83 number of samples 75 77 repeating 83 test number 74 75 Endpoint Program User Manual 87125 S Shake inserting in a test 22 23 shake modes 23 shake time 22 Short cut test selection 3 short menus 89 Sigmoid equation 151 Single and dual wavelength modes 7 8 Spectrum option 92 stats option 91 92 Template define template prompt 24 defining automatically 29 30 29 30 defining manually 25 28 editing 67 Test creating new 20 66 editing a 66 68 editing test options 67 making a copy of 66 password protected 21 repeating 83 running 73 83 Test name 21 Test number
20. 30 06 94 LANGUAGE DISPLAY KEYPAD PRINTER CE Language Select LANGUAGE to set the language options The Reader will display the current language setting Select ENTER to confirm this setting or CE to access the options LANGUAGE 4 45 30 09 94 ENGLISH FRANCAIS DEUTSCH ITALIANO OTHER OTHER accesses a second Language menu with the ESPANOL option Select the required language or select CE to return to the System menu The language chosen will be used to display all subsequent menus Display Select DISPLAY to view the Reader display format DISPLAY 2 X 40 4 45 30 06 94 ENTER Microplate Reader User Manual 87125 21 Chapter 2 Installation and Setup Press CE or ENTER to return to the System menu Keypad Select KEYPAD to view the Reader keypad format KEYPAD 21 KEY 4 45 30 09 94 ENTER select ENTER to move on The keypad has an optional beep which sounds each time a key 1s pressed The Reader will display the current kev beep setting Select ENTER to confirm the setting or select CE to access the options KEY BEEP 4 45P 30 06 94 YES CE Select YES to switch the beep on or NO to switch it off Printer Select PRINTER to view the printer settings EPSON LX 810 4 45P 30 00 94 NEXT LAST ENIER Select ENTER to accept the printer shown or use the NEXT and LAST commands to scroll through the list of printers The Reader is supplied with a number of standard printer drivers If your
21. Difference Data Test Printout DMPL Lab sJF Printed at 14 45 22 06 94 Page 12 TEST NO 04 TEST NAME 4 PASSWORD WAVELENGTH MODE DUAL TEST FILTER 410nm REF FILTER 690nm PLATE ID PROMPT NO O D MATRIX YES SHAKE NO BLANK MODE AIR l 2 3 4 5 6 7 8 9 10 11 12 NCL 1 TS 17 725 T33 741 149 T57 T65 T73 T81 T2 T10 T18 T26 T34 T42 150 T58 T66 T74 T82 3 T3 Til T27 T35 T43 T51 T59 767 T75 T83 4 4 T12 T20 T28 T36 744 152 160 T68 T76 T84 Coil TS T21 T29 T37 T45 61 769 T77 T85 2 T6 14 122 T30 0 738 T46 154 T62 T70 8 T86 G T7 T15 T23 T39 7147 T55 763 T71 T79 T87 H 2 T8 316 124 T32 T40 T48 T56 T64 T72 T80 T88 EQUATIONS AREA STATISTICS NO DIFFERENCE ALTERNATIVE NO FORMAT SUBTRACT ADJACENT SUBTRACT COLUMNS SUBTRACT ORDER Ist 2nd Endpoint Program User Manual 87125 137 Appendix B Sample Printouts Difference Data Results Printout DMPL Lab JF Printed at 14 45 on 22 06 94 Page 13 TEST NO 04 W L MODE SINGLE DATE 18 03 94 TEST NAME TEST FILTER 410 nm TIME 16 14 PLATE PLATE REF FILTER OPERATOR 1 2 3 4 5 6 8 9 10 11 12 0034 0 922 1 741 0 298 0 035 0 035 1 371 1 388 0 097 0 034 0 038 0 897 00 1 010 0 311 0 034 0 953 1 517 0 036 0 100 1 273 0 034 0 967 0 830 C 0 029 0 980 0 101 1 495 0 113 0 317 0 340 1 655 0 100 0 897 1 154 0 098 0 030 1 220 1 2
22. EE Zub eh Mg aT ha C T et eee ee Figure 3 The Microplate Reader Back Panel Mains Inlet 7 Optics Door 2 Voltage Selector 2228 Optics Cooling Vents See the Voltage Selector section below 3 Monitor Mains Socket 9 Serial Number Plate 4 Keyboard Socket 10 PSU Cooling Vents 5 Senial Port 11 Main Enclosure 6 Pnnter Port Note The warning symbols on the back panel indicate that the optics door be hot and that no appliances other than a monitor should be plugged into the mains outlet For more details refer to the discussion on Symbols earlier in this manual Note The positions of ports 5 amp 6 may not be exactly as shown but the number of pins or pin sockets in each port will remain the same Note Remove the port protectors connector protector and styrofoam packing inside 7 12 Microplate Header User Manuai 87125 Chapter 2 Installation and Setup Voltage Selector The position of the voltage selector see Figure 3 is very important and must be adjusted to match the line voltage of the mains power supply before switching the Reader on Position of Voltage Selector Mains Line Voltage 115V 100 120V 230V 200 240V CAUTION FAILURE TO FOLLOW THE PROCEDURES DETAILED BELOW MAY RESULT IN DAMAGE TO THE MICROPLATE READER DUE TO PARTS FALLING INTO THE POWER SUPPLY There are two types of plastic cover fitted to the voltage selector switch ff the plastic cover has a
23. LINEAR WELL VALUE CE These modes are described below For more information on these modes refer to the Wavelength Modes section in Chapter 2 LINEAR converts the secondary readings using a line of best fit calculated from the two sets of data WELL converts the secondary readings using the ratio between the primary and secondary ODs of a specified well The Reader will ask you which well type you want to use Blank Standard Test or Control WELL 4 45P 30 06 94 B S T OTHER Select a well The Reader will ask you for number of the well For example WELL 4 45 30 06 94 Enter well number using the keypad and press ENTER Note You cannot specify a well type and number which you have not defined on the template VALUE converts the secondary reading using a value which you enter using the keypad The secondary readings required will be multiplied by this factor The Reader will ask you for the value VALUE 4 45P 30 06 94 ENTER Enter value using the keypad and select ENTER Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Blanking The Reader asks which blanking mode you require It automatically uses air as a reference but for certain applications other reference levels may be more appropnate example vou may want to eliminate the absorbance of a reagent solution from the test result The Reader can hold the OD value of
24. Ratio and IB Equation Components summary of the components which can be used in ratio and JU equations is shown below together with a route showing you where to find them from the Ratio Matrix menu 1 Item Numbers Arithmetic Operators To the power of Brackets Logarithmic Functions log alog In Select OPTION MATH for example Select OPTION FUNCTION iablel Select OPTION FUNCTION 51 Select OPTION FUNCTION select OPTION FUNCTION 1 to 5 variables z z zis ele 7 a Minimum OD Maximum OD Maximum plate OD T tt Individual OD of every samp Select OPTION FUNCTION well ndividual replicate ODs for example Select OPTION FUNCTION samplel and enter the number on the alphanumeric kevpad Well ODs Well type 1 2 Select WELL Select the well and well number CO2 type and enter the number on the alphanumeric keypad Replicate ODs Well T12 Select WELL Select the well type number and NC2 3 type and enter the numbers on i PC4 2 52 1 the alphanumeric keypad T NC PC Select WELL C sr H mre ee Mrl Example To convert all ODs on the plate to a ratio of the average Positive Control to convert into different units 15 times smaller For the Ratio equation enter sample PC For the IU equation enter sample 15 When you have completed th
25. Reader has found an error equation or test If you cannot find an error in the test switch the Reader off and start again DOMAIN Error Contact an approved service center Error building DCB Check the communication settings and cables Contact the service center if the error persists Error in default Contact the service center if the error parameters persists Error in Equation The Reader has found an error in an equation Check all equations to make sure that they are valid and edit them if necessary Error Loading Module The Reader cannot find an executable file Contact an approved service center Error Opening File The software could not find the file you asked for Recreate the file Error setting comm state Check the communication settings and Troubleshooting Guide 87125 5 oection 1 Error Messages Fatal Error Bad Drive Request Structure Length Data Error CRC Error Drive Not Ready General Failure Read Fault Sector Not Found Seek Error Unknown Command Unknown Media Unknown Unit Write attempt Write Fault File Checksum Error File Error File is not the correct version cables Contact the service center if the error persists The Reader has detected problem with the floppy disk or the hard disk There may be no disk in the floppy drive or your floppy disk may be write protected or corrupted Switch the Reader off and remove the floppy disk fr
26. Tt will however produce reproducible shaking from machine to machine If you select USER The Reader asks you for the amplitude of the shake AMPLITUDE mm 4 45P 30 06 94 ENTER CE Enter a value for amplitude and select ENTER Minimum imm maximum 10mm The Reader asks you for the frequency of the shake FREQUENCY 4 45P 30 06 94 ENTER CE Enter a value for frequency and select ENTER Minimum 5Hz maximum 20Hz If the plate carrier is heavily loaded and the amplitude or frequency is very high the plate carrier may stail In this case press the Esc key to reset the Reader Always test run user shake mode settings before using them in actual tests Endpoint Program User Manual 87125 23 Chapter 4 Creating and Editing Tests Define Template Prompt The Reader asks whether you want to define the template manually or automatically DEFINE TEMPLATE 4 45 30 06 94 YES AUTO CE YES You must input the locations of each well type manually AUTO The Reader automatically assigns well locations once you have specified the number and format of the wells To define the template automatically refer to the Defining the Template Automatically section later in this chapter Defining the Template Manually Select YES at the Template menu to access the Manual Template menu The Reader asks which well type you want to assign to well location Al Al 4 45P 30 06 94 B S T C USER UTILITY FINISH CE B
27. for up to 12 tests The Reader asks if you want to assign all 96 wells samples to the currently open test NO OF SAMPLES 96 4 45P 30 06 94 ENTER Select ENTER to assign all 96 samples to the test To assign less than 96 wells select CE enter the number of wells and select ENTER Be sure to include the blanks standards and controls The section on Running More than One Test on a Plate below describes how the Reader assigns the wells The Reader asks if you want to assign any more wells to other tests ANY MORE SAMPLES 4 45P 30 06 94 YES NO CE Select NO to leave the rest of the wells unassigned or select YES to assign wells to another test The section on Leaving Wells Unassigned below explains how unassigned wells are discarded The Reader asks which test you require Open the test as described above in the Test Number section The Reader asks if you want to assign ali the remaining wells to the new test For example if you assigned 20 wells to the first test 76 wells will remain NO OF SAMPLES 76 4 45P 30 06 94 ENTER Select ENTER to assign all the remaining wells to the new test or CE to assign some to a further test The Reader will repeat the process until all 96 wells are assigned or wells are assigned to 12 tests or you select at the MORE SAMPLES prompt Endpoint Program User Manual 87125 7 Chapter 5 Running Tests and Recalling Plates If you have left any wells un
28. sample using the sample number or an individual replicate using the sample and replicate numbers For example mean of all Control wells C the mean of all C1 replicates 1 1 the OD of the first replicate of C1 OPTIONS inserts brackets mathematic functions and logarithmic functions into the equation RATIO _ 4 45P 30 06 94 FUNCIION MATH Endpoint Program User Manual 87125 53 Chapter 4 Creating and Editing Tests Inserts left and right brackets into the equation Six levels of parentheses are allowed FUNCTION Inserts a mathematical function into the equation Sample inserts the individual OD of every well on the plate into the equation Variable represents a variable which must be entered at runtime Five variables are allowed per test Example variablei You will have to enter this number runtime represents the maximum minimum OD on the plate or within a group of wells The group of wells may be a well type or a sample if it contains multiple replicates Example 1 Min T1 The lowest OD of replicates of Test sample 1 Example 2 Mi The lowest OD on the plate reg memabeeidnsm Ag mesasmeleg m 7 Tie inser natural logi OPER inserts an arithmetic operator into the equation Addon 54 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests
29. so that a record can be kept The Reader will display the current self test print setting Select ENTER to confirm the setting or CE to access the options PRINT SELF TEST 4 45 30 06 94 YES CE Select YES to print the self tests each time they are run om Note The printer must be connected directly to the Reader for the self test to print An extra self test retest is also available which is carried out before each plate is read The Reader will display the current setting for the test Select ENTER to confirm the current setting or CE to access the options TEST BEFORE READ 4 45P 30 06 94 YES NO CE Select YES to perform the extra test or NO to omit it Note Adding the extra test will lengthen the reading time Maintenance Reminder The Reader has a maintenance reminder which can be displayed at regular intervals on power up The reminder is mtended for use by laboratories which routinely verify the operation of their instruments Microplate Reader User Manual 87125 23 Chapter 2 Installation and Setup The Reader will display the current setting Select ENTER to confirm the current setting or CE to access the options MAINTENANCE 4 45 30 06 94 DAILY WEEKLY MONTHLY CE Select NO if you do not want any reminders to be displayed or select the appropriate frequency Comms Menu Select COMMS from the Setup menu to access the Communications menu and view PC communications settings Note Do n
30. 1111 79 0 1 6 6 0 11 The Reader Back 22 2 1 1 2 1 2 401 42 1 00 net enenatis 12 The Reader Front 22 2 1 nennen LA The Keypad and Display enne enne nennen nens 14 Fitting the Lamp and Optical nne 13 Switching the Reader 16 Switching between DOS 17 2 2 Setup Procedures esee essei nne aditus 18 Setup 9 Filters 19 Clock 1 2 4 DU System Maintenance nnne nnn 23 Comms Menu 24 Memory 4 22 1222 25 0 018 0 0 10 015 nta nennen nai nene tanc Do Param 42 0 nemen 26 Chapter 3 Printer Interface eere 29 Chapter 4 Mai
31. 163 71 T79 787 2 8 716 124 T32 140 T48 156 164 T72 T88 A gg m t U OG uw Q C EQUATIONS AREA STATISTICS NO THRESHOLD EON CO 0 9 EON CO 1 1 CO 1 5 CO 2 NO SEGMENTS 1 LABEL z 0 LABEL 0 LABEL Doc LABEL LABEL 126 Endpoint Program User Manual 87125 Appendix B Sample Printouts Threshold Data Results Printout DMPL Lab JF Printed at 14 45 22 06 94 Page 7 TEST NO 01 MODE SINGLE DATE 18 03 94 TEST NAME TEST FILTER 410 nm TIME 16 14 PLATE PLATEL REF FILTER OPERATOR 1 2 3 4 5 6 7 8 9 10 11 12 0 034 0 922 1 741 9 295 9 035 0 035 T1371 1 388 0 097 0 034 0 034 0 873 0 034 1 010 0 311 0 034 0 958 1 517 0 036 0 109 1 273 0 034 0 967 0 830 0 029 9 980 0 104 1 493 0 113 0 317 0 340 1 655 0 100 0 897 1 154 0 098 0 030 1 220 1 233 0 110 9 342 0 085 1 390 0 036 0 093 0 825 0 380 0 035 0 090 1 660 1 193 1 132 0 979 1 371 1 423 0 849 0 036 1 348 0 036 1 443 9 095 1 682 0 105 1 780 0 758 1 114 1 143 1 415 1 656 0 035 1 335 0 372 0 340 2 137 0 920 0 302 1 477 0 275 0 034 0 098 0 036 0 290 0 077 0 346 tid wy 0 345 1 864 0 035 1 311 1 111 1 185 9 084 0 291 1 004 0 538 0 113 0 998 THRESHOLD EON CO 2 0185 EON 9 1 5 0 138 EQN 1 0 102 BON CO D S 0 083 1 2 3 4 5 6 7 8 9 10 11 12 Nel 0 NC2
32. 60 Hz Plate Carrier Diagram The diagram on the inside of the floppy disk drive door shows the mechanism for moving the plate carrier in and out While the Main menu is displayed the plate carrier can be moved in and out using the up and down v cursor keys The up key moves the plate carrier in and the down key moves it out Do not place any objects or stand within 150mm 6 5 in of the front of the Reader as this will obstruct the plate carrier Microplate Reader User Manual 87125 5 symbols This page is intentionally left blank 6 Microplate Reader User Manual 87125 Chapter 1 Features of the Reader The Microplate Reader 15 microprocessor controlled photometer It is designed to measure the optical density OD of fluid samples in 96 well microplates in order to determine the leve of chemical reactions Figure 1 The Microplate Reader full list of the Reader s technical specifications can be found in Appendix C Reader provides the following features Endpoint Agglutination Software PC compatibility for additional contro and data storage Multi lingual display which guides you through menu choices Single and dual wavelength reading modes e Selection of up to six filter wavelengths Data analysis and presentation as OD matrices and or graphically using curve fitting routines Data output to printer Micropiate Reader User Manual 87125 7 Chapter 1 Features of th
33. 66 94 35 5 0 05 B 15 0 032 0 00 8 28 5 0 91 5 15 0 999 1 70 76 0 08 32 0 630 0 58 91 44 0 06 C 16 0 058 0 81 14 58 0 02 NC 4 0 817 0 77 94 66 5 0 03 A 0 533 0 58 dox ex ke x 4 0 786 0 83 1 05 9 01 PR 4 0 951 0 96 1 00 0 05 Endpoint Program User Manual 87125 139 Appendix Sample Printouts This page is intentionally left blank 140 Endpoint Program User Manual 87125 Appendix C Curve Fitting Appendix C Curve Fitting Linear Regression siss eetmentt eerie tae een eee ee 144 Polygon at enam enne 145 Non Linear Curve eene tane ener rennes LAG Quadratic Cubic and Quartic Regression BEER 147 Cubic Spline Curve Fitting eese sesenta 148 Other Equations MM NENNEN 149 Michaelis Menter 149 Sigmoid 0 151 Akima Curve LOG Axis Fitting HR 155 Semi Log LOD Log Log Fit LOD Endpoint Program User Manual 87125 141 Appendix C Curve Fitting This page is intentionally left blank 142 Endpoint Program User Manual 87125 Appendix C Curve Fitting Appendix C provides theoretical no
34. Data Sigmoid Fit Optical 2 500 Density 2 000 1 500 1 000 X 0 500 0 000 0 500 0 000 2 000 4 000 6 000 8 000 Concentration ug ml Michaelis Menten Fit Optical 2 500 Density 2 090 1 500 1 000 0 500 1 0 000 0 500 0 000 80 000 150 000 240 000 Concentration ug ml Endpoint Program User Manual 87125 133 Curve Fit Data Fit Optical 2 500 Density 2 000 1 500 1 000 0 500 0 000 0 500 1 000 3 000 5 000 7 000 Concentration ug ml 134 Endpoint Program User Manual 87125 Appendix Sample Printouts Ratio Data Test Printout DMPL Lab JF Printed at 14 45 on 22 06 94 Page 10 TEST NO 03 TEST NAME MRX3 PASSWORD WAVELENGTH MODE DUAL TEST FILTER 4l0nm REF FILTER 690nm PLATE ID PROMPT YES MATRIX YES SHAKE NO BLANK MODE AIR 1 2 4 5 6 7 8 9 10 11 12 1 Ti TS 117 125 123 41 149 T57 T65 T73 TEL B 2 T2 T10 T18 T26 T34 T42 T50 T58 T66 T74 782 C NC3 T3 T11 T19 T27 T35 T43 751 T59 T67 T75 NC4 112 T29 T28 T36 T44 152 T60 T68 T76 184 COL TS T13 T21 129 T37 T45 T53 T61 759 T77 T85 F COZ T6 114 T22 T20 138 146 T54 T62 770 78 186 ECI T7 15 T23 T3i T39 T47 155 T63 T71 T79 TS H PC2 TS T16 T24 T32 40 T56 4 T72 T80 T88 EQUATIONS AREA STATISTICS RATIO EQUATION Sample PC 0 9 I U EQUATION Sample 15 Endpoint Program User Manual 87125 135 Appendix B Sample Printout
35. ENTER Scale Graph The SCALE GRAPH option lets you scale the size of the graph up and down If vou do not specify range here the Reader will automatically scale the graph to the standard range SCALE GRAPH 4 45P 30 06 94 YES NO CE Select NO to proceed to sample dilution Select YES to scale the graph The Reader asks for the maximum and minimum points of the x and y axes For example X MINIMUM 4 45P 30 06 94 e ENTER Numbers are entered using the alphanumeric keypad the exponential notation e and the signs are entered by pressing the key below them When each point is correct select ENTER The Reader will increment to the next point for example x minimum to y maximum etc Sample Dilution The Dilution option lets you apply a dilution factor to any of the Test Control or User wells which have been diluted The Reader displays well location and its well type For example Al 1 1 4 45P 30 06 94 ROW COLUMN CLEAR FINISH 62 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing fests Al well location to move to a different well location scroll through the template using the cursor keys _ well type and number replicate number is not displayed e 1 1 dilution of the sample ROW lets you apply the dilution factor you enter to the whole row or part of the row COLUMN iets you apply the dilution factor you enter to the whole column or part o
36. ENTER The value which results from the equation 15 called the value The value which results from the equation is called the value If the and equations are identical for example NC 250 EQN 250 ODs below the value are negative ODs equal to or above the value are positive If the equation is higher than the equation as in an inverse assay for example EQN 0 2 NC PC 0 001 EQN 0 2 NC PC then ODs below or equal to the value are positive ODs above the value are negative WELL inserts a well type identifier Blank Standard Test Control or User well Select B S T or Blank Standard Test or Control to enter a well type or select OTHER to access a second menu If you have changed the name of any user wells refer to the User Wells section in Chapter 4 the appropriate label will be displayed In Threshold equations the well type identifier represents the mean OD of all the wells of that type For example represents the average reading for all the Test welis on the plate Using the keypad you can specify an individual sample using the sample number or an individual replicate using the sample and replicate numbers For example the mean of all Control wells C1 the mean of all C1 replicates 1 1 the OD of the first replicate of Endpoint Program User Manual 87125 47 48 Chapter 4 Creating and Editing Tests OPTIONS in
37. Enter these using the alphanumeric keypad Upper case letters lower case letters and symbols Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Plates Enter these in the following way a Choose upper or lower case letters or the symbols using the up and down direction keys v Scroll through the characters on the display with the left and right direction keys lt gt Enter the character shown by the flashing cursor by pressing the selection key Head Again A1 the end of test processing the option to repeat the test is given READ AGAIN 4 45P 30 06 94 YES NO Select YES to read the plate again or NO to return to the Endpoint menu 5 2 Recalling Plates The Recall option lets you recall data from previously read plates for further processing Plate data is stored after it has been read refer to the Plate ID Prompt section in Chapter 4 Data from up to 100 plates can be stored in the Reader s memory The Reader asks for the plate number and the plate ID For example PLATE 00 P11 4 45P 30 06 94 DIR ENTER scroll through the plates using the up and down cursor keys When the Correct plate 15 displayed select ENTER to recall the plate data Select DIR to print out a list of plates stored in memory When you recall a plate the Reader asks if you want to process the data using the test with which it was onginally run The number and name of the test under which the pla
38. H1 H7 AZ A8 H H12 Endpoint Program User Manual 87125 6 Chapter 4 Creating and Editing Tests 66 CET HALF and 2nd 156 calculates the following differences 7 Al B7 B7 H7 H1 A8 A2 H12 H6 Note Differences are always printed in the lowest well number of the operation For example the result of E2 EI will be printed in and the result of BI Al will be printed in Al The remaining wells that 15 in the examples above E2 and will appear as When you have completed the difference matrix section the display returns to the Output Options menu If you want to end the test select EXIT The Reader will ask if you want to protect the test with a password Refer to the Password section earlier this chapter 4 2 Editing a Test EDIT Copy Select EDIT from the Program menu to edit an existing assay test procedure The Reader will ask you for the number of the test you want to edit TEST 00 4 45P 30 06 94 DIR ENTER CE Select DIR to print a list of the stored tests Use the keypad to type in a test number and then select ENTER If you enter a number for which no corresponding test exists the test number prompt will reappear Re enter a valid test number When a valid test number has been selected you must confirm it For example NAME z RUBELLA 4 45P 30 06 94 COPY STOP ENTER CE COPY Copies the test to another test number STOP Stops editing and saves t
39. If the problem persists contact an approved Service center Make sure that the filters are installed in sequence in the filter wheel and that no slots have been skipped Then check the software setup and make sure the correct number of filters have been specified Filters get dirty and go bad over time Wipe the filters with a lint free cloth then run Calibration or Verification Plate to make sure that the filters are working properly If a filter is bad replace it An incorrectly installed lamp or a faulty lamp may be transmitting enough light Make sure the lamp is properly installed refer to Fitting the Lamp and Optical Filters in Chapter 2 in the Microplate Reader User Manuai If it is change the lamp to see if that will resolve the problem The optic assembly may not be pushed all the way inside the Reader If you just changed the lamp make sure it is fitted correctly and that the rear panel is back on Troubieshooting Guide 87125 7 section 1 Error Messages Filter n Bad Gain selection error 8 Hardware not present Incorrect Format Invalid Mode Invalid byte size Invalid Copy One of the filters is faulty or not installed n refers to the filter number Check that the filters are installed in the correct filter holders Check the filter for dirt or fingerprints and clean it carefully using a lint free cloth If the problem persists replace the filter Refer to
40. If you want to end the test select EXIT The Reader will ask if you want to protect the test with a password Refer to the Password section earlier this chapter Threshold Limits The threshold matrix will determine if your samples are Negative Positive Double Positive Triple Positive or if they fall between the Negative and Positive Equivocal The threshold limits are determined by entering either a specific number OD value or an equation floating cut off using well types and options The Reader prompts you as follows Everything less than this entry will be labeled denoted as negative Everything greater than or equal to this entry yet less than value will be labeled or denoted as positive Everything greater than or equal to this entry vet less than the value will be labeled or denoted as positive HEQN Everything greater than or equal to this entry will be labeled or denoted as positive Example 1 OD s that are less than 0 200 are negative and OD s greater than or equal to 0 200 and less than 1 000 are a 4 positive and OD s greater than or equal to 1 000 show a strong positive EQN 0 1999 4EQN 0 2000 EQN 1 000 Endpoint Program User Manuai 87125 51 52 Chapter 4 Creating and Editing Tests Example 2 Inverse Assays Test samples are negative if they are iower than the Negative Control well and are positi
41. N2 xy Ex When R 1 all data points lie along line of best fit When 2 0 the data points are bighly scattered Once a line of best fit has been established for a set of known Standards the concentration of an unknown sample can be determined for a measured sample as follows C concentration 144 Endpoint Program User Manual 87125 Appendix C Curve Fitting Polygon Fitting The polygon fitting procedure joins successive data points using straight lines ABSORBANCE CONCENTRATION Figure C1 Polygon Fitting Endpoint Program User Manual 87125 145 Appendix C Curve Fitting Non Linear Curve Fitting The remaining fitting routines all produce curves rather than straight line plots The Reader will only calculate one concentration value for each measured variable The user should examine the printed graph to determine if another curve would provide a better fit for the data points Some curves fit functions may not behave as expected if extrapolated beyond the range defined by the data points For example in a particular test the readings for a set of Standards increase in a non linear fashion with increasing concentration The user determines that a quadratic curve fit might give the best fit for such data However at concentrations lower than the concentration of the lowest Standard the curve might turn sharply upwards as shown in Figure C2 ABSORBANCE 0 5
42. TIS 19 T20 T21 122 123 T24 T25 T26 127 128 T29 130 T31 7132 133 134 135 T36 T37 138 T39 740 G 41 142 T44 745 T46 747 148 7409 150 Alternative Format Quadrupie Weli Standards in Columns Replicates in Rows 1 2 3 4 5 6 7 8 9 10 11 12 B S1 Si 51 51 T1 T1 T1 T1 52 52 52 52 T2 T2 T2 12 D S3 S3 S3 S3 T3 T3 T3 T3 54 54 54 54 4 4 T4 14 55 55 55 55 15 5 T5 5 G 56 56 6 6 T6 T6 T6 denotes unused wells denotes unused wells in altemative format 120 Endpoint Program User Manual 87125 Appendix Sample Printouts Directory Of 123 Directory of Plates eene nennen nnn nnne ar nnne aa 124 Directory of 20202 0021 nasa rasa esa 125 Results Matrix Labelled OD Matrix 200 2 0 0 000000 125 Threshold Data Test 0 2 12 126 Threshold Data Results Printout 127 Curve Fit Data Test Printout 128 Curve Fit Data Results Printout tentes 129 Curve Fit Data
43. ____ Ut See OPER Brackets Median of a list of ODs C Standard Deviation _ SD PCI Select OPTIONS STATS Coefficient of Variation CV T Select OPTIONS STATS Well ODs Well type TL NC2 Select WELL Select the well and weli number type and enter the number on alphanumeric keypad Replicate ODs Well 11 2 2 1 Select WELL Select the well type number and PC3 2 type and enter the numbers replicate number alphanumeric keypad Average ODs Well type S Select WELL RR e Sr L Example 1 Positive ODs above 1 0000 must be recorded as positive For the positive equation enter 1 0000 ODs below 0 9999 must be recorded as negative For the negative equation enter 0 9999 Example 2 Positive ODs above the result of Cut off Control 1 plus 0 4 must be recorded as positive For the positive equation enter CO1 0 4 Positive ODs above the result of Cut off Control 1 plus 0 6 must be recorded as double positive For the positive equation enter CO1 0 6 Positive above the result of Cut off Control 1 plus 0 8 must be recorded as triple positive For the positive equation enter CO1 0 8 Negative ODs below the result of Cut off Control 1 minus 0 4 must be recorded as negative For the negative equation enter CO1 0 4 Endpoint Program User Ma
44. a password Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Password When you select EXIT to save test the Reader lets you protect it with a password to prevent unauthorized changes PASSWORD PROTECT 4 45P 30 06 94 YES CE Select YES to enter a password Passwords may be up to 12 characters in length and consist of the following characters Numbers 0 9 and a decimal point These are entered using the alphanumeric keypad Upper case letters lower case letters and symbols Enter these as follows Choose upper or lower case letters or the symbols using the up and down direction keys A v Scroll through the characters on the display with the left and right direction keys lt gt Enter the character shown by the flashing cursor by pressing the A selection key The Reader will ask you to enter the password twice to make sure that it is correct When you have entered the password twice select ENTER The test will be saved and may be edited copied or overwritten if the correct password 1s entered Note The password protection option should be used with caution if you forget the password you will not be able to edit or overwrite the test Contact an approved service centre for advice Threshold Matrix Ouiput Option The threshold matrix is printed as table of symbols denoting OD data threshold matrix section lets you define ranges for positive
45. algorithm since it assumes that the data set is perfect The relevant eguations are given below without explanation S b e X j 1 09 209 ER Bo x p e X4 x a 7 0 X2X Where Difficulties can arise with spline fitting if data is highly erratic or the curve bends sharply severai times The curve may break up at high concentrations see Figure C3 The Reader will not be able to perform the calculations because of numerical rounding errors generated when attempting to fit the curve Using a sem log or log log axis fit rather than a linear fit will reduce this problem curve break ABSORBANCE CONCENTRATION Figure C3 Spline Curve Break Up 148 Endpoint Program User Manual 87125 Appendix C Curve Fitting Other Equations The Reader uses three other types of equation to fit curves to data Michaelis Menten Used to describe enzyme kinetics but its rectangular hyperbolic shape is useful for fitting curves to other types of experimental data Sigmoid A sigmoid 5 shaped curve is typical of many immunological reactions Akima Draws natura looking curve through all the data points Michaelis Menten The Michaelis Menten equation is used to describe enzyme kinetics but its rectangular hyperbolic shape is useful for describing other experimental responses see Figure C4 V LS Figure 4 Michaelis Menten Curve Endpoi
46. and negative ODs If there is a large neutral area between positive and negative you may defme segments within this area the positive cut off value is equal to the negative cut off value you can designate an assay as Inverse You can also use quality control QC equations to specify which Controls will be used and which will be rejected SELECT OPTION 4 45P 30 06 94 THRESH RATIO CURVE DIFF EXIT Endpoint Program User Manual 87125 45 Chapter 4 Creating and Editing Tests 46 To include a threshold matrix select THRESH The Reader asks if you only require QC equations Q C ONLY 4 45P 30 06 94 YES CE Select NO to specify threshold limits before inserting QC equations Select YES to insert QC equations and omit threshold limits Defining the Threshold Ranges Threshold Equations If you choose to use threshold ranges as well as QC equations the Reader will ask you to enter the limits for the positive and negative ranges These ranges are defined by threshold equations The Reader will ask you to enter the negative equation which defines the negative range and then the positive equation which defines the positive range A positive and negative range will always be required but two extra positive levels and are also available These can be used to show how positive each result is Threshold limits can be entered directly as absolute numbers that is a result will be recorded as positive or negati
47. barcode and then begin reading the plate Only barcode scan was included in the test refer to the Plate ID Prompt section in Chapter 4 Reading The test is started the plate 1s read and processed and a results matrix 1 printed if specified Variables Enter a figure for each variable which was specified in the ratio or IU equations Editing Areas Accept or reject wells with very high or low ODs Only if Area Statistics was included in the test refer to the Area Statistics section in Chapter 4 Curve Fit Output Determine if a graph should be calculated and printed and if it should be saved Only if a curve fit option was included the test refer to the Curve Fitting Output Option section in Chapter 4 Test Number Select START to run a test The Reader asks for the number of the test you want to run The name of the displayed test will be shown next to the test number TEST 00 4 45 30 06 94 DIR ENTER Select DIR to print a list of the stored tests Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Plates Use the keypad or scroll to type in a test number and then select ENTER When valid test number has been entered vou must confirm it For example TEST 10 RUBELLA 4 45P 30 00 94 ENTER Select ENTER to confirm and open the test Number of Samples The No of Samples option lets you assign wells samples on the same plate
48. beyond the range defined by data points sample Dilutions Apply dilution factors to test control and user wells i Curve Quality Control Apply a sertes of limits to the curve fit data Limits tu Equation Apply an TU equation 56 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Results Format The Reader asks for the results format RESULT FORMAT 4 45P 30 06 94 CONC TITER CE CONC The Reader will ask you to enter Standard concentrations in concentration values TITER Ihe Reader will ask you to enter Standard concentrations in titer values Stored Curve The Reader asks if you want to use a stored curve USE STORED CURVE 4 45P 30 06 94 YES CE The stored curve function lets you apply the parameters of a previously defined curve to new data Select YES to specify use of a stored curve The Reader will ask for the number under which the curve is stored CURVE 00 4 45P 30 06 94 DIR ENTER Enter the number of the stored curve and select ENTER Select DIR to print a list of all the stored curves ET Note If you have defined Standards in the template the Reader will ask you to enter the concentration of the Standards If you have not defined Standards in the template the Reader will ask you to enter the slope of the curve manually refer to the Slope and Y Axis Intercept section later in this chapter Reagent Concentrat
49. esee eene enne nnne teen 120 Linear Power Fit 2 2 1 11111 eene er ne eani eene 130 Quadratic Power 2220444 ereraa 30 Curve Fit Data eese raseetas 121 Cubic Power 1 nennen ritenere eene LOL Quartic Power 1 2 1 2 41 eren ttem nemine Lod Curve Fit 0 e esee e nnnm ann 132 Cubic Spline 132 Polygon 2 Curve Fit tern nnne atit eun nasa mas s 133 Sigmoid 2 1 41 01 4 4 6 6 0051 60111 Michaelis Menten 2 222 eene 3 Curve Fit 2 41 4 4 2 0000 134 Ratio Data Test 1 1 1 005 55 69 LOD Ratio Data Results 1 esses 136 Difference Data Test 22 22 2 12 20 0 renatus 137 Difference Data Results Printout 138 Area Statistics Test
50. example quartic or splme curve fits Refer to Appendix C Units The Reader asks for the concentration units which were used for the test These units will be printed out on the x axis of the graph UNITS 4 45P 30 06 94 YZ ABCD ENTER Use the up and down cursor keys to access the lower case letters and symbois and the left and right cursor keys to scroll through the characters Press the function key to enter a character or CE to delete a character Use the alphanumeric keypad to enter numbers When the units label is complete select ENTER to accept it Curve Fit Quality Control Limits Quality control limits can be applied to the curve fit data If the curve plotted from the Standards data does not meet the requirements of the quality contro expressions a FAILED message is printed CURVE FIT Q C 4 45P 30 06 94 YES NO CE Endpoint Program User Manual 87125 61 Chapter 4 Creating and Editing Tests Select YES to define values for the limits listed below seat ei et Uma MIN Y INT The minimum intercept of the curve fit plot through the y axis only for linear regression cubic quartic and quadratic fits The maximum intercept of the curve fit plot through the y axis only for linear regression cubic quartic and quadratic fits SLOPE The minimum slope value for a linear fit SLOPE Ihe maximum slope value for a linear fi E LT Enter values and select
51. in the test refer to the Curve Fitting Output Option section in Chapter 4 the Reader will print a table of Standard ODs against concentrations You may choose to print out a graph of this table CO Endpoint Program User Manual 87125 7 Chapter 5 Running Tests and Recalling Plates 80 Several stages are are involved in in determining the output of a test of a test h Determine if a graph should be caiculated and printed Edit Standards Delete and or insert the Standards which are used to plot the graph Save Curve Store the curve so that 1t can be recalled for use with another test If the template contained Standards Reader asks if you want to print the concentration graph obtained by plotting the known concentrations of the Standards against their ODs GRAPH 4 45P 30 06 94 YES NO SCALE Select YES to calculate and plot a graph and then edit the Standards Select NO to edit the Standards first Select SCALE to set the extent of the graph Editing Standards If the template contained Standards the Reader wil ask if you want to edit them EDIT STDS 4 45P 30 06 94 YES NO Select YES to edit the Standards For example STD NO 1 3 4 45P 30 06 94 ENTER CE Use the keypad to enter the number of the Standard you want to edit and select ENTER You must then select which wells you want to include in or delete from the curve fit calculations The Reader will
52. it remains in the same position relative to the end of the plate Columns 1 6 are read as normal but columns 7 12 are recorded as unread wells Template 1 Note control wells in positions 41 and H11 1 2 3 4 5 7 10 18 T24 132 140 TAS 154 172 TS T25 133 141 149 110 118 T26 134 42 I3 Te T35 143 T4 T20 T28 T36 744 T52 173 129 137 T45 14 T22 130 138 146 154 15 T23 T31 T39 4 155 163 c Template 2 Note contro welis in positions Al and H5 1 2 3 4 5 5 1 TG T16 T24 T32 T39 T25 T33 TAD T2 118 T26 T34 T41 111 119 T27 T35 142 T4 Ti T20 T28 T36 T43 T5 113 T21 T29 T37 T44 114 T22 T30 138 45 T7 T15 T23 T31 C2 1746 F G H Plate ID If the plate ID prompt option was included in the test the Reader prompts you to enter an ID for the plate This ID wil be used to store the plate data so that it can be recalled later if necessary Endpoint Program User Manual 87125 77 Chapter 5 Running Tests and Recalling Plates PLATE 4 45P 30 06 94 YZ ABCD DIR ENTER CE Plate IDs may be up to 12 characters in length and consist of the following characters Numbers 0 9 and a decimal point Enter these using the alphanumeric keypad Upper case letters lower case letters and symbols Enter these in the following way Choose upper or lower case letters o
53. n a Sce ide Dz 1 185 1 006 0 170 15 920 0 066 5 000 Se _ EZ 1626 Fz 1 648 1 637 0 015 0 950 0 034 6 000 ET Ge 2 103 amm 1 830 1 967 0 193 9 816 0 055 7 000 Endpoint Program User Manual 87125 129 Curve Data Linear Power Fit Optical Density 0 350 0 300 0 250 0 200 0 150 0 100 0 050 0 000 0 050 0 100 0 500 1 500 2 500 3 500 Concentration ug ml Quadratic Power Fit Optical 2 000 Density 1 500 1 000 0 500 0 000 0 500 0 600 2 000 4 000 6 000 Concentration ug m1 130 Endpoint Program User Manual 87125 Appendix B Sample Printouts Curve Fit Data Cubic Power Fit Optical 1 500 Density 1 000 0 500 0 000 0 500 0 000 1 000 2 000 3 000 4 000 5 000 Concentration ug ml Quartic Power Fit Optical 2 500 Density 2 000 1 500 1 000 x 0 500 0 000 0 500 1 000 3 000 5 000 7 000 Concentration ug ml Endpoint Program User Manual 87125 131 Appendix B Sample Printouts Curve Fit Data Cubic Spline Fit Optical Density 0 350 0 300 0 250 0 200 0 150 0 100 0 050 0 000 0 050 0 100 0 500 1 500 2 500 3 500 Concentration ug ml Polygon Fit RERO Optical Density 0 350 0 300 0 250 0 200 0 150 0 100 0 050 0 000 0 050 0 100 0 500 1 500 2 500 3 500 Concentration ug mi 132 Endpoint Program User Manual 87125 Appendix B Sample Printouts Curve Fit
54. number previously you must use the CLEAR command to clear the previously assigned number before entering a new one Quality Control Equations You can include up to 12 Quality Control QC equations per assay QC equations allow you to specify cnteria for the OD data If these criteria are not met you may choose to abort the assay You can introduce conditions into the equation That is well ODs are accepted or rejected using criteria such as comparison with another specified well or group of wells or the use of a constant The Reader asks if you want to include a quality control equation If you do not require quality control equations select ENTER to move on to the output options section WELL Inserts well type identifiers Blank Standard Test Control or User well into the equation OPTIONS Inserts brackets inequality symbols functions and statistical values into the equation OPER Inserts arithmetic operators into the equation ENTER Saves the equation The Reader checks the equation to test its validity If 1t is not correct the Reader displays it for editing e CE Deletes the character above the cursor or if no character has been added it returns the display to the previous menu Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Use the keypad to enter numbers into the equation Use the left and right cursor keys to scroll the equation left and night acr
55. of the filter that has the shorter distance from the groove to the end is toward the lamp Fit filter blanks into all unoccupied positions Ensure that the retaining springs grip the filter casing and are not bent forwards over the edge of the casing Slide the optics assembly back in if you have an older instrument you must also reconnect the 10 way connector and replace the optics door Attach the lamp connector to back of lamp Microplate Reader User Manual 87125 15 Chapter 2 Installation and Setup Figure 7 Fitting the Lamp and Filters Switching the Reader On Before switching the Reader on note the position of the voltage selector see Figure 3 The position of the selector is very important and must be adjusted to match the line voltage of the mains power supply Position of Voltage Selector Mains Line Voltage 115V 100 120V 230V 200 240V If the voltage selector is not in the correct position refer to the voltage selector discussion in The Reader Back Panel earlier in this section DO NOT place any objects or stand within 150mm of the front of the Reader as this will obstruct the plate carrier 1 sure that the instrument is switched off The power switch is ON when it is flush with the front panel and OFF when it stands out from the panel 2 For PR1100 Readers insert a Reader program disk into the floppy disk drive 9 Insert the power cord supplied into the socket at the rear o
56. specify that each reading is repeated a number of times and averaged into a single result For example to set the repeatability mode to repeat only STX241ETX The Over limit 1 used to set a range within which ODs should fall ODs above the limit will not be processed The limit is also used as an Under limit to set the negative limit of the range For example to set the Over limit to 3 500 and the Under limit to 3 500 STX 2 5 3 500 ETX 3 Filter Select STX 3 A B ETX 15 an ASCH number 0 1 or 2 Set sample filter 1 Set reference filter 2 Set mode B is an ASCI number 1 to 6 which identifies each filter Alternatively if A has been set to 2 set mode the ASCI numbers 0 and 1 represent single and dual wavelength modes respectively Filters Installed STX33ETX 106 Endpoint Program User Manual 87125 Chapter 7 Computer Control This command transmits the list of filter wavelengths as installed in the instrument The system supplies the data in the form 410 450 490 570 630 ETX separated by spaces 4 Blank Modification STX 4 BC D ETX is an ASCU number 0 to 5 Reset blank value to zero no additional arguments necessary Reset blank matrix to zero Defined blank matrix will be used 1 1s set as blank initially if matrix 1 not previously defined The next and subsequent readings are blanks until reset amp Ww Set matrix of blank values defined by the following argumen
57. the case of Spline Polygon Akima and Power modes data is transformed before curve fitting is performed Refer to Appendix For Sigmoid 4PLC and Michaelis Menten functions the best fit is calculated using untransformed data Select SIGMOID to define any of the four parameters of the sigmoid 4PLC curve FEX PARAMETERS 4 45P 30 06 94 LOGIT YES NO CE Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests LOGIT lets you fix just the A and D parameters YES lets you fix all four parameters Select LOGIT or YES to alter parameters A value for the relevant parameter will be displayed Select ENTER to accept this value or CE to change it Numbers are entered using the alphanumeric keypad the exponential notation e and the signs are entered by pressing the key below them Parallel Line Parallel line bioassays are used to calculate relative dosages between a set of BioassayS upto 12 curves A set of Standards defines the standard curve and sets of Test wells of identical size define the additional test curves If the test and standard curves are parallel the test data is valid Dosages can be determined from the position of the test curves relative to the standard curve The following conditions must be met for a parallel line bioassay to be available as a curve fit option Standard curve There must be at least two Standards and the Standards must be in double triple or quadruple replicates
58. the plate or adjacent rows or columns SUBTRACT 4 45 30 06 94 HALF ADJ 64 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Half HALF subtracts the reading in one half of the microplate from the readings in the other half of the plate The Reader will ask for the row column orientation of the difference matrix SUBTRACT 4 45 30 06 94 COLUMNS ROWS CE COLUMNS Sets the microplate halves as columns 1 to 6 on one side and columns 7 to 12 on the other ROWS Sets the microplate halves as rows to D on one side and rows E to H on the other Adjacent ADJ subtracts the readings in adjacent rows or columns from each other The Reader will ask for the row column orientation for the difference matrix SUBTRACT 4 45P 30 06 94 COLUMNS ROWS CE Select COLUMNS to subtract adjacent columns from one another or ROWS to subtract adjacent rows from one another Subtraction Order The order of the subtraction for rows columns or halves must be specified SUBTRACT ORDER 4 45P 30 06 94 1st 2nd 2nd 1st CE COLUMN and 1st 2nd calculates the following differences 1 2 3 4 5 6 7 8 9 10 11 12 COLUMN and 2nd 1st calculates the following differences 2 1 4 3 6 5 8 7 10 9 12 11 ROW and Ist 2nd calculates the following differences A B C D E F G H ROW and 2nd ist calculates the following differences B A D C F E H G HALF and ist 2nd calculates the following differences Al A7 B1 B7
59. the section on Changing the Optical Filters in the Reader User Manual Contact an approved service center An error has occurred in the temperature controller communications Contact the service center if the error persists The Reader 15 not correctly installed or not set up correctly in the Configure Reader box Check that the Reader is installed correctly refer to the Reader manual and configured correctly You have tried to load a test or data containing a chinese plate format but the test or data expected a 12x8 plate format Change the plate format using the Settings Configure Reader option You have selected Sigmoid 4PLC curve type with an invalid axis fit The Reader will change your axis fit to Semi Log Press key to continue Check the communication settings and cables Contact the service center if the error persists You have tried to copy a test and given the new test the same number as the original test The original test has now been lost Re write the test and copy it using a different number Troubleshooting Guide 87125 Invalid or unsupported ID Invalid shake parameters MATH Error Mathematical Error in an equation Module Not Loaded error nnn No Bulb Optic Channel n Bad Overflow Error Parallel Line Error Troubleshooting Guide 87125 Section 1 Error Messages Check the communication settings and cables Contact the service center
60. this reagent solution in memory and subtract from all subsequent OD readings Refer 10 the Blanking section in Chapter 2 The appearance of the Blanking menu depends on which wells you chose when vou defined the template 1 If your template contains no Blank wells the Reader will offer you air Jast or plate blanking BLANK ON 4 45P 30 06 94 AIR LAST PLATE CE 2 your template contains a total number of Blank wells equal to the sum of the Standard Test and Control wells the Reader will offer you paired blanking PATRED BLANKS 4 45P 30 06 94 YES NO CE If you choose NO the third Blank menu 15 displayed 3 your template contains from 1 to 95 blanks the Reader will offer you average individual row or column blanking BLANK ON 4 45P 30 06 94 INDIV AVERAGE ROW COLUMN CE 4 If 96 blanks were specified whole blank mode is automatically set These blanking modes are described in the sections below Air Blanking The Reader uses the absorbance of air as a reference level for 100 transmission This is the default blank mode Blank wells do not need to be specified in the template when using this mode Jf you choose this mode the display will move on to the Start mode menu Endpoint Program User Manual 87125 33 Chapter 4 Creating and Editing Tests Last Blanking Last blanking lets you use the blank value from the previously read plate If last mode is used after a test using whole mode the whole
61. to specify the standard format Heplicales Standards and Test wells can be arranged in groups of one to four replicates These replicates are averaged into a single value The Reader will ask how many replicates the wells must be arranged in For example 5 WELLS IN 4 45P 30 06 94 ENTER CE in 1 2 3 or 4 using the keypad and select ENTER Orientation of well type is arranged in replicates you must indicate whether these Replicates replicates are to be positioned along rows or down columns REPLICATES IN 4 45P 30 06 94 COLUMNS ROWS CE COLUMNS Positions replicates down the columns ROWS Positions replicates along the rows Endpoint Program User Manual 87125 2 Chapter 4 Creating and Editing Tests Well Type Orientation The Reader then asks whether the next well 1s to be positioned down the column or along the row T WELLS IN 4 45P 30 06 94 ENTER CE Enter replicates desired for test 3 WELLS IN 4 45P 30 06 94 COLUMNS ROWS CE Select COLUMNS to position the next well in the next available space down the column or select ROW to position the next well in the next available space along the row Note Test wells are entered just as standards are entered When Test wells and Standards have been specified the Reader assigns al the wells automatically The Reader will then ask you to confirm that the template 1 correct TEMPLATE CORRECT 4 45P 30 06 94 YES LIST CE Select YES to accept
62. values of absorbance can be obtained as long as equal volumes of Blanks Standards and Test samples are dispensed into wells of equivalent size and shape 2 3 Blanking The Reader Jets you subtract a reference value from all the ODs It automatically uses air as a reference but for certain applications other reference levels may be more appropriate For example you may want to eliminate the absorbance of a reagent solution from the test result The Reader can hold the OD of this reagent solution in memory and subtract it from all subsequently read ODs Blanks may be single wells or an average of wells Endpoint Program User Manual 87125 Chapter 3 Installation 3 1 Installing Endpoint in a PR 1100 Reader esses 13 3 2 Re Installing Endpoint a PR 2100 Reader 14 3 3 Upgrading from a Previous 2 14 3 4 Upgrading Assay Protocol Files in the PR 2100 15 Endpoint Program User Manual 87125 11 Chapter 3 Installation This page is intentionally left blank 12 Endpoint Program User Manual 87125 Chapter 3 installation CAUTION This installation procedure assumes that the Reader has been installed correctly and that the voltage selector is on the correct setting Refer to the Microplate Reader User Manual for instructions Note Before installing the Endpoint Program make a working co
63. wheel and replace with the new one Make sure the side of the filter that has the shorter distance from the groove to the end is toward the lamp Make sure the retaining springs grip the casing of the filter and are not bent forwards over the edge of the casing 5 Slide the optics assembly back in if you have an older instrument you musi also reconnect the 10 connector 6 Replace the optics door and reconnect the power supply 36 Microplate Reader User Manual 87125 Chapter 4 Maintenance Figure 11 Changing the Optical Filters Note If you install new filters you should run the test plate software Be certain to run PARAMS to establish new baselines Microplate Reader User Manual 87125 37 Chapter 4 Maintenance 38 Microplate Reader User Manuai 87125 Appendix Self Test Diagnostics Appendix A Self Test Diagnostics On power up and optionally before every read the Reader performs several self tests These cover A D Status Begins conversion and checks that the status line goes high and low that hardware can be detected and chosen Gain Selection Selects gain and compares with check back circuit results Additional hardware check Photodiode Selects all photodiodes and compares with check Selection back circuit results e Additional hardware check Plate Motor Moves the plate to Out position and then to the In position e Veri
64. you are using Refer to the Barcode Program User Manual Try scanning other barcodes of the same and different types If the problem persists contact an approved service center fault has occurred in the interface between the barcode scanner and Revelation Switch the Reader off and on again If the problem persists contact the service center data file has been corrupted If the file contains setup parameters or directory information the Reader will rebuild the file whilst displaying a rebuilding message If the file is a test plate data or a curve data file you will have to recreate it Check the communication settings and cables Contact the service center if the error persists Troubleshooting Guide 87125 section 1 Error Messages Curve File Error The Reader could not find the file required Recreate the file Curve Fitting Error An error has occurred when trying to calculate a curve fit Check your plate data and curve fit parameters Device already open Check the communication settings and cables Contact the service center if the error persists Device not open Check the communication settings and cables Contact the service center if the error persists Diode selection error Contact an approved service center Directory File Error The Reader could not find the directary file required The Reader will rebuild this file whilst displaying a rebuilding message Divide by Zero Error
65. you have set up the Barcode software in the Main menu refer to the Barcode User Manual This option only appears if the Barcode software is installed Shake Time and Shake Modes The Reader asks if you want to specify a shake time SHAKE 4 45P 30 06 94 ENTER CE If you insert a shake the Reader will shake the plate for the required time before reading it This will ensure that the reagents in the welis are completely mixed To insert a shake enter a number of seconds and select ENTER Minimum 1 second maximum 59 seconds If a shake is not required enter 0 seconds and select ENTER Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests If you have specified a shake time the Reader asks vou to specify a shake mode SHAKE MODE 4 45P 30 06 94 1 2 3 USER CE Select 1 2 or 3 to use one of the standard shake modes or select USER to specify your own shake parameters e Shake mode 1 The Reader will shake the plate for the specified time at a frequency of 14Hz 1Hz and an amplitude of 1 7mm e Shake mode 2 The Reader will shake the plate for the specified at a frequency of 9Hz 1Hz and an amplitude of 3 0mm Shake mode 3 The Reader will shake the plate for the specified time at a frequency of 852 4 1Hz and an amplitude of 3 0mm User shake Intended for experimental purposes only and will not mode produce the exact amplitude and frequency specified
66. 059 15 43 31 08 94 10 60 0060 16 42 31 08 94 11 61 0061 17 12 31 08 94 12 62 0062 17 13 31 08 94 13 63 0063 17 13 01 09 94 14 64 0064 08 43 01 09 94 15 65 0065 08 45 01 09 94 16 66 0066 09 03 01 09 94 17 67 0067 09 04 01 09 94 18 68 0068 09 09 01 09 94 19 69 0069 09 11 01 09 94 20 70 0070 09 52 01 09 94 21 71 0071 09 57 01 09 94 22 72 0072 09 58 01 09 94 23 73 0073 10 00 01 09 94 24 74 0074 10 02 01 09 94 25 75 0075 10 18 01 09 94 26 76 0076 10 18 01 09 94 27 77 0077 10 42 01 09 94 28 78 0078 10 43 01 09 94 29 79 0079 10 45 01 09 94 30 80 0080 10 47 01 09 94 31 81 0081 10 48 01 09 94 32 82 0082 10 50 01 09 94 33 83 0083 10 52 01 09 94 34 84 0084 11 18 01 09 94 35 85 0085 11 19 01 09 94 36 86 0086 11 56 01 09 94 37 87 38 88 39 59 40 90 41 91 42 92 43 93 44 94 45 0045 15 18 03 08 94 95 46 0046 15 19 03 08 94 96 47 0047 14 48 04 08 94 97 48 14 50 04 08 94 98 49 14 58 04 08 94 99 Endpoint Program User Manual 87125 Appendix B Sample Printouts Directory of Curves DMPL Lab Printed at 14 45 on 22 06 94 Page 3 CURVE DIRECTORY 00 01 02 03 04 05 06 07 08 09 10 11 12 13 14 15 16 1 7 18 19 Results Matrix Labelled OD Matrix 1 2 3 4 5 6 7 B 9 E 51 54 T T5 T9 117 T21 T25 BLANK 0 888 1 707 0 264 0 001 0 001 1 337 1 354 0 083 0 000 5 000 B1 54 1 Ti T5 T9 T13 T17 T21 T25 T29 33 ELANK 0 976 0 277 0 000 0 919 1 483 0 002 0 066 1 239 0 000 0 933 C
67. 119 Alternative Format Single Weli Standards in Rows 2 120 Alternative Format Quadruple Well Standards in Columns Replicates MENSEM 120 Appendix B Sample Printouts e 121 Directory of Tests casar s rrr sen ce 123 Directory of 402 2 0 00200 nete neret 124 Directory of Curves 125 Results Matrix Labelled OD Matrix 22 00 20 eher nnns 125 Threshold Data Test Printout 126 Threshold Data Results Printout 2 2 2 2 4 2 4122 Curve Fit Data Test Printout anta anre ris 128 Curve Fit Data Results 0 2010 129 Curve Fit Data ee une ne nene nns 130 Linear Power Fit ccs sa LIQ Quadratic Power cceeseeecsscseecceesecaeesenessaceessrsneseneesccercateseespeecessees Curve Fit 131 Cubic Power Fit eese ase Quartic Power 0 2 2 Curve Fit
68. 12 responses without data 115 uncontrolled transmission 113 Data storage 4 Define template prompt 24 Difference matrix output option 64 66 adjacent 65 half 65 subtraction order 65 66 Directories printing 69 E Editing a test 66 68 editing test options 67 editing the output options 68 editing the template 67 making a copy of 66 Endpoint Program See also the Reader User Manual features and specifications 3 menu 19 menu language 3 program load time 4 results output 4 version number 90 Wavelength modes 4 individual blanking mode 34 Installation of Endpoint in a PR 1100 11 re installing Endpoint in PR 2100 14 Uninstall option 91 inverse assay 47 50 52 L Last blanking mode 34 linear regression 144 Linear regression calculation mode 8 Menu language 3 Menus 89 Menus option 9 short menus 89 Michaelis Menten curve fit 4 58 81 Michaelis Menten equation 149 50 Microplate Reader 3 See also the Reader User Manual checksum algorithm 102 clock function 3 computer control commands 102 11 curve fitting algorithms 143 data format 111 13 data storage 4 handshaking 100 101 hardware specification 97 linking with an Apple Macintosh 99 linking with an PC 98 99 main menu 19 plate identification 3 short cut test selection 3 soitware specification 100 tests per plate 3 Multiple wavelength mode 8
69. 1997 Software versions Main Menu 2 02 Single Board 1 33 Multi Board English 8 360 87364 sanofi PASTEUR Chis document is copyright of DYNEX TECHNOLOGIES INC and must not be copied or reproduced in any form without pnor consent DYNEX TECHNOLOGIES reserves the right to make technical improvements to this equipment and documentation without prior notice as part of a continuous program of product development This manual supersedes all previous editions MS 0052 Licensing This product contains software licensed from Microsoft Corporation 1 The PR2100 contains intellectual property that is software programs that are licensed for use by the end user customer hereinafter referred to as the end user This is not a sale of such intellectual property The end user shall not copy disassembie or reverse compile the software program The software programs are provided to the end user as is without warranty of any kind either expressed or implied including but not limited to warranties of merchantability and fitness for a particular purpose The entire risk of the auality and performance of the software program is with you 5 DYNEX TECHNOLOGIES INC and its suppliers shall not be held to any liability for any damages suffered or incurred by the end user including but not limited to general special consequential or incidental damages including damages for loss of business profits business interruption l
70. 1s intentionally left blank 32 Microplate Reader User Manual 87125 Chapter 4 Maintenance IMPORTANT The first section in this manual contains safety information for all the equipment in the system You should be familiar with this information anyway but if not you must read through this section before carrying out any maintenance The warranty on the Reader may become void if vou do not follow the safety and maintenance instructions contained in this manual or ifthe covers are removed by anyone other than approved service personnel pum 4 1 Routine Maintenance Procedures The Reader requires very little maintenance however certain simple procedures should be cared out on a regular basis On a daily basis e Verify self test passes Remove the microplate from the plate carrier wipe the plate carrier down and return it to the In position Wipe down the external surfaces Section 4 2 contains more detailed cleaning instructions On a weekly basis Review the results of the self test that occurs when you switch the Reader on to make sure the instrument 1s functioning correctly If you want to retain this information for your records print out the self test results see Appendix A for a sample or save them to a file Back up the data files for PR1100 remove the disk and back it up using the File Manager program on an external PC On a yea
71. 32 D 73770 Denkendorf Germany Tel Mid 01093460 Fax 9 910108 934 6311 NOTICE TO OUR CUSTOMERS Addendum To PR Series Reader User Manual Affecting Chapter 2 Installation and Setup under Fitting the Lamp and Filters The Filter Blanks must be fitted into the unoccupied filter positions in the Filter Wheel Ensure the Filter Springs are around the sides of the Filter as shown in the top diagram The Springs must not extend past the rear face of the Filter bottom diagram Otherwise the Self test will fail due to Filter Motor Errors Correct Filter Spring Positioning View of Filter Wheel from filter spring side Incorrect Filter Spring Positioning 99001740 DOC Rev CERTIFICATE COMPLIANCE DYNEX Technologies certifies that PR2100 Serial No 1CXD is YEAR 2000 compliant according to the following definition Definitions Definitions Year 2000 Compliant DYNEX Technologies has adopted the following definition of Year 2000 compliance as set forth by the British Standards institute in DISC PD2000 1 The definition of Year 2000 conformity Requirements available on the Internet at http www bsi org uK disc year2000 2000 html has the qualification that the upper limit for compliance is the Year 2035 Year 2000 conformity shall mean that neither performance nor functionality is affected by dates prior to during and after the Year 2000 In particular Rule 1 No value for current da
72. 33 0 110 0 342 0 065 1 390 0 036 0 093 0 826 9 380 0 035 0090 1 660 1 193 1 132 0 978 1 371 1 423 0 849 0 036 1 348 0 036 1 443 0095 1 682 0 105 1 760 60754 1 114 1 143 1 145 1 656 0 035 1 335 0 372 G 0 340 2 137 0 920 0 302 1 247 0275 0 034 0 098 0 036 0 290 0 077 0 345 0 346 1 864 0 035 1 311 1 111 1 495 0 084 0 281 1 004 0 888 0 113 0 998 i 2 3 4 5 8 7 8 9 10 11 12 0 998 1443 40 017 0 063 0 845 Bids B 0 076 PERSE 027 wee 86 0564 0 064 1 239 0 197 C 091 1 592 0204 1315 mw 0797 1 056 D 41390 1123 diii 0 257 hee 1 354 0 733 say 0 345 1 570 0 061 M 052 0 574 AAEE 4 2112 44 407 3 587 He 4055 HUP 0360 0272 1 621 0 963 sete G 1 797 0 618 1209 sh 0 064 0254 0 269 4 518 2406 0084 0 207 gases 0116 it 0886 Sis INDICATES VALUE OUT OF RANGE INDICATES COMBINED DATA 138 Endpoint Program User Manual 87125 Appendix B Sample Printouts Area Statistics Test Printout AREA STATISTICS YES l 2 3 4 5 5 7 8 9 10 11 12 0 1 2 3 B 1 2 3 0 1 2 3 D Q 1 2 3 E 0 1 2 3 0 1 2 3 0 1 2 3 1 2 3 Area Statistics Results Printout VALID WELLS MEAN S D C V S E M AREA 0 B 0 775 0 69 89 07 5 0 05 AREA 1 8 0 690 0 51 74 03 0 02 AREA 2 8 0 709 0 62 87 15 0 04 AREA 3 8 0 598 0
73. 51 55 Po 6 Ti4 7118 722 T26 T30 0 005 0 946 0 057 1 459 0 076 0 283 0 305 1 621 0 056 0 863 1 1 D 1 55 PO T2 16 710 4 718 122 T2 T30 0 004 1 186 1 199 0 076 0 308 0 051 1 358 0 002 0 059 0 792 0 346 52 56 NC1 T3 t7 T T15 T19 T23 T27 0 055 1 626 1 159 1 098 0 945 1 337 1 389 0 815 0 062 1 314 2 56 T3 17 T11 T15 T19 T23 727 T 0 061 1 648 0 071 1 726 0 720 1 080 1 109 1 381 1 622 0 001 1 301 G 53 57 T4 TS Tt2 T16 T20 T24 T32 0 306 2 103 0 826 0 268 1 443 0 241 0 000 0 064 0 002 0 H 53 57 NC2 T4 Tt2 T16 T20 T24 0 312 1 830 0 001 1 277 1 077 1 161 0 050 0 257 0 970 1 2 3 4 D 6 7 9 INDICATES VALUE OUT OF RANGE INDICATES COMBINED DATA zx C4 HF BS 63 9 61 CE C2 D YS Endpoint Program User Manuai 8 125 125 Appendix B Sample Printouts Threshold Data Test Printout DMPL Lab Printed at 14 45 22 06 94 Page 6 TEST NO 01 TEST NAME MRX1 PASSWORD WAVELENGTH MODE SINGLE TEST FILTER 410nm REF FILTER PLATE ID PROMPT NO O D MATRIX YES SHAKE NO BLANK AVERAGE 1 2 3 4 5 6 7 8 9 10 11 12 NCL T9 17 T25 133 T49 157 T65 1773 T81 NC2 T2 T10 6 T34 142 150 T58 166 T74 T82 NC3 T3 711 19 T27 T35 T43 151 759 167 75 783 T4 T12 T20 T28 T36 144 T52 T60 T76 T84 COL T5 Tis 121 T29 T37 T45 T53 T61 T69 T77 T85 T6 14 T22 T30 T38 T46 T54 T62 T70 T78 T86 PCL T7 T15 T23 131 138 T47 155
74. 71 T72 T73 3775 THe T78 TH TsO 181 182 T83 4 gt Single Well Standards in Columns 2 3 4 5 6 7 8 9 10 11 12 51 Ti 19 T25 T33 T49 157 765 T73 52 12 TIO 142 T50 T58 T66 T74 53 T3 T27 7135 143 151 759 T67 T75 T83 54 T4 112 0 T28 T36 144 52 T60 7168 T76 T84 55 I5 T21 129 T37 T45 T53 T61 T69 T77 T85 56 114 122 T30 T38 746 154 162 T78 T86 57 T7 Ti5 23 131 139 147 155 3763 T79 7 58 T8 7 4 T32 T40 148 T56 T64 T80 T88 gt Endpoint Program User Manual 87125 117 Appendix Examples of Plate Formats Double Well Standards in Rows Replicates in Columns 1 2 3 4 5 6 7 9 10 11 12 51 52 3 54 55 56 57 58 59 510 511 512 51 52 53 54 55 56 7 8 59 510 511 512 2 5 T6 17 18 T9 TIO T12 Ti T3 T4 T5 T6 T7 T8 T12 13 5 6 TIS T19 120 121 122 T23 T24 4 TIS T18 T21 122 723 T24 T25 T26 127 T28 T29 T30 T31 132 T33 135 T36 T25 T26 T27 T28 T29 T30 T31 T32 T33 T34 T35 T36 w gt Double Standards Columns Replicates in Rows 1 2 3 4 5 6 7 8 9 10 11 12 Sl SI T9 19 Tl 125 125 133 T33 52 52 T 3 T2 TiO Ti8 T18 T26 T34 T34 53 53 T3 13 Til Tii 119 T19 127 127 T35 T35 54 54 T4 T4 2 112 T20 T20 128 128 T36 T36 55 55 5 5 T2 T21 729
75. 74 75 Test Number 20 21 Tests printing 68 69 Tests per plate 3 Threshold matrix output option 45 52 threshold limits 51 52 159 U W Upgrading Wavelength modes 4 30 32 assay protocol files in a PR 2100 Wavelength Modes 7 8 15 16 Well location calculation mode 8 from a previous version of Well types Endpoint 14 15 blank standard test or control 24 User Wells 27 creating new 27 Utihty menu orientation 25 accessing the 28 replicates 25 manual mode 88 89 Whole blanking mode 35 Utility Menu 87 93 LX Variables 79 Version number of Endpoint Program 90 160 Endpoint Program User Manual 87125
76. DIFF option 4 3 Printing Tests LIST Select LIST from the Program menu to print a test on connected printer Select the number of the test you want to print TEST 00 4 45P 30 06 94 DIR ENTER Select DIR to print a list of the stored tests Use the keypad to type in a test number and then select ENTER If you enter number for which no corresponding test exists the test number prompt will reappear Re enter a valid test number When a valid test number has been selected you must confirm it For example TEST 10 RUBELLA 4 45P 30 06 94 DIR ENTER Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tesis Select ENTER to confirm the test the test will be printed 4 4 Printing Directories DIR Select DIR from the Program menu to print the directory of Up 0 100 stored assay test procedures Upto 100 plate IDs Up to 20 stored curves DIRECTORY OF 4 45 30 06 94 TESIS PLATES CURVES CE Select TESTS PLATES or CURVES to print the appropriate directory Endpoint Program User Manual 87125 69 Chapter 4 Creating and Editing Tests This page is intentionally left blank 70 Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Plates Chapter 5 Running Tests and Recalling Plates 5 1 Running a Test 74 Number of Samples
77. ENTER CE Passwords are up to 12 characters in length and may consist of upper and lower case letters symbols numbers and a decirnal point These are entered using the display and the alphanumeric keypad Refer to the Password section later in this chapter the password 1s correct the Reader overwrites the test and asks you to enter the test name If the password is incorrect a PASSWORD ERROR message 15 displayed and the display returns to the Endpoint menu Test Name Once a valid number has been entered the Reader requests a name for the test NAME 4 45P 30 06 94 YZ ABCD ENTER CE Test names may be up to 12 characters in length and consist of the following characters Numbers 0 9 and a decimal point These are entered using the alphanumeric keypad Upper case letters lower case letters and symbols Enter these as follows a Choose upper or lower case letters or the symbols using the up and down cursor keys v Scroll through the characters on the display with the left and right cursor keys gt Enter the character shown by the flashing cursor bv pressing the function key below it Example To assign the name TEST A4 to test number 4 1 TEST 00 prompt select 04 and then select ENTER 2 Atthe NAME prompt press the lt or gt key till the letter T is indicated by the flashing cursor press the key to enter the letter Move to the letter E with the key and press th
78. ER 410 nm TIME 16 14 PLATE2 REF FILTER gt OPERATOR CALCULATION MODE ENDPOINT AVERAGE BLANKS Al 0 034 Bl 0 034 AVERAGE BLANK 0 034 1 2 3 4 5 6 5 9 10 11 12 BLANK 0 588 1 707 AOE sik de ee R BLANK 0 976 6 27 DPI C 43 005 0 9465 0 067 STILI LETTE FOR E Eo T ak e e ITI ee E D 0 004 1 186 1 193 k sia acie e pe afte ke me kkk 0 056 1 626 1 159 0 051 1 648 0 071 OK EE see e wok ese e FERRE aa RII G 0 306 2103 0 886 ako oie e ak aht e cae FOCI IIT H 0 312 1 830 0 001 se sk sie i ni we oe LEET E CURVE FITTING LINEAR POWER FIT WITHOUT TAILS Y 0 0587 0 0224 X R SQR 0 5136 STANDARDS LABEL LOC Q D MEAN amp D C M S E M CONC PRED CONC Sem RROR 51 C1 0 005 1 001 0 053 D1 0 004 0 005 0 001 15 713 0 051 1 000 52 Et 0 055 0 751 52 432 1 0 061 0 059 0 004 65 044 0 028 2 000 53 551 0 305 0 255 91 503 0 312 9 309 0 004 1 373 0 045 3 000 54 2 088 4 4 4 420 B2 0 976 0 932 0 062 6 677 0 083 4 000 Ss c2 J 3 m
79. ERA Threshold Matrix Output 49 Ratio Matrix Output Option ctc Curve Fitting Output 2 22 2221 5 Difference Matrix Output Option 2 64 4 2 Editing a Test 66 Copy V Editing Tests Options RENE T 4 3 Printing Tests LIST 68 4 4 Printing Directories 69 Endpoint Program User Manual 87125 i Table of Contents Chapter 5 Running Tests and Recalling Plates 71 5 1 Running 2 2 1 22 001 74 Belin AREE Number of Samples gt BO Plate ID 2 22044202020000111 77 Barcode Scan DEMNM 78 Variables MERE 79 Editing enarrare nnne nnne mener Curve Fit 79 Read 83 5 2 Recalling 4 2121 111 11 1 2 1 0 41 600 83 Chapter 6 85 h Utility MOI RARE 87 ET ES ET
80. Endpoint Program User Manual 87125 63 Chapter 4 Creating and Editing Tests Results Table The Reader asks if a table of Curve Fit results should be printed in the results output TABLE OF RESULTS 4 45P 30 06 94 YES NO CE GET Note If the test already contains a number of processing options the file may become very large and difficult to process if you also include a curve fit table If the test crashes when you run it try removing the curve fit table and running the test again When you have cornpleted the curve fit section the display returns to the Output Options menu If you want to end the test select EXIT The Reader will ask if you want to protect the test with a password Refer to the Password section earlier in this chapter Difference Matrix Output Option The Difference Matrix is a table of data showing the differences ODs between subsequent rows or columns of wells or between one half of the microplate and the other SELECT OPTION 4 45P 30 06 94 THRESH RATIO CURVE DIFF EXIT To include a difference matrix select DIFF Note If a difference matrix is inserted into the test all subsequent output options will use the difference matrix results The Reader asks if the test is using an alternative format template ALT FORMAT 4 45P 30 06 94 YES NO CE Select YES if you are using a non standard format that is not a 8x12 format The Reader will ask whether you want to subtract halves of
81. Format MR700 extended MRX Memory Menu Heset Select MEMORY from the Setup menu to access the Memory menu which allows you to reset the Reader memory or to upgrade the software SETUP MEMORY 4 45 30 06 94 RESET UPGRADE CE To upgrade the Reader follow the instructions provided with the upgrade disk The RESET command resets the Reader s default settings overwriting all user defined setup parameters The Reader will ask you to confirm this action ARE YOU SURE A45P 30 06 94 YES NO CE Select YES to reset all the Reader s parameters or NO to return to the Memory menu Upgrade The UPGRADE option allows you to upgrade the Reader with a software upgrade disk Only Reader application software obtained from your supplier should be used with this command If you are upgrading the Main menu Setup software refer to Upgrading From a Previous Version in Chapter 3 in the Endpoint Program User Manual Microplate Reader User Manual 87125 25 Chapter 2 Installation and Setup 26 Param Menu Select PARAM from the Setup menu to access the Parameters menu and view the OD limit data conversion plate type and repeatability settings Over Limit Data Conversior The Over limit is used to set a range within which ODs should fall ODs above the limit will not be processed The limit is also used as an Under limit to set the negative limit of the range For example If 3 500 is set as the over limit ODs
82. IL Lets you carry out a manual operation display the software version number define calculation modes and set menus PROGRAM Lets you create and edit assay test procedures While the Main menu or the Endpoint menu is displayed the plate carrier can be moved and out using the up and down cursor keys The up key moves the plate carner in the down key moves it out Note lf short menus have been selected using the Util menu up to tests may have been given short cut keys These will appear at the ENDPOINT READY display for example ENDPOINT READY 4 45P 30 06 94 TESTI TESI2 TESTS ENDPOINT The left and right lt gt cursor keys may be used to scroll along the list of tests and to access tests five to eight Refer to the Menus section in Chapter 6 The Utility Menu The Utility menu lets you carry out a plate read view the software version number of the Endpoint Program select long or short menus and carry out further data calculation Select UTIL from the Endpoint menu Endpoint Program User Manual 87125 87 Chapter 6 Utilities 88 ENDPOINT READY 4 45 30 06 94 OTHER MANUAL MENUS VERSION Select OTHER to access a second Utility menu ENDPOINT READY 4 45P 30 06 94 BACRUP STATS BATCH SPECTRUM CE Note If you are using a PR 1100 Reader the Backup option will be replaced by a C V option In the PR 2100 Reader this option is incorporated into the Stats option MANUAL Lets you
83. OCEED Lets you edit the Standards refer to the Editing Standards section earlier in this chapter Endpoint Program User Manual 87125 81 82 Chapter 5 Running Tests and Recalling Plates Sigmoid 4PLC Process When sigmoid 4PLC curve fit is being processed the Reader continuously updates the residual error value for the curve This value measures how well the sigmoid curve is progressing The lower the number the better the progress of the sigmoid RESIDUAL 0 1093 4 45P 30 06 94 ABORT If the residual value is too high you may abort processing and edit the Standards Curve Saving The curve you use can be saved for later use Refer to the Stored Curve section in Chapter 4 SAVE CURVE 4 45P 30 06 94 YES NO Select YES to save the curve The Reader asks for a number under which to store the curve CURVE 00 4 45P 30 06 94 DIR ENTER Up to 20 curves be stored print the directory of stored curves select DIR Use the keypad to enter a number for the curve and select ENTER If you enter existing curve number the Reader asks if you want to overwrite the curve or choose another number For example OVERWRITE 1 4 45 30 06 94 YES NO Once you have entered an available number you must enter a name 4 45P 30 06 94 YZ ABCD ENTER Curve names may be up to 12 characters in length and consist of the foliowing characters Numbers 0 9 and a decimal point
84. PGRADE CE 4 Select UPGRADE The Reader will prompt you to insert the Upgrade working disk and then the Endpoint disk if you are using a PR 1100 Reader 5 Reader 15 upgrading your disk it will come across filenames which are already being used on your disk When this happens it will display a message asking if you want to overwrite the old file If your disk contains pre defined PR Assay Data files You may have changed some of the pre defined assay data or curve files and want to keep the changes rather than overwrite them Select YES to overwrite files you do not require for example TXT EXE and INF files plus any assay curve and data files that you do not need Select NO to leave intact any files you want fo keep If you do not want to keep any of the pre defined assays select ALL to overwrite them all with the new assays files If your disk does not contain pre defined PR Assay Data files The upgrade disk will only overwrite the redundant executable and text files so you should select ALL to upgrade to the new version This will not affect the Reader s ability to open files created in a previous version on the software 6 When the upgrade is complete remove the disk from the disk drive You can access the Endpoint Program in the usual way 3 4 Upgrading Assay Protocol Files in the PR 2100 From time to time an assay protocol file upgrade disk may be supplied This disk will upgrade the library of assays ava
85. POINT to view the Endpoint menu ENDPOINT READY 4 45P 30 06 94 START RECALL UTIL PROGRAM CE START Lets you min assay test procedures which have been created using the Program menu RECALL Lets you recall data obtained from a previous assay test procedure for further processing UTIL Lets you carry out a manual operation display the software version number define calculation modes and set menus PROGRAM Lets you create and edit assay test procedures While the Main menu or Endpoint menu is displayed the plate carrier can be moved in and out using the up and down cursor keys The up key moves the plate carrier in the down key moves it out CS Note If short menus have been selected using the Util menu up to 8 tests may have been given short cut keys These will appear at the ENDPOINT READY display for example ENDPOINT READY 4 45P 30 06 94 TEST1 TEST2 TESTS TEST4 ENDPOINT The left and nght lt gt cursor keys may be used to scroll along the list of tests and to access tests five to eight Refer to the Menus section in Chapter 6 Endpoint Program User Manual 87125 19 Chapter 4 Creating and Editing Tests 20 4 1 Creating New Test NEW To create a new assay test procedure or edit an existing one select PROGRAM from the Endpoint menu The Program menu appears ENDPOINT READY 4 45 30 06 94 NEW EDIT LIST DIR CE e NEW Creates a new assay test procedure EDIT Modifies or copies an ex
86. S T C Assigns the well location to a well type Blank Standard Test or Control e USER Lets you create well types and then assign these to wells UTILITY Displays a Utility menu of tools which help you to define the template FINISH Saves the template Returns the display to Template menu B S T C Wells Select B S T C to assign Blank Standard Test or Control wells Al 4 45P 30 06 94 Si Select B1 51 T1 C1 to assign well location Al to a Blank Standard Test or Control well If you want to start with a different well location you can scroll through the wells using the cursor keys 24 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Heplicates Each sample of a well type can be arranged in groups of one to four replicates You can specify that each sample of a well type will contain the same number of replicates or that some samples will contain different numbers of replicates mixed replicates B WELLS IN 4 45P 30 06 94 MIXED ENTER CE If vou want to assign all the samples of this well type the same number of replicates type in the number of replicates on the keypad and select ENTER If you want to assign some samples in different numbers of replicates select MIXED and then seiect ENTER you select mixed replicates the Reader will ask you for the number of replicates in the first sample after you have specified the orientation of the re
87. T29 T37 T37 S6 56 716 T6 14 122 122 130 139 738 57 57 TT T 115 115 123 123 131 131 739 T39 58 58 178 T8 T16 124 T24 132 T32 7140 740 gt 118 Endpoint Program User Manual 87125 Appendix A Examples of Plate Formats Triple Well Standards in Rows Replicates in Columns 1 2 3 4 5 6 7 8 9 10 11 12 51 2 53 54 S5 56 57 58 59 10 511 512 5 52 53 54 55 56 57 58 59 10 511 512 51 52 53 54 55 56 57 58 59 10 511 512 T2 T3 14 T5 TS 19 10 T2 T3 T4 T5 16 T8 19 Tli T2 T3 14 T6 T8 19 d du q q so A FPO gt Triple Well Standards Columns Replicates in Rows 7 8 9 10 1 12 T9 19 1 2 3 4 6 12 T10 TiO 118 Tis 13 14 5 51 51 51 52 52 52 72 53 53 53 13 T3 7119 54 54 54 112 112 T20 T20 T20 5 55 55 15 TS 15 Tis 121 124 5 56 56 16 716 6 114 122 122 72 7 S7 5 7 317 5 5 T23 123 T233 58 58 58 5 1 T8 T24 T24 124 we Endpoint Program User Manual 87125 119 Appendix Examples of Plate Formats Alternative Format Single Well Standards in Rows 1 2 3 4 5 6 7 9 10 1 12 3 51 52 53 54 55 56 57 8 S9 SIO 12 13 14 15 16 TF 19 10 D Tii TIS
88. TATS Each well of a well type NCi Select OPTIONS Vijf Well type and i PCi Well ODs Well type T1 82 Select WELL Select the well and well number type and enter the number on the alphanumeric keypad 11 2 2 1 Select WELL Select the weil type and enter the numbers the alphanumeric keypad type number and replicate number mE Average ODs Well type T NG PC See WELL MinimmOD Select OPTIONS FUNCTION Maximum OD Max S1 __ Select OPTIONS FUNCTION phiru Examples of equations are shown below Example 1 Template includes 3 Negative Controls and 2 Positive Controls If any Negative Control OD 1s more than 2590 higher or lower than the mean of all the Negative Controls it must be rejected For QC1 enter 0 75 NC lt NCi lt 1 25 NC If more than one Negative Control OD is rejected the test fails For QC2 enter valid NC gt 2 Endpoint Program User Manual 87125 43 Chapter 4 Creating and Editing Tests Example 2 The average of the Negative Control ODs must be more than 0 5 For QC3 enter gt 0 5 The average of the Positive Control ODs must be less than 20 of the average of the Negative Control ODs For QC4 enter PC 0 2 NC Template includes 4 Negative Controls and 2 Positive Controls If any Negative Control OD 1s more than three times higher than the sum of the other three it must be r
89. UAGE AASP 30 06 94 ENGLISH FRANCAIS DEUTSCH ITALIANO OTHER Select one of the languages displayed by pressing the function key directly below it or select OTHER to access the Spanish option LANGUAGE 4 45 30 06 94 ESPANOL CE To select Spanish as the display language press the function key below ESPANOL The menus will then be displayed in Spanish Filters Menu The Filters menu allows you to install new filters and enter filter wavelengths Select FILTERS from the Setup menu to display the number of filters installed OF FILTERS 2 4 45 30 06 94 ENTER Microplate Header User Manual 87125 19 Chapter 2 Installation and Setup 20 ENTER Confirm the number of filters shown CE Clear the number of filters and enter new number Minimum 1 filter Maximum 6 filters Once the number of filters has been entered the Reader prompts you to enter the wavelength of each filter in turn Note When installing new filters remember that the filter with the lowest wavelength should be in position 1 on the filter wheel and so on in ascending order of wavelength The Reader will display Filter 1 and a wavelength for example FILTER 12410 nm 4 45P 30 00 94 ENIER CE Select ENTER to confirm the wavelength shown and move on to Filter 2 Select CE to clear the wavelength shown and enter a new wavelength Press ENTER When wavelengths have been entered for all the filters installed the display
90. Under no circumstances does the PR series Reader have any direct patient contact or perform therapeutic patient function Specific diagnostic results are not provided by the device Diagnostic decisions are made only after independent confirmation additional methods under the supervision of a qualified professiona WARNING If this equipment is used in a manner not specified by the manufacturer then the protection provided by the equipment may be impaired Before using any decontamination method except those recommended by the manufacturer users should check with the manufacturer that the proposed method will not damage the equipment This page is intentionally left blank Contents Table of Contents About This Safety Information ee ETL LLL N 3 Symbols ee te sese nne eese Chapter 1 Features of the Reader 7 Chapter 2 Installation and Setup 9 2 1 Installation tene ennt nente en nennt 11 Unpacking Reader 222
91. User Manual 87125 Chapter 6 Utilities RESTORE Copies the data files held on floppy disk onto the Reader hard disk UNINSTALL Removes the Endpoint Program from the Reader hard disk Note Before using the Backup or Restore commands make sure that you have a blank disk labeled Back up in the floppy disk drive Note The Uninstall command should be used with caution You will not be able to restore the Endpoint Program onto the hard disk unless you have a copy of the Endpoint disk If you are upgrading the Endpoint Program use the Memory upgrade command in the Main menu refer to the Upgrading from a Previous Version section in Chapter 3 C V This option 15 replaced by the Backup option on PR 2100 Readers refer to The Utility Menu section earlier in this chapter To use the C V option refer to the Coefficient of Variation section below Stats Fhe Stats option checks the repeatability of laboratory procedures and calculates statistical data for all stored plates This option incorporates both Stats and C V option on PR 2100 Readers refer to The Utility Menu secton earlier in this chapter ENDPOINT READY 4 45P 30 06 94 C V STATS CE Coefficient of Variation C V The option checks that the readings from a selected group of plates have an acceptable variation You may step through all the plate data files stored 1n memory and the Reader asks if you want to include each in CV check For exam
92. above 3 5 will not be stored and will be printed as OVER ODs below 3 5 will be printed as UNDER The Reader will display the current Over Limit Select ENTER to confirm the value shown and move on to the Param Plate Type menu Select CE to clear the value shown and enter a new value Minimum 0 000 Maximum 4 000 Note Take care when setting the Over limit if it is too low valid test results may be rejected The normal limit is 3 500 If the Over limit is altered the Reader asks if ODs which lie outside the range should be assigned a conversion value for use in quality control equations If no value is assigned to these ODs the OC equations which contain them will substitute five asterisks for a well which is marked as OVER DATA CONVERSION 4 45 30 06 94 YES ENTER CE Select YES to enter a value for Over and Under ODs or select NO to define the plate type The Reader will ask for the Over value followed by the Under value For example OVER VALUE 29 999 4 45 30 06 94 ENTER CE Enter Over and Under values and select ENTER Min Over value 0 000 Max Over value 9 999 Min Under value 9 999 Max Under value 0 000 Plate Type Two types of plate format can be used with the Reader One is the standard 12 rows by 8 columns format and the other is the 10 rows by 4 columns format or the Chinese plate format The Reader will display the current plate type setting Microplate Reader Us
93. al operation display the software version number define calculation modes and set menus PROGRAM Lets you create and edit assay test procedures While the Main menu or the Endpoint menu is displayed the plate carrier can be moved and out using the up and down cursor keys The up key moves the plate carrier in the down key moves it out Note If short menus have been selected using the Util menu up to 8 tests may have been given short cut keys These will appear at the ENDPOINT READY display for example ENDPOINT READY 4 45P 30 06 94 TEST TEST2 TESTS TEST4 ENDPOINT The left and right lt gt cursor keys may be used to scroll along the list of tests and to access tests five to eight Refer to the Menus section in Chapter 6 Endpoint Program User Manual 87125 73 74 Chapter 5 Running Tests and Recalling Plates 5 1 Running a Test Option The START options let you operate the Reader using previously created and stored assay test procedures Several stages are involved in running a test Test Number Select the test to be run TEE n M Number of Samples Select the number of wells on the plate to be assigned to each test Plate ID Apply an ID to the plate being used the Reader will store the plate data under this name Only if plate ID prompt was included in the test refer to the Plate ID Prompt section in Chapter 4 The Reader will scan the
94. and 16 wells are assigned Test2 The templates are arranged in rows The Reader will use the first 20 wells that is Al to B8 for 1 It will use the next 16 wells that is B9 to C12 for Test2 76 Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Plates Leaving wells you assign less than 96 wells the Reader will try to reduce the template unassigned X taking into account the wells you defined when you created the test It does so by removing Test and if necessary Blank wells from the end of the template until the required number of wells is left Control Standard and User wells are left in the same positions you defined relative to the last full column or row on the plate If is not possible using this method to reduce your template to the correct number the Reader will print an error message and it will not reduce the template Hows and Jf you arrange the template in rows the Reader will reduce the template Columns upwards from Row If you arrange the template in Columns the Reader will reduce the template backwards from Column 12 Example Wells and Hil are Controls and the remaining wells are Test wells Using the No of Samples option 48 wells are assigned to Testi and using the Any More Samples prompt the rest of the wells are left unassigned The template is reduced in terms of columns The Reader will relocate the second Control well formerly Hil to H5 so that
95. assigned or chosen more than one test the Reader will ask if you want to arrange the test templates in columns or rows WELLS IN 4 45P 30 06 94 COLUMNS ROWS CE See the sections below on how the Reader runs more than one test on a plate and reduces templates Note If you have arranged your template rows you should reduce it in rows If you have arranged it in columns you should reduce it in columns You should not include tests on the same plate if they were arranged in different orientations For example one test was arranged in rows and one was arranged in columns a Note If you want to see how the template has been reduced your test must include Data matrix with labels Running you assign wells to more than one test the Reader will assign the wells to than One Test tests in the following way on a Plate If you selected ROWS ihe first block of wells assigned to the first test will be placed in the first wells on the pjate reading along the plate from Al toA12 B1 to B12 etc If you selected COLUMNS the first block of wells assigned will be placed in the first wells on the plate reading down the plate from Ai to A2 to H2 etc The Reader counts all wells along the columns or down the rows until it reaches the number you specified It then moves on to the second block of wells for the second test and so on Example Using the No of Samples option 20 wells are assigned to
96. ation OPTIONS Inserts brackets functions and logarithmic functions into the equation OPER Inserts arithmetic operators into the equation ENTER Saves the equation The Reader checks the equation to test its validity If it is not correct the Reader displays it for editing Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests e Deletes the character above cursor or if no character has been added it returns the display to the previous menu Use the keypad to enter numbers into the equation Use the left and right cursor Keys to scroll the equation left and right across the display Use the up and down arrows to move to the start and end of the equation When you have entered the ratio equation the Reader moves on to the IU equation ff you do not want to enter an IU equation or after you have finished the IU equation select ENTER Ratio and IU equations may be up to 50 characters in length and may be used to scale the data up or down WELL inserts a well type into the equation RATIO EQN 4 45P 30 06 94 8 OTHER Select B S or C Blank Standard Test or Control to enter a well type or select OTHER to access the User wells In RATIO equations the well type identifier represents the mean OD of all the wells of that type For example T represents the average reading for al the Test wells on the plate Using the Keypad you can specify an individual
97. ber of rows in the reduced matrix 110 Endpoint Program User Manual 87125 Chapter 7 Computer Control This command be used to reduce the size of the matrix For example if only 40 wells are needed for a test a reduced matrix of 5 columns by 8 rows could be used 7 6 Data Format The following conventions are used for data format b represents a space ASCH 20H XX represents a numeric value 0 12 of the X well position right justified and with leading space if necessary y represents the Y position is the home Y position ASCH 40H q represents the sign of the number Space for positive values and minus sign for negative ASCII 2DH u represents an underline ASCII 5 cr represents carnage retum ASCH represents the number of the reference filter used means reference filter not applicable S represents sample filter number represents numeric value Response with Data There are three different possibilities for data streams that may be sent by the Reader when under computer control Single Value This occurs when the single filter mode is selected and a single well read and Read Mode transmit command has been issued The following data stream will result Normal Head This is normal operation where the whole plate is read after the start Mode command has been issued The data stream is divided into two parts a header and a body The header 1
98. connected to the Reader using the interface cable shipped with the instrument This 1s a ribbon cable terminated a standard IEEE Centronics style 36 way connector see Figure 8 Figure 8 Printer cable connector Centronics Microplate Header User Manual 87125 29 Chapter 3 Printer Interface The table below shows the relevant pin assignments 30 Signal Name STROBE DATA 1 DATA2 DATA 3 DATA 4 DATA 5 DATA 6 DATA 7 DATA 8 ACKNLG BUSY PE SLCT Not Used Not Used Not Used Not Used Signal Name _ GROUND GROUND GROUND GROUND GROUND GROUND GROUND GROUND GROUND GROUND GROUND INIT Not Used Not Used Not Used Not Used Not Used Microplate Reader User Manual 87125 Chapter 4 Maintenance Chapter 4 Maintenance 4 1 Routine Maintenance 2 2 2 2 1 2 60121000001101000 4488 33 4 2 Cleaning 33 AWLOCIAVING tenis satin sitae OF External Painted and Plastic Surfaces 222 22 1 0 1 eene e nene OF 1 c RM 34 34 4 3 Repacking 34 4 4 Replacing the 35 4 5 Changing the Optical Filters 02220 36 Microplate Reader User Manual 87125 31 Chapter 4 Maintenance This page
99. contains multiple replicates Endpoint Program User Manual 87125 41 Chapter 4 Creating and Editing Tests Example valid PC gt 3 The number of valid PC wells that is those which pass the quality control FUNCTION Inserts a function into the equation Valid Inserts a validity expression that is valid well type identifier expression equations must be greater than or equal to 3 or the test fails quality control Max Min Represents the maximum minimum OD on the plate or within a group of wells The group of wells may be a well type or a sample if it contains multiple replicates Example 1 Min T1 The lowest OD of all replicates of Test sample 1 Example 2 Min The lowest OD on the plate Represents a variable which must be entered at runtime Five variables are allowed per test Example variablel You will have to enter this number at runtime 42 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Equation Components A summary of the components which can be used in quality control equations is shown below together with a route showing you where to find them from the Equation menu Example unen Keypad Arithmetic Operators Median of alist of ODs median T Select OPTIONS STATS Standar Deviation SDcCD Select OPTIONS STATS Coefficient of Variation Select OPTIONS S
100. d potentially lethal voltages are contained within If any fault occurs with the Reader for which you cannot find an explanation in this manual contact the nearest approved service center immediately Troubleshooting Guide 8 125 1 About This Manual This page is intentionally left blank 2 Troubleshooting Guide 87125 Section 1 Error Messages Section 1 Error Messages The Reader carries out a series of self tests immediately after it is powered up Failure of some of these tests does not necessarily stop the Reader from working Two types of failure can occur fatal and non fatal errors e Self Test Fatal Errors some fatal errors may prevent the Reader from working completely Others will display a warning message but allow the self tests to continue If the Reader displays fatal error message switch the Reader off and disconnect it from the main power supply Contact the nearest approved service center for help and advice Self Test Non fatal Errors these will allow the Reader to carry on operating but the Reader s measurements will be subject to certain restrictions The Reader generates a number of messages during normal operation However if a fault occurs the Reader may display an error message These messages are designed to help you locate the cause of the problem and they often suggest possible solutions If the problem persists contact an approved service center Error Message Prob
101. d by PROCESSING and SAVING PLATE messages 78 Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Pilates Note While the plate is being read do not block the front of the machine as the plate carrier will move to the Out position so that vou can remove the plate Variables If any variables were specified in any equations the Reader asks you to enter a figure for each variable For example VARIABLE 1 4 45 30 06 94 ENTER Enter a value for each variable and select ENTER The Reader will not store the values you enter here If you want to run the test again using the same variable values you shouid make a written record of the values and store them safely Editing Areas If the Area Statistics option was included in the test refer to the Area Statistics section in Chapter 4 the Reader will ask if you want to edit these areas You may eliminate wells with very high or very low ODs EDIT AREAS 4 45P 30 06 94 YES NO Select NO if the readings are as expected these are printed out on the results matrix Select YES to remove specific well ODs from the calculations EDIT WELL 4 45P 30 06 94 ENTER Use the alphanumeric keypad to enter a well location and select ENTER The well will be omitted from the calculations Repeat the process for each well location Select ENTER on its own to finish editing the areas Curve Fit Output if a curve fit option was included
102. d matrix Slope and Y Axis Intercept If you have not defined Standards in the template only linear regression is available You will have to input the slope of the line and the Y axis intercept point manually SLOPE 4 45P 30 06 94 e ENTER CE Minimum 0 0001 maximum 12200 Enter the value for the slope using the keypad and select ENTER The Reader wiil ask for the Y axis intercept point Y INT 4 45 30 06 94 e ENTER CE Minimum 0 000 maximum 1e200 Enter the value for the slope using the keypad and select ENTER Axis Fit The Reader asks for the type of axis fit required This option lets you choose how data is fitted onto the axes of the printed graph AXIS FIT 4 45P 30 06 94 LINEAR SEMI LOG LOG LOG AUTO CE LINEAR Linear scales for both axes SEMI LOG Uses a2 logarithmic scale for the x axis e LOG LOG Uses a logarithmic scale for both axes AUTO The Reader selects the best axis fit automatically only available for the linear regression quadratic cubic and quartic fits Note For Sigmoid 4PLC curve fit you should use a Semi Log axis fit Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Tails The curve shown on the printout can be extrapolated beyond the values defined by the test data by selecting the tails option USE TAILS 2 4 45P 30 06 94 YES NO CE This option should be used cautiously particularly with the higher order polynomial for
103. display a prompt for each replicate well of the chosen Standard For example 1 DELETE 4 45P 30 06 94 YES NO Note If the replicate has been previously removed from the Standard the Reader will ask if you want to re include it Endpoint Program User Manual 87125 Chapter 5 Running Tests and Recalling Plates O D 1 INCLUDE 4 45P 30 06 94 YES Select YES to include or deleie the dispiayed replicate When all replicate wells of a particular Standard have been displayed the EDIT STDS prompt will be re displayed Edit any remaining Standards as required Select NO at the EDIT STDS prompt to finish editing The display will return to the GRAPH prompt and you may choose to print the concentration graph again When all the necessary Standards have been edited the Reader re processes the results Too Few curve cannot be calculated because there are not enough Standards the Standards following error message is displayed TOO FEW STANDARDS 4 45P 30 06 94 The following table summarizes the number of Standards required for the various curves Too Many Jf acurve contains some Standards which are making it very uneven the Standards Reader will display a Multi Valued Curve error message This gives you the option to edit the Standards and remove the ones which are making the curve uneven ABORT Abandons the curve fitting processes and continues with the next part of the test PR
104. e key to enter the second letter 3 Repeat this process for the other letters unti the name is complete and the number 4 on the keypad 4 Select ENTER to record the name Endpoint Program User Manual 87125 21 22 Chapter 4 Creating and Editing Tests Plate ID Prompt If a plate ID prompt is inserted into the assay test procedure the Reader will ask you to enter a plate ID when the plate is read PLATE ID PROMPT 4 45P 30 06 94 YES YES NO BARCODE NO BARCODE CE At runtime the Reader will ask you to enter a plate ID prompt This ID will be used to label the unprocessed plate data for storage and you can use it to recall the plate data if necessary If you do not assign an ID the Reader will assign a default one the Reader has a total capacity of 100 plates default IDs are numbered 0000 0099 unless you have assigned IDs of your own In this case there will be less default IDs available Once the Reader reaches its 100 plates capacity it reuses all the available default IDs overwriting the plate data they hold It begins at 0000 and works upwards until all the default IDs are used up again It does not inform you when it begins overwriting old plate data If yon intend to recall plate data at a later date you should always insert a plate ID prompt or a barcode scan At runtime the Reader wil look for a barcode on the side of the microplate To use this option make sure that
105. e Reader e Storage of assay test procedures and microplate data on 3 5 floppy disk drive or hard disk Modular internal design making it quick to service and repair e Barcode option Test plate option Temperature Control option 8 Microplate Reader User Manual 87125 Chapter 2 Installation and Setup Chapter 2 installation and Setup 2 1 Installation LL Unpacking Reader oo 11 The Reader Back 1 2 12 The Reader Front Panel eee esee an nnne nennen nnne nen i4 The Keypad and Display rhet etae tasas ternas 14 Fitting the Lamp and Optical 15 Switching the Reader te sett ra nh nhi 16 Switching between DOS Applications 2 2 Setup Procedures s esee es eeeee nana nena tentent nean nn nre nent 18 Setup 19 Filters Menu LD Clock Menu MV System 0 42 4 4 4 21 Maintenance 23 Comms MEDU MEE 24 Memory eseeeeeeeeseceesese seen sa moreno atate sse ate 9 Param M
106. e ratio matrix section the display returns to the Output Options menu If you want to end the test select EXIT The Reader will ask if vou want to protect the test with a password Refer to the Password earlier in this chapter Endpoint Program User Manual 87125 55 Chapter 4 Creating and Editing Tests Curve Fitting Output Option The curve fitting routines can be used to interpret data ODs are quantified by comparing them to a concentration graph which is constructed from the concentrations and ODs of Standards The curve fit section lets you specify which type of graph is used and other conditions about how the data is to be treated SELECT OPTION 4 45P 30 06 94 THRESH RATIO CURVE DIFF EXIT To include a curve fit select CURVE Several stages are involved in defining a curve fit TF on Results Format Select the results format for the curve concentration or titer Use Stored Curve Use a previously defined and stored curve Reagent Concentration Enter the reagent concentrations used 1n the Standard wells Standards are defined in the template Curve Fit Type Select a curve fit type if Standards are defined in the template Slope Enter the slope and the y axis intercept of the curve if Standards are not defined in the template Axis fit Select the type of scale to be used forthex and y axes of the printed graph Use Tails Extrapolate the curve
107. efer to the Microplate Reader User Manual for more information The Reader powers The line voltage setting 1s incorrect or the up but does not access Reader is defective the disk drive Switch the Reader off and adjust the voltage setting If the problem persists contact the service center The Reader powers The disk is corrupt or not one of the Reader s up but only accesses disks the disk drive briefly Try using the backup disk If this does not work contact an approved service cenier Readings in rows F Stray light may be entering the reading G and H are compartment unusually low Check that plate carrier door closes correctly The hardware and Verify that you have changed the floppy disk software setup you were using Setup options are stored with options have been the software programs So every program you lost are running may have different setup option Speaker beeps several A fatal self test error has occurred times in succession The Reader will probably crash When it does power up restart it and count the number of beeps which occur on power up Contaci an approved service center informing them of the number of beeps Troubleshooting Guide 87125 15 Section 2 Solving Problems 11 Printing Problems Printing Problem The Reader produces an unrecognizable printout Results are printed on the night of the page overlapping each other The Reader reverts to No Printer mode each t
108. ejected For enter 4 NC NCi gt NCi If more than two Negative Control ODs are rejected the test fails For QC2 enter valid NC gt 2 The average of the Negative Control ODs should not be greater than 0 2 However if the average of the Positive Control ODs is greater than 0 7 then average Negative Control ODs of up to 0 3 will be accepted For QC3 enter If PC gt 0 7 then NC lt 0 3 elseNC lt 0 2 The average of the Positive Control ODs must be more than 0 5 For QC4 enter gt 0 5 Inserting Output Options Into Test The output options command gives vou a choice of various data processing options SELECT OPTION 4 45P 30 06 94 THRESH RATIO CURVE DIFF EXIT THRESH Inserts a threshold matrix into the test which lets you define the ranges for positive and negative results and to perform quality control checks on the Control well ODs RATIO Inserts a ratio matrix into the test which lets you transform the ODs of Control and Test wells into different unit measurements CURVE Inserts a curve fit section into the test which lets you plot a graph of Standard ODs against concentrations DIFF Inserts a difference matrix into the test which lets you calculate the difference between ODs from two sets of wells For example the top and bottom halves of a microplate EXIT Results are output in the form of a results matrix only The test is saved and the Reader asks if you want to protect the test with
109. en read Wells are read in the order Al to HI A2 to 2 etc Average Blanking Average blanking averages the chosen series of wells into a single blank value which is subtracted from each well OD on the plate 34 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Paired Blanking In paired blanking one blank 1s associated with each Test Standard or Control well The blank may consist of one well or the average of a series of replicates The total number of blank values must be equal to the total number of all the wells PAIRED BLANKS 4 45P 30 06 94 YES NO CE e NO If paired blanking ts not selected the next display offers the individual and average blanking menu YES Blanks are assigned to different types of wells in the following order Standards Tests Controls Positive Controls Negative Controls Cut off Controls Positive Reference Controls Example For a plate with 3 S 5 C and 8 T wells 16 Blanks are required Blanks I 3 will be assigned to Standard wells 1 53 Blanks 4 11 will be assigned to Test wells T T8 Blanks 12 16 will be assigned to Control wells C5 Whole Blanking Whole blanking mode shouid be used in conjunction with last mode The Reader reads the plate and holds memory an average of all 96 ODs If last mode is selected for the next test this average blank value is subtracted from each OD on the next plate Row Blanking In row blanking B
110. endix B Accessories for reference Filter 630nm 87119 6329780630 Filters 3 Pack 450 490 620 87109 13000600 Filters 6 Pack 87114 13000610 405 450 490 550 620 630 Lamp UV shipped standard with 87128 6360408002 single board unit PR Dust Cover 87380 9119780012 PR Lens Cleaning Cloth 87108 41000070 PR Quick Servicing Guide Service 87121 99000500 Manual singie board RS 232 Filter 9 way D Connector 7122 50400380 SDP Endpoint Software for PR2100 87379 04000261 SDP Endpoint Software for PR1100 04000391 Test Plate 12 way UV 450nm 87127 00140010 with Manual Insert and Software 2 0 Test Plate Software version 2 0 for use 87124 04000400 with single board unit only 04000410 Microplate Reader User Manual 87125 41 Appendix Accessories US Power Cord 87129 6090405009 User Manual version 2 0 87125 99001720 42 Microplate Header User Manual 87125 Appendix Specifications Appendix C Specifications Software Specifications Menu language English French German Italian Spanish Clock function Day date and time DOS Software Endpoint program option Agglutination program option Program Load Time Using PR1100 40 seconds Using PR2100 1 second Hardware Specifications Keypad 2 key tactile membrane Display 2 line by 40 character backlit LCD No of fiiters 2 6 Performance Read cycle time Single Wavelength 4 seconds Dual Wavelength 6 seconds Microplate Reade
111. ent contact an approved service center Warning Although this instrument is fully insulated and earthed grounded ii 15 Electric important for users to be aware of the potential hazard of using liquids in Shock close proximity to an electrical supply If any liquids are spilled disconnect the Hazard instrument from the mains electrical supply immediately and clean the liquid up DO NOT reconnect the electrical supply until the instrument has been fully inspected by an approved service engineer Take when using non rigid non standard microplates as spillages are more likely to occur To switch this instrument off press the power switch on the front panel Remove the mains power cable from the socket on the rear panel Warning Operating this equipment in ways other than detailed in this manual may impair Incorrect the protection provided by the instrument Operation DO NOT operate this equipment with the covers removed as potentially lethal voltages are contained within DO NOT operate this equipment with the safety earth ground disconnected e DO NOT install unauthorized cards spare components or accessories as this may impair the safety of the Reader and will invalidate its warranty e DO NOT place any objects or stand within 150mm of the front of the Reader as this will obstruct the plate carrier DO NOT overfill the microplate wells as this may lead to liquid contamination of the wells and impa
112. entered Enter the correct password If vou cannot remember the password vou will have to re enter the test Contact the service center Try repeating your last command and contact the service center if the error persists The Reader could not find the file you asked for Recreate the file An incorrectly installed lamp or a faulty lamp not be transmitting enough light Make sure the lamp is properly aligned refer to Fitting the Lamp and Optical Filters in Chapter 2 in the Microplate Reader User Manual If it is change the lamp to see if that will resolve the problem The reference holes on the plate carrier located at Al and H12 may be dirty or obstructed Blow air through the holes and remove any obstructions Make sure the sprint clips are not bent The Reader cannot start the Plate Motor Check for obstructions to plate carrier movement and whether any of the plate carrier index holes are blocked then press any key If the plate carrier is stuck you may carefully attempt to free it by hooking a suitable implement around the edge You typed a well location that does not exist in the correct well location You have entered a value which is out of range Enter a valid value Contact an approved service center Troubleshooting Guide 87125 section 1 Error Messages Printer switched off Printer Offline Printer Paper Empty Reader Overheat Set point is below amb
113. enu 20 Microplate Reader User Manual 87125 9 Chapter 2 installation and Setup This page 1s intentionally left blank 10 Microplate Reader User Manual 87125 Chapter 2 Installation and Setup 2 1 Installation CAUTION DO NOT connect the instrument to the mains electrical supply or switch it on before you have completed this installation procedure Unpacking the Reader If you ordered an upgrade you will only receive an upgrade disk and manual The Reader is packed to provide maximum protection during shipment Take care when unpacking it and examine it carefully for any damage Report any damage to the carrier immediateiy Check the contents against the shipping checklist enclosed and report any omissions to your supplier Remove the Reader from the carton and place it on a surface free of dust moisture vibration draughts and away from direct sunlight Keep the packing materials so that they can be used if the Reader has to be transported Figure 2 Example Packing Contents Reader 5 Software disks 2 Manual Set 6 Power Cord 3 Optical Filters 7 Printer Cable 4 Lamp 8 Interface Cable 9 RS 232 Filter not shown Microplate Reader User Manual 87125 11 Chapter 2 Installation and Setup The Reader Back Pane i 1 1 ir ME SCA r Eet
114. er Manual 87125 2 2 Optical Path Figure 3 is schematic diagram illustrating the optica path through the Reader A tungsten halogen lamp projects a light beam horizontally through a heat absorbing filter This beam is focused and passes through a filter located 1n the filter wheel Here the beam 15 separated into 13 channels One of these channels is used as a reference channel to monitor the light output of the lamp The other 12 beams are directed upwards through a row of 12 wells on the microplate onto an array of silicon photodiodes The photodiodes accurately measure the intensity of light transmitted through each well Figure 3 Reader s Optical Path 1 6 Optic Fibres 2 Field Stop 7 Lenses 3 Heat Filter 8 Optic Stops 4 Lens 9 Microplate 5 Filter 10 Photodiodes 11 Reference Diode Endpoint Program User Manual 87125 9 Chapter 2 Understanding the Endpoint Program Effect of Pathlength Light absorption by a material is determined by the Beer Lambert law This states that the Absorbance of Light is directly proportional to the product of Pathleneth and Concentration Pathlength is the distance in cm which the light beam travels through the absorbing material Absorbance is usually expressed in terms of a standard cell of lem pathlength Concentration is expressed as moles per litre of fluid The pathlength through a solution in a microplate well is less than 1 cm But accurate
115. er Manual 87125 Chapter 2 Installation and Setup Select ENTER to confirm the current plate type setting or CE to access the Options PLATE TYPE 4 45P 30 06 94 12x8 10 4 CE select 12x8 or 10x4 to the specify the plate type Repeatability Mode Using the repeatability mode you can specify that each reading the Reader takes is repeated a number of times and averaged into a single result The Reader will display the current repeatability setting Select ENTER to accept the current setting and return to the Setup menu or select CE to enter a different number REPEATABILITY MODE 4 45 30 06 94 ENTER Minimum 1 no reading repeats Maximum 4 Note Repeated readings will require a longer reading time and this option should be used with caution for time critical plate readings Microplate Reader User Manual 87125 27 Chapter 2 Installation and Setup 28 Microplate Reader User Manual 87125 Chapter 3 Printer Interface Chapter 3 Printer Interface If the Reader has been supplied with a printer this printer will be completely compatible with it The following information 15 for users whose printer was not supplied with the Reader printer which communicates through a Centronics paralle printer interface will operate successfully with the Reader Note Once the printer has been correctly installed it should always be switched on before switching on the Reader external printer can be
116. est will fail Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Inserts a conditional expression into the equation The Reader offers if the first time this option is selected then the second time and else the third time However else is optional If condition then expression else expression Example If PC 0 2 then NC gt 0 5 else NC 0 1 If the average of the PCs is less than 0 2 then the average of the NCs must be more than 0 5 or else the average of the NCs may be less than 0 1 Inserts inequality symbols gt gt lt lt into the INEQUAL equations STATS Inserts a statistical value into the equation Represents the median of a group of ODs ODs in the group are listed the median is the OD in the middle of the list If the list contains an even number of ODs the median is the mean of the middle two ODs The group of wells may be a well type or a sample if it contains multiple replicates Example Median PC The value calculated w1ll be the median of all the Positive Contro ODs Represents the standard deviation between the ODs in a group of wells The group of wells may be a well type or a sample if it contains multiple replicates Represents the coefficient of variation between the ODs in a group of wells The group of wells may be a well type or a sample if it
117. et the Plate Type option to Standard format using the Setup menu You wish to recall plate The Reader can store 100 sets of plate ID data you did not assigna and it assigns a defauit plate ID numbered plate ID 00 to 99 for any plates which you do not assign an ID or a barcode Once the Reader reaches capacity it starts overwriting plates stored under default IDs without informing you If the you require has not been overwritten you may be able to find it by printing the directory of plates This will tell you when each set of data was obtained so you can work out which plate ID you need Troubleshooting Guide 87125 17 Section 2 Solving Problems This page 1s intentionally left blank 18 Troubleshooting Guide 87125 PR Microplate Reader Endpoint Program User Manual Manual code 87362 Revision of the manual October 1997 Software versions End Point 2 0 Single Board 1 3 Multi Board English 87360 87364 sanofi PASTEUR This document is the copyright of DYNEX TECHNOLOGIES INC and must not be copied or reproduced in any form without prior consent DYNEX TECHNOLOGIES INC reserves the right to make technical improvements to this product and documentation without prior notice as part of a continuous program of product development This manual supersedes ali previous editions MS DOS Licensing This product contains software licensed from Microsoft Corporation 1 ThePR 2100 contains
118. f the column CLEAR clears the currently displayed dilution allowing vou to enter new one FINISH ends the dilution option If a Test Control or User wel has not been diluted enter 1 1 Jf any samples have been diluted scroll through the template unti you reach well Select clear to delete the 1 1 ratio The Reader will ask for the new dilution Al Tl 1 4 45P 30 06 94 ENTER Enter the new dilution using the keypad For a dilution of 1 volume of reagent to two volumes of diluent enter 1 2 and so on When the dilution factor is correct select ENTER The Reader will return to the dilution prompt To assign the displayed dilution factor to the row vou are in select ROW If you are at the start of a row all the dilutions in that row will be overwritten and replaced with the displayed dilution factor If you are not at the start of the row and you select ROW the dilutions in the well locations after the displayed location will be overwritten and replaced with the displayed dilution factor The COLUMN command works in the same way as the Row command above international Units Equations This option applies an International Units equation to the data LU 4 45P 30 06 94 WELL OPTIONS OPER ENTER CE If you do not require an IU equation select ENTER The curve fitting IU equation is entered in the same way as the ratio matrix IU equation Refer to the Ratio Matrix section earlier in this chapter
119. f the instrument gt Connect the power cord to a suitable power source with protective earth ground Connect the printer cable from the Reader to the printer Switch the printer on Switch the Reader on by pressing the power switch on the front panel Venfy that the Reader completes the self test routine successfully 16 Microplate Reader User Manual 87125 Chapter 2 Installation and Setup Self Tests When the Reader is switched on it carries out several self tests to check that the instrument is working correctly Appendix A shows a list of these tests and sample printout During self tests a series of symbols are displayed on the bottom line of the LCD these indicate the optional extras that are installed in your Reader If the Reader fails any of the tests an error message is displayed If the Reader s data files have been corrupted the Reader requests your serial number this can be found on the Reader s back panel or inside of the floppy disk drive s door an error message persists contact the service center Maintenance Reminder On first power up the Reader may display a maintenance reminder HAVE YOU PERFORMED YOUR MAINTENANCE CHECKS To clear the message press any key The reminder is intended for use by laboratories which routinely verify the operation of their instruments The self test printouts and the frequency of the maintenance reminders may be altered from
120. fies that the plate carrier position sensors are Operating correctly Checks motor and sensors Background Checks for light leakage into the reading Light compartment Verifies that current is flowing through the bulb when it 1 switched on Checks that the bulb has not blown Moves the filter motor to the first position Checks the filter motor and optical alignment Transmission e Verifies that all fibres are capable of transmitting Levels at least 3396 of the maximum transmission level Checks for blocked channels or broken diodes Checks that gains can be selected for all filters Checks for damaged or missing filters Temperature Checks to see of the temperature control hardware Control Is present e Checks that communication can be established with the controller software Microplate Reader User Manual 87125 39 Appendix A Self Test Diagnostics Self Test Sample Printouts SELF DIAGNOSTIC SEQUENCE Reader Serial A340 Technologist Date 14 06 94 Time 08 53 Test 1 A D Pass Test 2 Gain selection Pass Test 3 Photodiode Pass selection Test 4 Plate motor Pass Test 5 Background light Pass levels Test 6 Bulb Pass Test 7 Filter motor Pass Test 8 Transmission levels Pass Test 9 Filters Pass Self Diagnostic Summary Reader Status READY 40 Microplate Reader User Manual 87125 Appendix Accessories App
121. gh the data point The fitted curve will appear smooth and natural and approximates to a manually drawn curve Figure C6 Points joined by the Akima Curve Fit Method The Akima curve fit consists of a set of polynomials which are applied to the set of data points The slope of the curve at each point 1s determined by these polynomials The fit is based the assumption that each data point 15 determined locally by five points The point of interest and two points on either side of it Note The Akima method is discussed more fully in the Journal of the Association of Computing Machinery Val 17 No 4 October 1970 pages 589 602 A new Method of Interpolation and Smooth Curve Fitting Based on Local Procedures Endpoint Program User Manual 87125 153 Appendix C Curve Fitting The slope of the curve Numbering the points 1 2 3 4 5 the slope of the curve at the point of interest point 3 is assumed to be determined by i Im m m Im m m m Where t is the slope of the curve and m1 m2 m3 and m 4 are the slopes of the following line segments 12 23 34 45 interpolating between a pair of points With the slopes of the points determined the portion of the curve between two points is calculated so that the curve passes through both points the slopes at the data points are the same as previously determined portion of the curve 1s expressed as a uniquely deter
122. graphs 56 60 axis fitting 155 B S T C Wells 24 Backup 90 Barcode 22 Barcode scan 78 Batch option 92 Beer Lambert law 10 Blank wells 33 77 92 Blanking 3 10 33 35 air blanking mode 33 average blanking mode 34 column blanking mode 35 individual blanking mode 34 last blanking mode 34 paired blanking mode 35 plate blanking mode 34 row blanking mode 35 whole blanking mode 35 Brackets equations 38 39 40 43 46 48 49 52 53 54 55 Endpoint Program User Manual 87125 C C V See Coefficient of variation Calculation mode 32 Clock function 3 Coefficient of variation 41 43 48 49 91 92 Column blanking mode 35 Computer control commands blank modification 107 8 computer control 110 display control 110 filter select 106 print control 108 9 read mode 106 reduced matrix 110 start stop 304 step x y 103 Constant value calculation mode 8 cubic spline curve fitting 148 curve fitting algorithms 143 Curve fitting output option 56 64 axis fit 60 curve fit output 79 83 curve fit quality control limits 61 curve fit type 58 60 editing standards 80 82 80 82 international units equation 63 printing as graph 80 reagent concentration 57 58 results format 57 results table 64 sample dilution 62 63 scale graph 62 slope and Y axis intercept 60 stored curve 57 tails 61 units 61 157 p Data control response with data 111
123. he following information refer to the Microplate Reader User Manual Safety information Installation and configuration instructions Maintenance instructions For explanations of error messages and possible solutions refer to the Troubleshooting Guide Endpoint Program User Manual 87125 1 About This Manual This page is intentionally left blank Endpoint Program User Manual 87125 Chapter 1 Features and Specifications Chapter 1 Features and Specifications The Endpoint Program is designed for use with the Microplate Reader Figure 1 The Microplate Reader The features and specifications of the Reader can be found in the Microplate Reader User Manual The features and specifications of the Endpoint Program are as follows Menu language Enghsh French German Italian Spanish Blanking Air Last Plate Paired Wells Row Individual Wells Column Average Each well on the Whole Plate Average plate Clock function Day date and time Plate identification Manuat Barcode option Tests per plate 12 Short Cut Test Fight function keys available Selection Endpoint Program User Manual 87125 3 Chapter 1 Features and Specifications Data storage 3 5 1 44Mb floppy disk or optional hard disk drive storage of up to 100 tests 100 plates and 20 curves Program Load Time Using a 1100 Reader 40 seconds Using a PR 2100 Reader 1 second Wavelength Modes Single Dual Multiple Results Output Optical Densi
124. he test ENTER Confirms the test and moves to the next display e CE Cancels the test and lets vou choose another Select COPY to make a copy of the test before editing the original The display prompts you to give the copied test a new number TEST 00 4 45 30 06 94 ENTER Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests If you enter the number of an existing test the Reader will ask if you want to choose another test or overwrite this test For example CLEAR TEST 10 4 45P 30 06 94 YES NO CE YES makes the copy overwriting the old test of that number NO cancels the copy instruction and returns to the TEST NUMBER prompt Noie Do not use the original test number for the copied test If you do the original test will be lost when you select CLEAR TEST and it will no longer exist to be copied If this occurs an INVALID COPY message is displayed Editing Tests Options When a valid number has been entered you must confirm it then you may begin editing the test The Reader displays each step of the test and lets you confirm the step or edit it The first step displayed will be the plate ID prompt ID YES 4 45P 30 06 94 SIOP ENTER CE At any time during editing e STOP Saves the test and returns to the Program menu ENTER Accepts the displayed test step and moves on through the test Lets you alter the displayed test step You can move thr
125. heses are allowed Represents each defined well type Example 1 Each Control C well OD must be within 25 of the mean of the ail the Control weils or that well fails quality control and 1s removed from the calculations You have 4 Control wells defined as C1 C2 C3 C4 The equation is written as 0 75 C Ci 1 25 C Example 2 Referencing Example 1 this time you have two Control wells each with a replicate of 3 defined as C1 1 C1 2 C1 3 and C2 1 C22 C2 3 The equation is written as 0 75 lt 1 1 lt 1 25 and 0 75 C C2 1 1 25 C If you need to have each replicate Control well OD fall within 25 of the mean of just the 1 or C2 s then the equation is written 0 75 CI C14 1 25 CI and 0 75 C2 C2 1 1 25 C2 Also if you cannot accept any replicate wells above the Over Limit see the Reader User Manual the equation 15 written C1 i lt 4 0 or 24 lt 4 0 To fail the equation for any OVER readings in the replicate wells use the Valid statement for example Valid 1 gt 3 and Valid 2 gt 3 Expressions containing i often lead to ODs being excluded from the calculations every OD in a certain well type is excluded and this well type 1s used in another QC equation the QC operation will not work properly For this reason each equation containing the i expression should be accompanied by a valid wells expression This will ensure that if too many ODs are rejected the t
126. ient 4 SING Error Slate Error Test File Error The temperature controHer cannot be found Troubleshooting Guide 87125 The Reader has detected a problem with the printer If necessary select ABORT the Reader will reset all your printer options so vou will have to set these again using the Setup menu refer to the Setup menu section in the Reader User manual Swiich the printer on press the on line button or replace the paper according to the specific instruction Contact an approved service center The temperature controller is set to a temperature 1t cannot achieve Make sure the set temperature is above ambient 4 C Ambient is defined as the temperature in the thermal chamber This temperature is higher than room temperature and increases with normal Reader activity plate shaking plate reading and other incubations If you have been running a large number of readings or shake operations leave the Reader to cool or set a higher temperature If you have just run a high temperature incubation the Reader will only ailow you to set the lower temperature if it is within range However you should leave the Reader to cool before inserting the piate Contact an approved service center Contact an approved service center Reader could not find the required file the file An error has occurred in the temperature controller Contact the service center if the error persists
127. if the error persists The settings you have entered for the User shake facility are too high Choose a different combination of shake settings Contaci an approved service center The Reader has found an error in an equation Check all equations to make sure that they are valid and edit them if necessary You are trying to run an assay which contains operations not available for your Reader model Remove the unsupported operation Contact the service center if the error persists The Reader cannot detect the bulb Check that the bulb is correctly connected and that it lights correctly Replace it if necessary Refer to Fitting the Lamp and Optical Filters in Chapter 2 in the Microplate Reader User Manual One of the optics channels is faulty n refers to the channel number Ihe Reader can still work but the readings from the column containing the faulty channel must be ignored Contact the service center Contact the service center The parallel line fit contains too many lines Reduce the number of lines in the parallel line fit by removing Test wells Refer to the Parallel Line Bioassays section in the Endpoint Program User Manual Section 1 Error Messages 10 Password Error Photodiode selection Plate drive sensor error Plate File Error Plate Motor Error Please enter a valid well location Please enter an integer between x and y PLOSS Error The wrong password has been
128. ilable on your PR 2100 hard disk drive To install the upgrade disk 1 Switch the Reader on It will carry out its self tests refer to the Microplate Reader User Manual for details and then display the Main menu The appearance of this menu will depend on which software options are installed but the SETUP option will always be present For example READY 4 45P 30 06 94 ENDPOINT SETUP Endpoint Program User Manual 87125 15 Chapter 3 Installation 16 2 Select SETUP and then OTHER to access the second Setup menu SETUP 4 45 30 06 94 MAINT COMMS MEMORY PARAM Select MEMORY from the setup options The Reader will ask you want to reset the memory or to upgrade the Reader software SETUP MEMORY 4 45P 30 06 94 RESET UPGRADE CE Insert the upgrade disk in the drive and select UPGRADE The assay protocol files are copied to the hard drive When the Reader has finished the process press the CE key several times to return to the Main menu Remove the upgrade disk from the disk drive Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Chapter 4 Creating and Editing Tests 4 1 Creating a New Test sentia 20 Test 20 Test Name MERE Plate ID REP Shake Time and Shake Modes NEMINEM Define Template 24 Defining the Template Manually
129. ime it is switched on Parts of the output are overwritten and vertical lines appear on the screen On 2 tractor fed printer the printout is not the correct place on the page On a laser printer The last page of any printout does not print automatically Recommended Action An incorrect printer driver is installed Verify that the driver Setup menu corresponds to printer type if not contact an approved service center Increase the page width using the Setup menu Refer to the Setup menu section in the Reader User Manual The Reader is being switched on before the printer Switch the printer on before the Reader Trim down the output by removing processing options or if you are using a number of tables remove one or more of them Position the printer paper So that the top of the page is just above the print head for correct page position Switch the printer off line and select Form Feed Switch the printer on line before trying to print again Troubleshooting Guide 87125 Section 2 Solving Problems General General Problem Recommended Action Problems 2 self test 15 camied out The Self test Retest option is toggled on on read Set the Retest option to NO using the Setup meni All readings are Over The Over limit is too low Reset the Over limit using the Setup menu The Reader does not The Plate Type option is set to Alternative process the full 12x8 Format matrix S
130. in Menu 2 02 Single Board 1 33 Muiti Board English 87360 8 7364 Sanofi PASTEUR This document is the copyright of TECHNOLOGIES INC and must not be copied or reproduced in any form without prior consent DYNEX TECHNOLOGIES INC reserves the nght to make technical improvements to this equipment and documentation without prior notice as part of a continuous program of product development This manual supersedes all previous editions Copyright amp 1997 DYNEX TECHNOLOGIES INC rights reserved Table of Contents Table of Contents About This e ennt 1 Section 1 Error 1 2 2 1 000 entente tenent 3 Section 2 Solving Problems 15 Troubleshooting Guide 87125 Table of Contenis This page is intentionally left blank Troubleshooting Guide 87125 About This About This Manual This manuai contains two sections messages section that provides an alphabetic list of the error messages with an explanation of what they mean and possible solutions problem solving section that provides a list of hardware prin ng and general problems which may occur but are easily rectified WARNING ELECTRIC SHOCK HAZARD Reader contains no user serviceable parts The instrument must not be operated with the covers remove
131. in the table below and described in detail in this section Menu Setting Vale o 619 p 20 German Spanish p 20 Ram _ COMMS 0 2 Note If you are using a 1100 Reader and you make changes to the Setup settings these changes will only apply to the current software program If you insert a different program disk you will have to re enter the settings 18 Microplate Reader User Manuat 87125 Chapter 2 Installation and Setup Setup Menu The Setup menu allows you to view and if necessary alter the Reader settings SETUP 4 45 30 06 94 OTHER FILTERS CLOCK SYSTEM CE Select OTHER to access a second Setup menu SETUP 4 45 30 06 94 MAINT COMMS MEMORY PARAM CE In the menus shown on the following pages the options available are shown on the bottom line of the display To select an option press the function key below it or where appropriate key in a value Note In most of the menus the default or previously defined value is shown To enter a different value you must press CE This will access the alternatives available To change display language from English to Spanish Select SYSTEM from the Setup menu to access the System menu Select LANGUAGE from the System menu to access the Language menu The default or previously defined menu language is displayed LANGUAGE ENGLISH 4 45 30 06 94 ENIER To access the alternative languages select CE LANG
132. inal Ready 2 Data Set Ready 5 Ground 4 6 Data Set Ready 7 Request to Send Clear to Send 3 4 5 9 pin female Reader 9 pin D Macintosh 9 pin port Pin Name type port Pin Name pin Data Terminal Ready Data Set Ready Signal Ground Signal Ground I m l Data Set Ready Endpoint Program User Manual 87125 99 Chapter 7 Computer Control 7 2 Software Specification Software is defined by the standard ASCII character set together with the following specific control characters for handshaking SIX 02H ETX 03H ENQ 05H 06H XON 11H 15H 7 3 Handshaking Start of text End of text Enquiry Acknowledge Start Stop Not Acknowledge Begins transmission Terminates transmission Sent by Reader to indicate ready to transmit Used to indicate proper reception of transmission Start transmitting data Stop transmitting data Used to indicate faulty transmission The RS232C port is bi directional when used in computer control mode The DSR DTR handshake signals as well as software handshake are used to maintain communication status and synchronisation Computer control is established as follows DSR asserted STX COMMAND ARGUMENTS checksum ETX Sends command character string 100 ACK NAK Indicates proper improper reception Bxecutes task ENQ Asks 1f computer 1s ready t
133. intellectual property that 1s software programs that are licensed for use by the end user customer hereinafter referred to as the end user 2 This is not a sale of such intelectual property 3 The end user shall not copy disassemble or reverse compile the software program 4 The software programs are provided to the end user as 1s without warranty of any kind either expressed or implied including but not limited to warranties of merchantability and fitness for a particular purpose The entire risk of the quality and performance of the software program is with you 5 DYNEX TECHNOLOGIES INC and its suppliers shall not be held to any liability for any damages suffered or incurred by the end user including but not limited to general special consequential or incidental damages including damages for loss of business profits business interruption loss of business information and the like arising from or in connection with the delivery use or performance of the software program MS DOS is a registered trademark of Microsoft Corporation IBM isa registered trademark of International Business Machines Corporation Apple and Macintosh are trademarks of Apple Computer Inc Copyright 1997 DYNEX TECHNOLOGIES INC rights reserved Table of Contents Table of Contents About This ManuaL e eeeeseseesssee ee rese 1 Chapter 1 Fea
134. involved with the number of the section The Reader will then look for all the wells with the same number and view this as a discreet area AREA STATISTICS 4 45P 30 06 94 YES NO CE Select YES to include area statistics and divide the template up into sections Select NO to move on to the Quality Control equations Al 4 45P 30 06 94 ROW COLUMN CLEAR FINISH CE 36 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests ROW Places a row or part of a row within an area COLUMN Places a column or part of a column within an area e CLEAR Removes the displayed well from its area Clear can be used with ROW or COLUMN to remove rows and columns from areas FINISH Ends the area statistics option The Reader asks you to confirm that the template is correct If necessary you can print out the template using the LIST option to check that it 1 correct Placing Random Welis or Blocks of Wells in Areas To place a random well in Area 0 scroll through the well locations using the cursor keys until you reach the required well Enter the number 0 using the alphanumeric keypad this well location is now assigned to Area 0 To place a block of wells in Area 0 scroll through the plate and place each well individually Anv other wells you label number 0 will also be included in Area 0 Placing Rows in Areas To piace a row 1n Area 1 scroll through the well locations using the cursor keys until you reach the f
135. ion The Reader asks you to enter the concentrations of the Standards You will either have to enter a concentration value or a titer value depending on which was chosen in the Results Format menu CONC OF Si 4 45P 30 06 94 e ENTER CE For Sigmoid 4PLC semi log and log log fits Minimum 0 001 maximum 1 200 1x10 9 o Endpoint Program User Manual 87125 58 Chapter 4 Creating and Editing Tests For all other fits Minimum 0 0 maximum 1e200 1 10200 TITER 51 1 4 45P 30 06 94 e ENTER CE Minimum 1 maximum 999999 Specify the concentration and select ENTER Numbers are entered using the alphanumeric keypad the exponential notation is entered by pressing the key below it Curve Fit Type The Reader will ask you which type of curve fit you require CURVE FIT TYPE 4 45P 30 06 94 POWER SPLINE POLYGON OTHER CE Select POWER SPLINE or POLYGON to specify a fit type or select OTHER to access a second menu CURVE FIT TYPE 4 45P 30 06 94 SIGMOID MICHAEL AKIMA CE POWER 22 Polynomial regression routine linear regression quadratic equation cubic equation or quartic equation are available SPLINE Cubic spline fit POLYGON Successive points are jomed by straight lines SIGMOID 4PLC Sigmoidal S shaped fit MICHAEL Michaelis Menten hyperbolic fit AKIMA Curve which passes through every point and appears smooth and natural much like a manually drawn curve In
136. ir the safety of the Reader PREPARED for unexpected plate carrier movement when the Reader is controlled by an external computer MAKE SURE that the voltage ratings on the rear panel of the Reader correspond to the local mains supply Microplate Reader User Manual 87125 3 Safety Information MAKE SURE that the mains power cable 1s correctly wired Color codes are as follows Europe United States Brown Live Black Live Blue Neutral White Neutral Green vyellow Earth ground Green Ground Fuses The instrument does not contain any user replaceable internal fuses However the power supply contains an internal fuse in the primary circuit If the fuse needs to be changed it must be replaced with a CSA approved 20x5mm 4 cartridge fuse with a voltage rating of 250V This fuse should not be replaced by the user If the fuse blows contact an approved service center 4 Microplate Reader User Manual 87125 symbols symbols Warning Symbol For vour safety the Reader 1 marked with a warning symbol to remind you of certain hazards Qn the back panel this indicates that the optics door may be hot If you want to remove the optics door make sure that you allow the Reader to cool before touching it e Adjacent to the mains outlet this indicates that the outlet should only be used for an external monitor with a power rating of up to 120V A and an earth leakage current of less than 1 mA at 264V and
137. irst well in the required row Enter the number 1 using the alphanumeric keypad and select ROW This row is now assigned to rea 1 To place a portion of a row in rea 1 select the first well required enter 1 and select ROW other wells you label number will also be included in Area Placing Columns in Areas To place a column in rea 1 scroll through the wel locations using the cursor keys unti you reach the first well in the required column Enter the number 1 using the alphanumeric keypad and select COLUMN This column is now assigned to rea 1 To place a portion of a column in Area 1 select the first well required enter 1 and select COLUMN Any other wells you label number 1 will also be included in Area 1 Endpoint Program User Manua 87125 37 Chapter 4 Creating and Editing Tests 38 Removing Rows and Columns from Areas To remove an entire row from an area scroll through the well locations using the cursor keys until you reach the first well of the required row Select CLEAR and then ROW To clear a portion of a row select the first well used select CLEAR and then ROW To remove an entire column from an area scroll through the well locations using the cursor keys until you reach the first well of the required column Select CLEAR and then COLUMN To clear a portion of a column select the first well used select CLEAR and then COLUMN Note If you move to a well which has been assigned an area
138. isting assay test procedure LIST Prints all the steps in an assay test procedure DIR Prints directories of tests plates or curves When you create a new test you Assign a test number test name plate ID shake time and shake mode e Define the template manually or automatically e Select wavelength and blanking modes e Specify whether you want to print a results matrix include area statistics and quality control equations Specify the output options Select NEW from the Program menu to create a new assay test procedure Test Number The Reader requests an test number TEST 00 4 45P 30 06 94 DIR Use the keypad to enter a number or use the cursor keys to increment and decrement the number The up and down cursor keys change the number in single units The left and right cursor keys change the number in tens If you enter the number of an existing test the test name is displayed next to the number The Reader will ask if you want to overwrite the existing test for example CLEAR TEST RUBELLA 4 45P 30 06 94 YES NO CE Select NO to leave the test intact and return to the Program menu Select YES to overwrite the test Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Password If the test you want to overwrite is protected by a password you must enter Protected the password before the Reader will overwrite it Tests PASSWORD 4 45P 30 06 94 YZ ABCD
139. its for the host to send an XON character 11H control code Endpoint Program User Manual 87125 113 Chapter 7 Computer Control This page is intentionally left blank 114 Endpoint Program User Manua 87125 Appendix Examples of Plate Formats Appendix A Examples of Plate Formats Single Well Standards in ROWS esee eerie 117 Single Well Standards in 117 Double Well Standards in Rows Replicates in Columns 118 Double Well Standards in Columns Replicates in Rows 118 Triple Well Standards in Rows Replicates in Columns 119 Triple Well Standards Columns Replicates in 119 Alternative Format Single Well Standards in 120 Alternative Format Quadruple Well Standards in Columns Replicates Bd RENE 120 Endpoint Program User Manual 87125 115 Appendix A Examples of Plate Formats This page is intentionally left blank 116 Endpoint Program User Manual 87125 Appendix Examples of Plate Formats Single Well Standards in Rows 1 2 3 4 5 6 7 5 9 19 11 12 51 82 53 54 55 56 57 58 59 510 511 512 T2 T4 fT T6 17 15 T9 Til 12 TI3 15 Tis 120 121 3122 T23 T25 T27 128 129 130 T31 132 T33 T34 T35 T37 138 T39 T40 141 142 7143 144 745 146 T47 T48 149 150 151 152 153 154 155 T56 T57 T58 T59 17060 T61 T62 T63 164 7165 T66 T67 T68 769 3T
140. lanks may be specified within each row The blank value is used within that row only Each row is treated as separate from the others with its own set of blanks Column Blanking In column blanking Blanks may be specified within each column The blank value is used within that column only Each column is treated as separate from the others with its own set of blanks Endpoint Program User Manual 87125 35 Chapter 4 Creating and Editing Tests Results Matrix A results matrix is table of values printed out when the OD data is processed The Reader asks if you want to print a matrix of ODs O D MATRIX 4 45P 30 06 94 NO YES BOXED LABELLED e YES Includes an OD matrix in the results BOXED Includes a matrix with curve fit threshold difference or ratio sections if these have been specified LABELLED Includes a matrix which shows the label of each well for example 51 T5 C2 with curve fit threshold difference or ratio sections if these have been specified Area Statistics The Reader asks if you want to include area statistics in the results You can divide the template into up to 50 sections numbered 0 49 and for each of these sections the Reader will caiculate the mean standard deviation standard error mean and coefficient of variation These will then be output in the results Areas can range from a single well to the complete microplate Each area is defined by labelling the well locations
141. lect DIR to print a list of the stored tests Use the keypad to enter the test number and select ENTER When you have selected all the plate data and tests that vou need select CE The Reader will process ail the results and print them on an attached printer Spectrum The Spectrum option lets you produce a spectral response curve for a specified well WELL LOCATION 4 45P 30 06 94 ENTER Use the keypad to enter the well location and then select ENTER The Reader wil perform readings of the specified weil using all the mstalled filters The spectral response curve and suggested test and reference filters will then be printed out Endpoint Program User Manual 87125 Chapter 6 Utilities SPECTRAL RESPONSE CURVE WELL LOCATION Al 9 450 9 339 069 420 000 480 000 540 600 600 600 665 000 Warelength inm SUGGESTED TEST WAVELENGTH 419 rum SUGGESTED REF WAVELENGTH 630 CEU Note use the Spectrum option three or more filters must be installed Endpoint Program User Manual 87125 93 Chapter 6 Utilities This page is intentionally left blank 94 Endpoint Program User Manual 87125 Chapter 7 Computer Control 7 1 Hardware Specification 97 Linking with an IBM Compatible 8 Linking with an Apple Macintosh esee E 99 7 2 Software Specification 100 7 3 Handshaking HERR 100 7 4
142. lem Recommended Action A D Status error Contact an approved service center Agglutination assays You cannot combine agglutination assays cannot be run together onto the same plate unless they have the unless they have the same wavelengths readings per well and same speed plate speed settings Change the assays so that they can be run together Agglutination assays You cannot combine agglutination assays cannot be run with other onto the same plate with non types of assay agglutination assays Remove all the agglutination or all the non agglutination assays from the combined plate Troubleshooting Guide 87125 3 section 1 Error Messages Background light error Barcode COM Error Barcode Not Found Barcode retry error Barcode timeout error Checksum Error in File Command Time out There is excess light in the reading compartment Check that the plate carrier door closes correcily If it does close correctly but the problem persists contact an approved service center A fault has occurred in the interface between the barcode scanner and the Barcode Program Switch the Reader off and on again If the problem persists contact an approved Service center The barcode scanner was unable to read the barcode correctly Check that the barcode label is printed correcily and that it is positioned correctly on the side of the microplate Check that the Barcode Program has been set up to scan the type of barcode
143. mined polynomial in the form Y Do p x x where Po Y t aly y 2t t X X amp t 2y v s x Ms X 154 Endpoint Program User Manual 87125 Appendix Curve Fitting Axis Fitting The normal method of fitting data to the axes of a graph is to use linear scales for the x concentration and y measured variable axes Two other axis fitting methods are available Semi Log Fit Log Log Fit Semi Log Fit All x are transformed in the following way x log concentration Thus to obtain the concentration of a sample using linear regression concentration antiod Log Log Fit All x and values are transformed as follows x log concentration log measured variable Thus to obtain the concentration of a sample using linear regression 4 concentration antilo m Note These examples use linear regression but Log Log and Semi Log Axes Fits may be used with other curve fitting routines as well Endpoint Program User Manual 87125 155 Appendix C Curve Fitting This page is intentionally blank 156 Endpoint Program User Manual 87125 Index Air blanking mode 33 Akima curve fit 4 58 153 Area statistics 36 38 editing 79 Anthmetic operators in equations 38 43 46 49 52 55 Automatic template definition 29 30 Average blanking mode 34 Axis fit for curve fit
144. n key The test name will be displayed Select ENTER to confirm the displayed test name or CE to return to the Menus display Type in the desired number and press ENTER Each tirne the Reader is switched on the Endpoint menu allow you to choose from the tests you have assigned to short cut keys Test I to 4 are shown on the display ENDPOINT READY 4 45P 30 06 94 TESTI TEST2 TESTS TEST4 ENDPOINT Tests 5 to 8 can be accessed using the and right cursor keys Note All eight function keys must be assigned a test If for example you only have one test to assign you must assign this test to all eight function keys 8 Note Test names be up to 12 characters long but only the first seven letters will be used for the short menus display Make sure that you do not assign two tests with the same first seven letters to short cut keys Version The Version option lets you view the software version number of the currently installed Endpoint Program For example ENDPOINT VERSION 1 0 4 45P 30 06 94 Backup This option is not available for PR 1100 Readers refer to The Utility Menu section earlier in this chapter The Backup option lets you copy data files from hard disk to floppy disk or from floppy disk to hard disk or to remove the application from the hard disk ENDPOINT READY 4 45P 30 06 94 BACKUP RESTORE UNINSTALL CE BACKUP Copies the data files held on the Reader hard disk onto floppy disk Endpoint Program
145. nETX This command recalls data from memory by plate number n n is the plate storage number from plate directory entered as a decimal value between 0 and 99 Following this command OD data will be transmitted in the same data format as if the plate had just been read Transmit Stored Data by Plate ID SiXl1l7 nnnnnnnnnnnnETX This command recalls data from memory by plate ID nnnnnnnnnnnnisthe plate ID number from plate directory entered as letters numbers or special characters Following this command OD data will be transmitted in the same data format as if the plate had just been read Endpoint Program User Manual 87125 Chapter 7 Computer Control Switch the Lamp On Off SIX15ETX Switch the lamp on STX 1 6 ETX Switch the lamp off Users should exercise caution when using these commands allowing the lamp to remain on unnecessarily will shorten its life Shake Mode Command This command sets the Shake made STX i ETX n is the ASCH number 1 to 4 denoting shake modes with different frequencies and amplitudes Frequency 14Hz 2Hz Amplitude 1 7mm 2 Frequency 9Hz 2Hz Amplitude 3 0mm 3 Frequency 8Hz 2Hz Amplitude 3 0mm 4 Sets Custom Shake mode which is defined using commands 1 9 and 1 Custom Shake Mode Frequency Command This command sets the frequency of the Custom Shake operation STX 19 nn ETX nn is adecima number denoting the frequency Minimum 5 H
146. ng instructions 1 Remove the optics door and take out the lamp and filters When you replace the optics door insert the optics door packing materials 2 Pack the lamp and each of the filters separately 3 Make that there is no microplate in the plate carrier and no disk in the floppy drive 4 Place the Reader in the original anti static plastic bag 5 Place the bottom end caps into the carton and lower the Reader into the carton Fit the top end caps to the Reader 6 Place the filters and lamp in the accessories box and fit this between the end Caps T Seal the box carefully and securely Make sure that the box is not dropped handled in a rough manner 34 Microplate Reader User Manuali 87125 Chapter 4 Maintenance Figure 9 Repacking the Reader 4 4 Replacing the Lamp Warning If the Reader has been used recently the optics door and the lamp in the optics assembly still be hot Allow time for the Reader to cool before teuching it Take care when removing the optics door as there may be broken glass in the optics assembly Figure 10 summarizes the lamp replacement instructions Note DO NOT touch the bulb or reflector directly 1 Switch off the mains power supply and disconnect the cable 2 Usinga No 1 Posi driver remove the optics door 3 Slide the optics assembly out of the instrument If you have an older instrument check your serial number panel newer Readers have 1CXCxxxx or 2CXCxx
147. nt Program User Manual 87125 149 Appendix Curve Fitting The relationship between OD and concentration x can be written in the following general form a x OD x b Where a and b are constants It can be shown that a equals the limiting OD as x and that b is the concentration at half The equivalent formula applied to enzyme reaction rates is 5 Vo S K Where S Enzyme concentration V max Maximum reaction velocity constant Km Enzyme concentration at which the reaction velocity is half Vi The constant Kj is known as the Michaelis constant For practical applications it is best to transform the Michaelis Menten equation into a linear form known as the Lineweaver Burk equation 1 OD OD OD x If 1 OD is plotted against 1 x a straight line is obtained whose slope is max With an intercept on the VOD axis 1 0Dma and an intercept on the L x axis of The Reader performs this calculation automatically and determines the best straight line fit by linear regression printed as Vinx and Kp are evaluated and printed out 150 Endpoint Program User Manual 87125 Appendix C Curve Fitting Equation Many immunological reactions are characterised by a S shaped or sigmoid curve d LJ C lt CO x C U D s a CONCENTRATION Figure C5 Sigmoid Curve The Sigmoid equation can be written as
148. ntenance 5 552 21 4 1 Routine Maintenance 22 33 4 2 seu 33 Autoclaving 7 External Painted and Plastic Surfaces 34 Filters OF Decontamination TE 4 3 Repacking the Reader 34 4 4 Replacing the 35 4 5 Changing the Optical 36 Microplate Reader User Manual 87125 table of Contents Appendix A Self Test Diagnostics 39 Self Test Sample 22 22211 40 Appendix 41 Appendix Specifications eee eee tese 43 Software 1222 1 1 2 43 Hardware 1 entente 43 ses tha pense uten asa amas 43 405 to 850 Wavelength 44 340 to 400 Wavelength Range
149. nual 87125 49 Chapter 4 Creating and Editing Tests 50 Labels If there is a large difference between the lower limit of the positive range and the upper limit of the negative range many readings may fall between the two This neutral area may be divided into as many as ten segments which are numbered to 9 For example if there are two segments and the OD for weil A1 fails into the second segment it will be recorded in the matrix by the number 1 NO OF SEGMENTS 4 45P 30 06 94 ENTER CE To define the number of segments other than one enter the number using the alphanumeric keypad Notes 1 When doing an inverse assay and the positive and negative equations are the same there is no neutral area therefore this prompt will not appear 2 segments are numbered upwards from the negative end of the neutral area So that the highest number 15 the closest to a positive result The Labels option lets you choose how the positive and negative results will appear in the printed threshold matrix The default labels are for negative for positive for double positive for triple positive and 0 for the neutral area if only one segment has been defined The Reader displays the current label Select ENTER to confirm this label CE to change it and access the letters and symbols For example LABEL 4 45P 30 06 94 YZ ABCD ENTER CE Use the up and down cursor keys to access the lowe
150. o enter a character or CE to delete a character Use the alphanumeric keypad to enter numbers User well names may be up to three characters in length When the label is complete select ENTER to accept it User wells are positioned in the same way as for Blank Standard Test and Control wells Refer to the B S T C Wells section earlier in this chapter Endpoint Program User Manual 87125 27 Chapter 4 Creating and Editing Tests Utility Finish Select UTILITY from the Manual Template menu to access the Utility menu Al 1 4 45P 30 06 94 RESET DELETE RHENUM FILL CE The Utility menu will display the first occupied well followed by a list of tools RESET Clears all the existing well assignments allowing you to redefine the template from scratch DELETE Deletes the currently displayed well assignment The cursor keys can be used to scroll through the well locations RENUM Renumbers all well types into unbroken sequences This is useful if the plate has been edited and some wells have been removed leaving gaps in the numbered sequence FILL Completes the rest of the template once the locations of specified wells have been defined CE Returns the display to the Manual Template menu Once all the required well types have been specified the remaining empty wells can be assigned to Test wells using the FILL command If no Test wells have yet been specified the Reader will ask for the number of
151. o receive Endpoint Program User Manual 87125 Chapter 7 Computer Control 16 ACK NAK Indicates ready not ready to recerve SIX RESULTS ANSWER checksum ETX Sends answer ACK NAK Indicates proper improper reception steps 2 to 8 are repeated for subsequent transmissions provided the data link remains connected Results may require more than a single transmission in which case steps 5 to 8 must be repeated If 1n either step 6 or step 8 the computer has not acknowledged receipt of data the Reader will return to step 5 and retransmit the results The following example illustrates the data stream for initiating computer control mode for the Reader Hardware handshaking step 1 has been omitted Computer STX 7ETX HEX 02 37 03 Reader ENQ STX ACK ETX Note The example shown above does not use checksums Checksums are optional and are initiated by the 72 command Endpoint Program User Manual 87125 101 Chapter 7 Computer Control 102 7 4 Checksum The Reader 15 equipped with a Fletcher s checksum algorithm to protect against any communication problems The checksum is calculated as follows sumi 0 sum2 0 for i from 1 to message length do sumi sumi message 1 modulo 255 sum2 sum2 sum 1 modulo 255 end for checksum sum2 255 sumi This checksum is transmitted as a 4 digit hexadecimal 16 number in ASCI format Example Normal command ST X 5 0 ETX
152. of the previous piate is used as blank for the next Refer to the discussion of Whole Blanking larer in this section Plate Blanking In plate blanking the Reader reads and processes a plate of ODs It then holds these ODs in memory and when the plate is read again it subtracts the previous set of 96 readings This means that you can measure a change 1n sample concentrations over a period of time without monopolizing the Reader Two tests are needed 1 Create an assay test procedure for the first reading which uses air blanking The data from this plate will be stored with an ID 2 When the first test has been run create a second test for the next reading This test must use Plate blanking The Reader will ask for the plate ID from the first test PLATE 00 4 45P 30 06 94 DIR ENTER Scroll through the plates using up and down cursor keys When the correct plate is displayed select ENTER Select DIR to print out a list of plates stored in memory d Note You may enter a plate number here which does not yet exist For example you may use the plate number which will correspond to the first of these two tests Individual Blanking Individual blanking lets you position a series of Blank wells across a microplate Each time the Reader encounters a Blank well the blank value is updated This value is then subtracted from subsequent ODs unti the next Blank well is encountered This is repeated until the whole plate has be
153. ollows pin pot _ Pin Name Request to Send Clear to Send Clear to Send Request to Send ader 25 7 9 pin port Pin Name port Pin Name i DNI gt g Data Set Ready Data Terminal Ready Request to Send Clear to Send Clear to Send Request to Send Reader 25 port Pin 2 mm Data Terminal Ready 6 Data Set Ready Signal Ground Signal Ground Data Set Ready Data Terminal Ready To Request to Send Clear to Send s fe Clear to Send Request to Send Endpoint Program User Manual 87125 Chapter 7 Computer Control 25 female Reader 25 PC 25 pin E onere mee me mesape 7 p I CCC 5 tare Sent Linking with an Apple Macintosh The cable supplied with the Reader is for an IBM compatible PC To link with an Apple Macintosh computer the cable will have to be modified The RS232C cable connection between the Reader and a Macintosh is as follows OE 771 9 pin female Reader 9 8 pin Macintosh 8 pinpot Pin Name DIN port Pin Name pin DIN Ee A esee s 4 Data Term
154. om the disk drive if necessary Switch the Reader back on Place the floppy disk in the drive If the disk is write protected slide the tab back to the closed position If the Reader cannot read your disk it may be corrupted If this is the case stop using the corrupted disk and copy your files from your backup disk onto a new disk data file has been corrupted If the file contains setup parameters or directory information the Reader will rebuild the file whilst displaying a rebuilding message if the file is a test plate data or a curve data file you will have to recreate it The software could not find the file you asked for either because it was not there or because of memory problems Recreate the file if it does not exist If this error occurred during copy operation switch the Reader off and restart it then again The file you asked for has been saved using a different software version Upgrade the software version of the program you are using Contact an approved service center Troubleshooting Guide 87125 Section 1 Error Messages Filter Motor Error 1 The Reader cannot initiate the Filter Filter Motor Error 2 Motor Check that number of filters specified in Ihe Reader s Filter menu corresponds with the number of filters installed in the filter wheel and check that the filter wheel index holes are not blocked Refer to the section on Changing the Optical Filters in the Reader User Manual
155. oss of business mformation and the like arising from or in connection with the delivery use or performance of the software program MS pos and Microsoft are registered trademarks and Windows and Excel are trademarks of Microsoft Corporation BM is a registered trademark of International Business Machines Corporation Apple and Macintosh are trademarks of Apple Computer Inc Copyright 1997 DYNEX TECHNOLOGIES INC All rights reserved Limitations of Warranty Relating to Software 1 Sanofiaccepts no liability for the maintenance or support of Microsoft software 2 Installation of any software or Microsoft software other than MS DOS Windows or Excel will void the warranty of the product 3 DYNEX TECHNOLOGIES INC accepts no liability for consequentia loss arising from the use of software on this product outside the scope of the above definition Limitations of Use The user of the PR series Reader must foliow the specific manufacturer s assay package insert when modifying parameters and establishing results calculation methods The performance characteristics of the PR series Reader have not been established with specific serology or antigen detection assays The user must evaluate the PR series Reader in conjunction with the specific serology and or antigen detection assays This evaluation must include the establishment of performance characteristics for the specific assays
156. oss the display Use the up and down arrows to move to the start and end of the equation As you enter each quality contro equation the Reader increments to the next equation for example from to QC2 etc When no more equations required select ENTER OPER inserts an arithmetic operator into the equation Addio Subuacton _ WELL inserts a well type into the equation EQN 4 45P 30 06 94 B 5 Select B S or Blank Standard Test or Control to enter well type or select OTHER to access the User wells In QC equations the well type identifier represents the mean OD of all the wells of that type For example T represents the average reading for all the Test wells on the plate Using the keypad vou can specify an individual sample using the sample number or an individual replicate using the sample and replicate numbers For example C the mean of all Control wells the mean of all replicates C1 1 the OD of the first replicate of C1 OPTIONS inserts brackets inequality symbols functions and statistical values into the equation EQN _ A A5P 30 06 94 0 i ifINEQUAL STATS FUNCTION Endpoint Program User Manual 87125 39 40 Chapter 4 Creating and Editing Tests Inserts brackets index counter 1 into the equation or conditions if then and else When inserting brackets six levels of parent
157. ot alter the default settings unless you are proficient in RS232 communications protocols SETUP 4 45 30 06 94 MR700 MRX USER CE MR700 Select MR700 to set the Reader communication parameters to a format suitable for all Dynex application programs The MR700 settings are Baud Rate 9600 Stop Bits 1 Data Bits 8 Parity even Data Format MR700 Communications Reader asks which communication port is being used Select COMI or 24 Port COM2 to specify the port or select CE to return to the Comms menu MRX Select MRX to set the Reader communication parameters to an enhanced format suitable for most application programs When MRX is selected the display flashes bnefiy and then redisplays the setup menu The settings are Baud Rate 9600 stop Bits 1 Data Bits 8 Parity even Data Format Microplate Reader User Manual 87125 Chapter 2 Installation and Setup Communications Ports User The Reader asks which communication port is being used Select COMI 2 to specify the port or select CE to return to Comms menu Note When using PR1100 or a multiboard PR2100 no COMZ option exists Select USER to custornize the communication settings The User options aliow you to set the values for baud rate stop bits data bits parity and data format The settings available are Baud Rate 110 150 300 600 1200 2400 4800 9600 Stop Bits 1 2 Data Bits 7 8 Parity none even odd Data
158. ough the test step by step by selecting ENTER at each step In this way the steps in a test can be viewed To change any of the test steps select CE to access the alternatives Editing the Template You may edit the template scrolling through the test steps to the TEMPLATE section TEMPLATE CORRECT 4 45P 30 06 94 YES LIST CE Select YES to continue to the next step the test or LIST to print out the template Select CE to view the template well by well and redefine it if necessary 4 Endpoint Program User Manual 87125 6 Chapter 4 Creating and Editing Tests 68 Editing the Output Options No Option When the THRESH RATIO CURVE or DIFF options are displayed severa additional editing tools become available For example INCLUDE includes the named option as previously defined and displays the next option tn the test DELETE Deletes the displayed option STOP Saves the test and returns to the Program menu EDIT Lets you modify the displayed option INSERT Inserts an additional option from the Output Options menu Refer to the Inserting Output Options Into the Test section earlier in this chapter If there are no output options in the test if they have all been deleted or if INCLUDE has been incremented past the last option the following message will be displayed NO OPTION 4 45P 30 06 94 STOP INSERT Select STOP to save the test or INSERT to insert a THRESH RATIO CURVE or
159. phcates and the well type Orientation Of 1f you selected more than one replicate or mixed replicates the Reader asks Heplicates the replicates are to be positioned along rows down columns or randomly REPLICATES IN 4 45 30 06 94 COLUMNS ROWS RANDOM CE COLUMNS Positions all replicates down the columns ROWS Positions all replicates along the rows RANDOM Lets vou position all replicates randomly The onentation of the replicates applies to all the samples in the well type even if the samples are arranged in mixed replicates Well Type Reader asks whether the next well of that type is to be placed in the next Orientation available space down the column or along the row B WELLS IN 4 45P 30 06 94 COLUMNS ROWS CE Select COLUMNS to position the next well in the next space working down the columns Select ROW to position the next well in the next space working along the rows This determines the next well location offered bv the B S T C menu Number of Each time you select a well type which has been assigned in mixed Mixed replicates the Reader will ask you how many replicates you want to assign to Replicates this sample For example G10 4 45 30 06 94 BIX CE Select number of replicates required for this sample a Endpoint Program User Manual 87125 2 Chapter 4 Creating and Editing Fests 26 Example The Reader returns to the B S T C menu and offers you
160. ple 01 A11 4 45 30 06 94 DIR FINISH CE NO Excludes the displayed plate e YES Includes the displayed plate in the calculation DIR Prints a directory of plates FINISH Prints the results of the calculation Endpoint Program User Manual 87125 91 Chapter 6 Utilities 92 Stats Batch Results are printed showing the mean standard deviation and coefficient of variation for all the valid wells on of the plates listed Blank wells and wells outside the Reader s Over and Under range are excluded To scroll the Plates directory backwards and forward use the up and down cursor keys The Stats option calculates statistical data for all the plates stored in memory This option can be used in a similar way to C V above but it operates on areas of the selected plates identified the Area Statistics option Refer to the Area Statistics section in Chapter 4 The Batch option recalls stored plate data and reprocesses it using a different test BATCH operates like RECALL refer to the Recalling Plates section in Chapter 5 but operates on a series of plates rather than a single plate First you must select a plate PLATE 01 Pll 4 45P 30 06 94 DIR ENTER Use the up and down cursor keys or the alphanumeric keypad to find the plate you need and select ENTER to accept it You must then choose the test to which the plate data will be applied TEST 01 A1 4 45 30 06 94 DIR ENTER Se
161. printer is not listed here contact the service center Page Size Reader asks you to enter the page size in inches For example PAGE LENGTH 11 000 445P 30 06 94 ENTER Select ENTER to accept the page length and width shown or press CE to enter new values Lab Name Reader asks if you want to print a laboratory name at the top of each print out sheet LAB AASP 30 06 94 YZ ABCD ENTER CE Enter a laboratory name or select ENTER to return to the System menu Laboratory names may be up to 16 characters in length and consist of the following characters Numbers 0 9 and a decimal point Enter these using the keypad e Upper case letters lower case letters and symbols 22 Microplate Reader User Manual 87125 Chapter 2 installation and Setup Enter these in the following way Choose upper or lower case letters or the symbols using the and v cursor keys b Scroll through the display characters on the display using the lt and gt cursor keys C Enter the character shown by the flashing cursor by pressing the A function key below it When the name is complete select ENTER Maintenance Menu Select MAINT from the Setup menu to access the Maintenance menu and view the self test printouts and mamtenance reminder settings Self Tests Self tests are performed when the Reader is switched on to make sure everything is working correctly The self test can be printed 1f necessary
162. programmer then the versatility of the Reader can be extended even further It must be emphasized however that this information has been prepared for the computer professional Therefore it may be confusing for those not versed 1n computer communication protocol and peripheral handling CAUTION The applications programmer must take great care to prevent the Reader from starting plate carrier movement when the user is unprepared This could result in spilled liquids or pinched fingers 7 1 Hardware Specification The Reader computer interface 15 as specified by ELA 5232 interface standard for a data terminal device Baud rates between 110 and 9600 may be selected from the Setup menu refer to the Microplate Reader User Manual Data characters comprise e Start bit e 8 data bits e Pantybit Stop bit The following information describes RS232C cable configuration between the Reader and computers of various different serial outputs The cable supplied with the Reader conforms to the DB 25 pin serial output specification Connections for IBM compatible PCs and Apple Macintosh computers are shown 1n the sections below Endpoint Program User Manual 87125 97 98 Chapter 7 Computer Control Linking with an IBM Compatible PC 9 pin female 9 pin female 25 pin female 9 pin female 9 pin female 25 pin female The RS232C cable connection between the Reader and an IBM or compatible PC is as f
163. py of the Endpoint disk and store the original disk safely The be made an external PC using Windows File Manager or the MS DOS diskcopy command 3 1 InstaHing Endpoint in a PR 1100 Reader Note If you are using the Endpoint Program disk for the first time it will contain all the default hardware and software setup options To reset these options refer 10 Chapter 2 of the Microplate Reader User Manual 1 Switch the Reader off 2 Ifthe Reader was already running a software program remove the original disk from the floppy disk drive 3 Insert the Endpoint working disk into the floppy disk drive 4 Switch the Reader on When the Reader has completed its self test routines refer to the Microplate Reader User Manual for details the Main menu appears showing the Endpoint option READY 6 65P 30 006 94 ENDPOINTSETUP To access the Endpoint Program press the key below the ENDPOINT option The Reader will now run the Endpoint Program until you insert a different software program disk Endpoint Program User Manual 87125 13 Chapter 3 Installation 14 3 2 Re Installing Endpoint in a PR 2100 Reader The Endpoint Program is supplied pre installed on the PR2100 hard disk drive In the event that the software 15 accidentally deleted or one or more files have been corrupted vou will need to re install the software To re install the software 1 Locate the Endpoint Program disk which wa
164. r User Manual 87125 43 Appendix Specifications 405 to 850nm Wavelength Range Dynamic range Linearity 0 000 to 2 000 OD 2 001 fo 3 500 OD Filter band width FWHM Center Wavelength Accuracy Precision 0 000 to 2 000 OD 2 001 to 3 000 OD 3 001 to 3 500 OD Accuracy 0 000 to 3 500 OD 0 100 to 4 000 OD i 1 0 1 5 10 nm z 2 nm 2 0 2 CV or 0 005 OD whichever is greater 0 6 CV 1 0 CV 2 5 or 0 005 OD whichever 15 greater 340 to 400 Wavelength Range Option Dynamic range Linearity 0 000 to 2 500 OD Filter band width FWHM Center Wavelength Accuracy Precision 0 000 to 2 000 OD 2 001 to 2 500 OD 0 100 to 3 000 OD 2 0 18nm 2 nm 2 nm 0 6 CV or 0 005 OD whichever is greater 1 0 CV 1 Linearity is the maximum percentage deviation of a reading from the ideal straight line plot of OD versus concentration Measured by the manufacturer at 410nm in the visible range and 340nm the UV range Precision is the mean Coefficient of Variation CV figure for all wells on a plate that has been read 20 times in succession Measured by the manufacturer at 4 in the visible range and 340nm in the UV range 44 Microplate Reader User Manual 87125 Appendix Spectfications Interface Printer interface Parallel Centronics Compatible with up to 850 printers All printers must be compliant with EMC directive 89 336 number of standa
165. r case letters and symbols and the left and right cursor keys to scroll through the characters Press the function key to enter a character or CE to delete a character Use the alphanumeric keypad to enter numbers Labels may be up to five characters in length When the label is complete select ENTER to accept it The Reader also assigns default labels to other types of data such as unread wells and out of range readings These labels cannot be changed Week Unread well Out of range data Combined data This symbol denotes difference data It is found in the higher level of wells which have been used 1n difference calculations Difference data will only be included in a threshold matrix if a difference matrix was placed before the threshold matrix Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests QC Equations When you have defined the labels or if YES was selected at the ONLY prompt the Reader asks you to enter QC equations You can include up to 12 Quality Control QC equations per assay QC equations allow you to specify criteria for the calculated results If these criteria not met you may choose to abort the assay The threshold quality control equations are entered in the same way as the ordinary QC equations Refer to the Quality Control Equations section earlier in this chapter When you have completed the threshold matrix section the display returns to the Output Options menu
166. r the symbols using the up and down direction keys v Scroll through the characters on the display with the left and right cursor keys Enter the character shown by the flashing cursor by pressing the selection key If a plate is already stored with the same ID the Reader will ask if you want to choose another plate ID or overwrite this plate ID and the corresponding plate data For example OVERWRITE A3 4 45P 30 06 94 YES NO CE Select YES to overwrite the plate data stored under the plate ID or select NO to keep the old plate data and enter a different ID for the new plate Barcode Scan If the Barcode option was included in the assay the plate carrier will move to the In position and the Reader will scan the barcode If it reads the barcode successfully it will go on to start the test If it cannot read the barcode it will display an error message which lets you abort or retry the scan If you want to retry the scan check to make sure that the barcode is correctly positioned and that it 1 the same type as you defined in the Barcode setup options Refer to the Barcode User Manual If you choose to abort the Reader will ask you to input the piate ID manually Enter the barcode number in the same way as for a normal plate ID This 1s described above Reading Once you have started the plate and input the information required the test will begin The Reader will display READING message followe
167. rd printer drivers are included if your printer is not one of these contact the service center Computer Interface Bi directional RS232C with user definable protocol Electrical Light source tungsten halogen lamp Mains input 100 to 120 200 to 240V 50 to 60 Hz Power consumption 500 VA Fuses There are no internal user replaceable fuses The power supply contains a CSA approved 20x5mm 4A cartridge fuse with a voltage rating of 250V in the primary circuit If the fuse biows contact the service center Mains Power Fuse mains plug powercord Safety Class apparatus Physical Environmental Conditions Weight 12 5 kg 27 55 Dimensions 0390 x W360 x H220 Operating Temperature 10 40 C Operating Humidity 10 90 RH Storage Temperature 0 509 Storage Humidity 10 90 Altitude 2000m Microplate Reader User Manual 87125 45 Appendix Speciications 46 Microplate Reader User Manual 87125 Index Index Accessories 4 Alphanumeric Keys 14 Back Panel 12 CC Cleaning 33 34 Clock Menu 20 21 Comms Menu 24 25 Cursor Keys 14 p Decontamination 34 Display 14 Electric Shock Hazard 3 External Painted and Plastic Surfaces cleaning the 54 F Filters cleaning the 34 Filters Menu 19 20 Front Panel 14 Function keys 14 Fuses 4 Microplate Reader User Manua 87125 H Hardware Specifica
168. replicates and the orientation Refer to the discussions of Replicates and Orientation of Replicates earlier in this section When the template is finished select CE to return to the Manual Template menu and then select FINISH Select FINISH from the Manual Template menu to end the template option The Reader asks you to confirm that the template is correct TEMPLATE CORRECT 4 45P 30 06 94 YES LIST CE Select YES to accept the template LIST to print the template or CE to return to the Manual Template menu allowing you to edit the template Note You should always print out a copy of the template before running the test to make sure that it is correct Example templates are shown in Appendix Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Defining the Template Automatically Select AUTO from the Template menu to access the Auto Template menu Only Standards and Test wells may be defined in this mode The Reader asks you to define the Standards and then the Tests The display requests the number of Standards NO OF STDS 4 45P 30 06 94 ENTER CE Enter the number of standards required Minimum 1 maximum 24 Format Two types of format can be used with the Reader the standard 8 by 12 format or the alternative 4 by 10 format The Reader asks whether or not you are using the alternative format ALTERNATIVE FORMAT 4 45P 30 06 94 YES NO CE Select YES to specify alternative format or NO
169. rly basis Remove the filters and clean them Section 4 2 contains more detailed cleaning instructions Periodic maintenance should be determined by the user 4 2 Cleaning Warning Always switch the instruments off and disconnect the power cable before cleaning the Reader The Reader is constructed from high quality materials nevertheless spilt saline solutions solvents acids or alkaline solutions must be removed from outer surfaces immediately to prevent damage Microplate Reader User Manual 87125 33 Chapter 4 Maintenance Autoclaving DO NOT autoclave any part of this instrument External Painted and Plastic Surfaces Ciean external surfaces with a mild laboratory detergent followed by 10 bleach or 7046 alcohol Always dilute detergents according to the manufacturer s instructions Filters Clean the filters by wiping them with a lint free cloth or a lens tissue If necessary a little alcohol may be used with the cloth or tissue Decontamination If you need to return the Reader to the service center and it has been in contact with human blood other potentially infectious body fluids pathological samples toxic or radioactive materials must be decontaminated Clean the surface with a mild laboratory detergent followed by 10 bleach before shipping the instrument 4 3 Repacking the Reader This procedure assumes that the original Reader packaging materials are being used Figure 9 summanzes the repacki
170. s Ratio Data Results Printout DMPL Lab JF Printed at 14 45 22 06 94 Page 11 RATIO MATRIX RATIO EQUATION Sample PC 0 9 Sample PC 0 95 l 2 3 4 5 5 7 8 9 10 11 12 2119 2 987 5 640 0 965 0 113 0 113 4 441 4 496 0314 0 110 0 110 2 847 0110 3 272 1 007 0 110 3 087 4 914 0117 0 324 4424 0110 3 132 2 689 C 009 3 175 0 327 4 836 0 366 1 027 1 101 5 361 0324 2 906 3 738 0 317 D 0 097 3 952 3 994 0356 1 108 0 275 4503 0117 0 301 2 767 1 231 0 113 0292 5 377 3 865 3 667 3 171 4 441 4610 2750 0117 4387 0 117 4 674 0308 5 449 0 340 5 701 2443 3 609 3703 4584 5364 0 113 4 325 1 205 G 1401 6 923 2 980 0 978 4 785 0 891 0 110 0317 0117 09 0 249 1 121 1421 6 038 0 113 4 247 3 599 3 871 0272 0943 3 252 2877 0 366 3 233 I U EQUATION Sample 15 Sample 15 1 2 3 4 5 6 7 8 9 19 11 12 007 0 199 0 376 0 064 0 008 0008 0296 0 300 0 021 0 007 0 007 0 190 B 007 0 218 0 057 0 007 0 26 0 328 0008 0022 0275 0007 0 209 0 179 C 006 0 212 0 022 0 322 0 024 0068 0 073 0 357 0 022 0 194 0 249 0 021 0 006 0 263 0 266 0 024 0 074 0 018 0 300 0 008 0 020 0178 0 082 0 008 0019 0 358 0 258 0 244 0 211 0 296 0 307 0 183 0008 0 201 0 008 0 312 001 0 363 0 023 0 380 0 163 0 241 0247 0 306 0 358 0 008 0 288 0 080 G 095073 0 462 0 199 0 065 0 319 0 059 0007 0021 0 008 0063 0 017 0 075 9075 0 403 0 008 0 283 0 240 0 258 0 018 0 063 0 217 0192 0 024 0 216 136 Endpoint Program User Manual 87125 Appendix Sample Printouts
171. s originally supplied with your PR 2100 Reader 2 Insert the disk into the PR 2100 Reader disk drive and turn on the instrument The software is automatically installed and the Main menu appears on the display READY 6 65 30 006 94 ENDPOINT SETUP 3 Remove the disk from the drive and return it to its storage place for safekeeping Note Your assay protocol files and plate data will not be affected by the re installation proc dure 3 3 Upgrading from a Previous Version If you receive an updated version of the Endpoint Program use the following procedure to upgrade the Reader Note This upgrade procedure will not affect tests you have created previously These tests are fully compatible with the new software version To upgrade from a previous version 1 Switch the Reader on It will carry out its self tests refer to the Microplate Reader User Manual for details and then display the Main menu The appearance of this menu will depend on which software options are installed but the SETUP option will always be present For example READY 4 45 30 06 94 ENDPOINT SETUP 2 Select SETUP and then OTHER to access the second Setup menu SETUP 4 45P 30 06 94 MAINT COMMS MEMORY PARAM Endpoint Program User Manual 87125 Chapter 3 Installation 3 Select MEMORY from the setup options The Reader will ask if vou Want to reset the memory or to upgrade the Reader software SETUP MEMORY 4 45P 30 06 94 RESET U
172. s transmitted first MR700 data format 1 bBMODEDbREFbSAM c ETX 2bsSNGLbb bbbscr ETX Lbbrbbbscr ETX HLD 2b1 00cr EFX bbbbbl1 00cr ETX uuuuuuuuucr ETX uuuuuuuucr ETX lt gt Note Lines 3 to 6 do not contain valid data and are only included to maintain compatibility with existing MR700 software Endpoint Program User Manual 87125 111 Chapter 7 Computer Control 112 Five Filter Head Mode Extended and Reader data format LbMODEDREF D7 SAM ETX 2bSNGLbb bbbscr ETX TIME cr ETX 4DATE cr ETX SID F cr ETX OPER uuuuuunuuucr ETX The body consists of twelve data blocks representing the twelve columns of a microplate The data blocks consist of the following i x x b y b b b d 2 X x b y b cr 8 X x b y b b 8 8 cr 9 ETX There are three possible exceptions to the field well is blank or out of range the following is transmitted x x b y b b b b or x x b y b b b or x x b y b b b cr cr mm b O V U N D CT b b This occurs when the five filter mode has been specified before the start command has been issued The header is the same as before and the body also consists of twelve data blocks each representing the columns of a microplate filter 1 filter 2 filter 3 filter 4 filter 5 2 TE 7 JHET 3 dH 1997
173. serts brackets and statistical values into the equation Inserts left and right brackets into equation Six levels of parentheses are allowed STATS Inserts a statistica value into the equation EE Represents the median of group of ODs ODs in the group are listed the median is the OD in the middle of the list if the list contains an even number of ODs the median is the mean of the middle two ODs The group of wells may be a well type or a sample if it contains multiple replicates Example Median PC The value calculated will be the median of all the Positive Control ODs Represents the standard deviation between the ODs in a group of wells The group of wells may be a well type or a sample if it contains multiple replicates Represents the coefficient of variation between the ODs in a group of wells The group of wells may a well type or a sample if it contains multiple replicates OPER inserts an arithmetic operator into the equation Subwacton Manican 7 Division Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Threshoid Equation Components A summary of the components which can be used in threshold equations is shown below together with a route showing you where to find them from the Threshold menu ltem Example Wherefound Arithmetic Operators SelectOPER To the powerof
174. slot cut 1n it and the voltage selector 1s not in the correct position insert a suitable small flat bladed screwdriver through the slot and move the selector to the desired voltaze DO NOT LOOSEN THE SCREWS USED TO RETAIN THE PLASTIC COVER the plastic cover does not have a slot cut in it and the voltage selector 15 not in the correct position use a No 1 Posi driver to remove one of the screws and loosen the other screw to allow the plastic cover to be pushed aside Move the swiich to the desired voltage replace the cover and tighten the screws DO NOT REMOVE BOTH SCREWS USED TO RETAIN THE PLASTIC COVER Microplate Header User Manual 87125 13 Chapter 2 installation and Setup The Reader Front Panel Figure 4 Microplate Reader Front Panel 1 Power Switch marked for on off 4 Floppy Disk Drive 2 Power Light 5 Keypad and display 3 Plate Carrier Door The Keypad and Display The Reader is controlled by menu driven software which responds to the user s menu choices The menus are displayed on a liquid crystal display which can show up to five options at a time Choices are entered using the Keypad Figure 5 Function Keys and Display Function keys menu options are shown on the bottom line of the display and selected by pressing the function key below Figure 6 Alphanumeric Keys and Cursor Keys 14 Microplate Reader User Manual 87125 Chanter 2 installation and Setup Alphan
175. ssay WARNING HAZARD EXISTS PLATE WILL BE RECALLED WITH CURRENTLY SELECTED ASSAY AND NOT ORIGINAL ASSAY Endpoint Program User Manual 87125 Chapter 6 Utilities The Utility Menu 87 Marital 88 Li 1 ra Backup 4 TURRRRORRARSERERERENRNENZumnmmummuraumauhmamu ruuvrzdhumurtrurrurmuerrtuuskhtmhushuumukhihctmmuuauhmrmmumumimkhkhwrumurmsmmmuuusumaqeEFAST ZAEUNNAR 91 Endpoint Program User Manual 87125 85 Chapter 6 Utilities 86 Endpoint Program User Manual 87125 Chapter 6 Utilities Once the instrument is switched on and the self test routines are successfully completed the Main menu is displayed This shows the choice of programs The appearance of this menu will depend upon the application programs installed if the Endpoint Program 15 the only software program installed the Main menu will show only the Endpoint and the Setup options READY 4 45P 30 06 94 ENDPOINT SETUP Select ENDPOINT to view the Endpoint menu ENDPOINT READY 4 45 30 06 94 START RECALL UTIL PROGRAM e START Lets you run assay test procedures which have been created using the Program menu RECALL Lets you recall data obtained from a previous assay test procedure for further processing UT
176. st direction C is the number of steps in the second direction that 1s the Y direction when 2 This command is analogous to an 700 instruction for incrementing plate movement but in this case will step through well locations stored in memory The arguments and are derived by finding the ASCII equivalent of adding 30H 48 decimal to the number of steps required Consequently if an ASCII character A was the argument 17 steps would result If the number of steps is more than is left in the row or column then the pointer will return to the equivalent of the home position in memory and continue to step until complete If B or C is missing then the default value of 1 results Endpoint Program User Manual 87125 103 Chapter 7 Computer Control 104 1 Start Stop STX 1 A ETX is an ASCI number 0 or 1 G STOP START STOP stops operation and return plate carrier to the Out position START will start reading operation in the mode currently selected Shake Commands SIX 12 Shake the plate for 1 to 59 seconds and then read the plate the mode currently selected nn is shake period in seconds entered as a decimal value For example STX 1234 ETX shake for 34 seconds S1X1208ETX shake for 8 seconds STX 13 nn ETX Shake the plate for 1 to 59 seconds without reading n nis the shake period in seconds entered as a decimal value Transmit Stored Data by Plate Number STX 14n
177. subsequent wells In normal read mode up to a maximum of 32 blanks can be set across the plate 5 Print Control STX 5 A character string ETX is the ASCII number 0 or 1 Disable printer Printer wil not print until the computer resets or relinquishes control X Enable printer a character string follows maximum 196 characters it will be printed otherwise the printer will function as usua Print control characters can also be sent refer to the printer manual 108 Endpoint Program User Manual 87125 Chapter 7 Computer Control Print Installed Files lt 52 This command transmits codes indicating installed programs Data takes the form nnannnnannnnnnnnElX lt separated by spaces where means page unoccupied indicates page accessing Reader software 2 indicates inaccessible program cartndge 5 Barcode Agelutination H Kinetics Test Backup Commands STX 53 ETX This command will cause the Reader to transmit all tests stored in memory The data will be variable in length but the end will be marked an ETX character Normal Reader communications protocol should be observed STX54ETX This command will replace ali tests stored in the Reader memory with tests downloaded from a computer Once this command has been acknowledged data follows terminated by an ETA signal Receipt of the data 15 acknowledged following ENQ sent by the computer The Reader will respond
178. take manual control of the Reader MENUS Gives you the choice of long or short menus VERSION Displays the software version number of the currently instalied Endpoint Program e Produces a statistical analysis of plate data BACKUP Lets you copy data files from hard disk to floppy disk or from floppy disk to hard disk or to remove the application from the hard disk STATS Produces a statistical analysis of plate data e BATCH Recalls a series of stored plates for processing SPECTRUM Produces a spectral response curve for a well Manual Manual mode lets you operate the Reader manually Its purpose 15 to let you to make a manual check of specific resuits after many plates have been tested The Reader asks you to enter the wavelength mode WAVELENGTH MODE 4 45P 30 06 94 SINGLE DUAL CE The Reader may be operated in single or dual wavelength mode Single wavelength mode invoives the use of a test filter only Dual wavelength mode involves the use of a test filter and reference filter Refer to the Wavelength Modes section in Chapter 2 Select SINGLE or DUAL to specify the wavelength mode The Reader asks for the wavelength of the test filter Endpoint Program User Manual 87125 Chapter 6 Utilities Select ENTER to confirm the wavelength displayed Select LAST or NEXT to scroll backwards or forwards through the available filter wavelengths If DUAL wavelength mode was selected the Reader asks for the
179. te If the test filter wavelength is the same as the reference filter wavelength ODs are averaged instead of subtracted Refer to Wavelength Modes in Chapter 2 Multiple Mode Multiple wavelength mode lets you take a primary and secondary reading for every sample using different filter wavelengths The primary reading is normally used but the secondary reading will be used if any well ODs are above the Reader s Over limit The Reader uses a calculation mode chosen the user to convert secondary readings into the primary reading range Primary and Secondary modes can be both be run in dual or single wavelength mode For further information refer to the Wavelength Modes section in Chapter 2 The Reader asks which wavelength mode you want to use for the primary reading PRIMARY MODE 4 45P 30 06 94 SINGLE DUAL CE Select SINGLE or DUAL mode and then select the filter wavelengths by scrolling through the available filters refer to the sections above Endpoint Program User Manual 87125 31 32 Chapter 4 Creating and Editing Tests The Reader asks which wavelength mode you want to use for the secondary reading SECONDARY MODE 4 45 30 06 94 SINGLE DUAL CE Select SINGLE or DUAL mode and then select the filter wavelengths as before Once you have selected the filter wavelengths the Reader asks which calculation mode to use to convert secondary readings to the primary reading range CALCULATION MODE 4 45P 30 06 94
180. te was read are displayed select ENTER to process the plate data with the indicated test If you want to process the plate data using a different test use the keypad to type in a different test number This option is useful if you want to assess the OD data of the test using a technique not inserted into the original test you enter a number for which no corresponding test exists the test number prompt will reappear Re enter a valid test number Recalling 1f you did not assign an ID to a plate but you want to recall the plate data the plates with Reader will have assigned a default plate ID to the data To find this ID print default IDS directory of plate IDs This will list the date and time that the test was run You may then be abie to work out which plate ID you require Endpoint Program User Manual 87125 83 Chapter 5 Running Tests and Recalling Plates Note As the Reader has a total capacity of 100 plates default IDs are numbered 0000 0099 unless you have assigned IDs of your own this case there will be less default IDs available Once the Reader reaches its 100 plates capacity it reuses all the available default IDs overwriting the plate data they hold It begins at 0000 and works upwards until all the default IDs are used up again It does not inform you when it begins overwriting ald plate data Note Partial Plates will have the entire plate recalled recalculated for only the selected a
181. te will cause interruption in operation Rule 2 Date based functionality must behave consistently for dates prior to during and after Year 2000 Rule 3 interfaces and data storage the century in any date must be specified either explicitly or by unambiguous algorithms or inferencing rules Rule 4 Year 2000 must be recognized as a leap year John L Eccles Director of Quality amp Regulatory Affairs SANOFI DIAGNOSTICS PASTEUA Main menu versions 2 02 1 33 End versions 2 01 3 User Manual Codes 87350 67354 PR2100 PRI100 CONTENTS 1 Microplate Reader User Manual 2 Troubleshooting guide 3 Endpoint Program User Manual Page 4 Last modification Oet 1997 User manua opde 87362 PR Microplate Reader User Manuals Software Upgrades When you receive software upgrades the manuals will be supplied in shrink wrapped form These manuals are designed to replace the old manuals in your PR Manual Set Binder you wish to purchase another binder please contact vour Reader supplier To replace old manuals Remove the old manual from the binder and discard it e Replace it with the new manual taking care to mix up pages Remove old troubleshooting guide from tbe binder and discard it Replace it with the new troubleshooting guide taking care not to mix up pages PR Microplate Reader Microplate Reader User Manual Manual code 87362 Revision of the manual October
182. tes for the curve fitting algorithms used in the Reader For all curve fitting routines data 15 always plotted in the following way X axis Represents concentration Y axis Represents measured variables 1 optical density time or rate of change with time This appendix describes the following types of curve fit Linear Regression Straight line of best fit Polygon Fitting Joins successive data points with straight lines Quadratic Cubic Curved line of best fit similar to linear Quartic Regression regression Spline Curve Fitting Curve fit which passes the curve through all the data points Other Equations Curve fits which include the Michaelis Menten equation the Sigmoid equation and the Akima curve fit The following types of axis fit are also described Log Log Fit Semi Log Fit Endpoint Program User Manual 87125 143 Appendix Curve Fitting Linear Regression Linear Regression is used to put a best fit straight line through a set of data points The equation for a straight line 15 where m the slope the v intercept defining the line x the value for concentration y the value for the measured variable The linear regression formulae for determining the best straight line through series of data points are 2 2 c y m x Where x and y are the mean values of x and 1 The linear regression coefficient R is defined by R
183. the SETUP menu Main Menu If no faults are detected the instrument displays the Main menu which shows ali the available software programs and SETUP If there are more than four software programs installed use the lt and gt cursor keys to view them While the Main menu is displayed the plate carrier can be moved in using the cursor key and out using the v cursor key The plate carrier should not be left out of the Reader for more than a few minutes at a time as it will gather dust and may become damaged it is left for five minutes without using the software the Reader will move the plate carrier in automatically Switching between DOS Applications On a PR1100 1 Press the Esc to return the Reader to the Main menu 2 Switch the Reader off 3 Change the software disk 4 Switch the Reader on again Note If you have changed any settings the Setup menu you will have to enter them for the new program Microplate Reader User Manual 87125 17 Chapter 2 Installation and Setup On a PR2100 4 Press the Esc key to return the Reader to Main menu 2 Select the required program using one of the function keys 2 2 Setup Procedures The Reader has a number of settings which can be adjusted to suit the assays which will be run on it The settings are altered using the Setup menu To use the Setup menu options select SETUP from the Main menu The options accessed by this menu are summarized
184. the next available well location If you want to move to a different well location you can do so using the cursor keys All Test samples must be arranged in replicates of four which must be positioned along the rows Each new group of Test well replicates must be positioned down the columns The first well must be located in well In total six groups of Test wells must be placed on the template the Template menu select YES to manually define the template The Reader will ask which type of well 15 required Al z 4 45P 30 06 94 B S T C USER UTILITY FINISH Select B S T C to assign Test wells Al 4 45P 30 06 94 B1 51 1 1 Select T1 to place first Test well in location 1 Reader will ask for the number of replicates T WELLS IN 4 45P 30 06 94 MEXED ENTER To define Test wells in groups of four replicates type 4 in using the keypad and select ENTER The Reader will ask for the orientation of the replicates REPLICATES IN 4 45P 30 06 94 COLUMNS ROWS RANDOM CE Select ROWS to position the replicates along the rows The Reader will ask for the orientation of subsequent groups of Test weils T WELLS IN 4 45P 30 06 94 COLUMNS ROWS CE Select COLUMNS to position subsequent groups of Test wells in the next available space down the columns The display will return to the 5 menu displaying the next available well location This well location will be because COLUMNS was defined in
185. the template LIST to print the template or CE to return to the Template menu allowing you to edit the template You should always print out a copy of the template before running the test to make sure that it is correct Example templates are shown in Appendix A Wavelength Mode 30 The Reader asks which wavelength mode 15 required The plate may be read in Single wavelength mode with a test filter only in Dual wavelength mode with a test filter and a reference filter or in Multiple wavelength mode with a combination of filters Refer to the Wavelength Modes section in Chapter 2 WAVELENGTH MODE 4 45P 30 06 94 SINGLE DUAL MULTIPLE CE Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Single Mode Select SINGLE to use a test filter only The Reader asks for the test filter wavelength TEST FILTER 410NM 4 45P 30 06 94 NEXT LAST ENTER CE Use the NEXT and LAST commands to scroll through the list of filter wavelengths Select ENTER to accept the displayed wavelensth or CE to return to the Wavelength Mode menu Dual Mode Select DUAL to use reference and test filters The Reader asks vou to enter a test filter wavelength in the same way as for Single mode above It will then request the reference filter wavelength FILTER 550NM 4 45P 30 06 94 NEXT LAST ENTER CE Select the reference filter wavelength 1n the same way as you selected the test filter wavelength No
186. tions 43 Incorrect Operation 3 14 1 Lamp fitting the 15 16 replacing 35 36 M Main Menu 17 Maintenance 33 34 Maintenance Menu 23 24 Maintenance Reminder 17 23 Memory Menu 25 Microplate Reader See Reader 0 Optical Filters changing the 36 37 fitting the 15 16 Over Limit 26 p Param Menu 26 27 Performance specifications 43 44 Plate Carrier Diagram 5 Plate Type 26 Printer interface 29 30 47 48 R Reader accessories 41 back panel 12 connecting a printer to it 29 electrical specifications 45 features of 7 8 front panel 14 hardware specifications 43 illustration of 7 interface 45 keypad and display 14 performance specifications 43 44 physical environmental conditions 45 repacking the 34 35 resetting its memory 25 self tests 17 software specifications 43 switching it on 16 unpacking the 11 Repacking the Reader 34 35 Repeatability Mode 27 Resetting the Reader memory 25 Safety Information 3 4 Self tests 17 23 39 sample printout 40 Setup menu 18 19 Software Specifications 43 Specifications 43 45 System Menu 21 23 V Voltage Selector 13 W Warning Symbol 5 Microplate Reader User Manual 87125 Microplate Reader Troubleshooting Guide Manual code 87362 Revision of the manua October 1997 Software versions Ma
187. tive limits you have defined are not in sequence relative to the positive and negative limits Change the limits so that they follow the sequence of the positive and negative limits Troubleshooting Guide 87125 B section 1 Error Messages Warning Multiple The Multi Wavelength mode calculation wavelength calculation did not work correctly error If you specified Well calculation mode check that the well does exist on the template and check that the OD for this well was not OVER Check vour data to make sure that the calculation mode specified could be used Change the calculation mode if necessary Warning Nominal value The dilution value you have set for the is ouf of range change between positive and negative threshold ranges was not correct within the 2 tolerance Run the test again using a different nominal value or use the Titration Multiplier facility to correct the value Warning Plate ID does The plate ID you entered or the barcode not match assay scanned does not match the tag specified prefix suftix format in the test Check that the plate in the plate carrier is the one you wish to process If this message was generated after a barcode scan check that the barcode label is not damaged and check that the software is set up to recognise the correct barcode type Warning Quality The criteria for the defined QC equations Control Failed have not been met Warning Unable to The Standard samples you ha
188. transmitting STX ETX if data has been received successfully Note Users are advised to obtain data transfer software from the Reader supplier The above commands use large data sets and the data format is non standard Writing successful programs to handle these data sets is not straightforward Endpoint Program User Manual 87125 109 Chapter 7 Computer Control 6 Display Control STX 6 control character sting ETX This command allows the computer to access the 2 x 40 LCD display It recognises the following special control characters CHARACTER Writing position moves left one character Writing position moves right one character Display is cleared writing position moves to night end of display Writing position moves to left end of the display 7 Computer Control STX 7 A ETX This command acts as a toggle beginning or ending computer control The Reader will not accept other commands from the computer until control is restarted is the ASCI number 0 1 or 2 where G Stop 1 Start 2 Start with Checksums 7 1 ETX This command is used to begin computer control once the data link is established SIX 7 0 ETX This command is used to end computer control STX 7 This command acts as a toggle SIX72ETX This command begins computer control and enables checksums 9 Reduced Matrix STX 9 A B ETX is the number of columns in the reduced matrix B is the num
189. ts explained beiow 5 The previous reading is used as blank value for subsequent readings this command resets argument A 3 B is the column indicator in the matrix command defined by the ASCH numbers 1 to 9 and the following special characters 10 11 lt 12 ASCII number symbol 1 to see table below for indication of blank wells affecting the wells D through Dis an ASCII number or symbol 1 to see table below for indication of blank wells affecting the wells H through E 2 3 4 5 6 7 8 9 Endpoint Program User Manual 87125 107 Chapter Computer Control an example STX 44221 ETX would cause blanking in column 2 on wells C and H Each B C D set represents one row Further B C D sets can be added in the command to set additional blanks that is STX 44221554 ETX will set blanks in column 2 on wells C and H and also column 5 on wells B D and F Arguments A 0 5 and 5 should be used collectively when data from individual wells are transmitted singly as in MANUAL mode STX 2 A 2 Similarly arguments 1 2 and 4 are used in normal read mode STX 2 0 since they affect a matrix of blanks across plate If argument 3 1 setin MANUAL mode blanks will be assigned for each well position addressed until the command is reset by argument 5 the plate is read when a new blank well is encountered the blank value is updated and is subtracted from al
190. tures and Specifications 3 Chapter 2 Understanding the Endpoint Program 5 2 1 Wavelength Modes 2 Single and Dual Wavelength Modes 7 Multiple Wavelength Mode t cd 2 2 Optical 2 4 stent 9 Effect of Pathlength 1 0000 10 2 3 Blanking ERR 10 Chapter 3 Installation A eere eere eere eenese LL 3 1 Installing Endpoint in a PR 1100 Reader 13 3 2 Re Installing Endpoint in a PR 2100 Reader 14 3 3 Upgrading from a Previous Version esee eene 14 3 4 Upgrading Assay Protocol Files in the PR 2100 15 Chapter 4 Creating and Editing Tests 17 4 Creating New Test 20 Test 20 Test Name Plate ID Prompt NENNEN Shake Time and Shake Modes Defme Template Prompt ttc D Defining the Template Manually eee sesenta 24 Defining the Terplate Automatically Wavelengtb Mode ee HERR 1 Results Matrix NENNEN Area Statistics MERERI V Quality Control Equations NENNEN Inserting Output Options into the Test N
191. ty OD data matrix Threshold Difference and Ratio matrices Graphical Curve Fit output Spline Polynomial regression linear quadratic cubic and quartic functions Point to point straight line fitting Michaelis Menten equation Sigmoid 4PLC Parallel Akima fit AXIS Fits Linear Semi log Log log Auto function for regression coefficient Echo of calculated results to RS232 Endpoint Program User Manual 87125 Chapter 2 Understanding the Endpoint Program 2 1 Wavelength Modes MM Single and Dual Wavelength Modes HR 7 Multiple Wavelength Mode sess 8 2 2 Optical 9 10 2 3 Blanking RE 10 Endpoint Program User Manual 87125 Chapter 2 Understanding the Endpoint Program This page is intentionally left blank Endpoint Program User Manual 87125 Chapter 2 Understanding the Endpoint Program This chapter describes certain aspects of the theory of photometry including wavelength selection optics and blanking These processes are described simply so as to give you the basic information necessary to create effective microplate tests 2 1 Wavelength Modes The Reader is able to take readings in three different modes Single using one test filter Dual using one reference and one test filter Miultiple using a combination of filters Single and Dual Wavelength Modes Using dual
192. umeric keys used to enter numbers and well locations Esc key returns the display to the Main menu Cursor keys used to scroll through well locations and menus and in some menus to move the plate camer in and out Note When the Reader is operating under the control of an external computer the keypad will not operate Fitting the Lamp and Optical Filters Warning 1 2 Disconnect the mains cable before fitting lamp amp filters Note DO NOT touch the filters bulb or reflector directly Using a No 1 Posi driver remove the optics door and if fitted remove the packing materials from behind the door Slide the optics assembly out of the instrument If you have an older instrument check your serial number panel newer Readers have 1CXCxxxx or 2CXCxxxx numbers you need to disconnect the optics assembly s I0 way connector and then slide the assembly out of the instrument Insert the lamp into the assembly and plug the connector into its back see Figure 7 For Osram type lamps Make sure that the lamp 1s seated correctly with the locating pip on the lamp fitted into the notch on the optics assembly For Philips type lamps Make sure that the lamp 1s seated correctly and that the lamp pins are horizontal as shown in Figure 7 Insert the filters into the filter wheel Place the filter with the lowest wavelength in position 1 the next lowest in position 2 and so on Make sure the side
193. ve if it falls above or below a specified number It may be necessary to introduce conditions into the equation that is a result will be recorded as positive or negative using certain other criteria such as comparison with a specified well or group of wells or the use of a constant The Reader asks you to enter the negative equation to define the negative range WELL Inserts well type identifiers Blank Standard Test Control or User well into the equation OPTIONS Inserts brackets and statistical values into the equation OPER Inserts arithmetic operators into the equation Note Two characters together indicate the power e g T1 PC ENTER Saves the equation The Reader checks the equation to test its validity If it is not correct the Reader displays it for editing CE Deletes the character above the cursor or if no character has been added it returns the display to the previous menu Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Use the keypad to enter numbers into the equation Use the left and right cursor keys to scroll the equation left and right across the display Use the up and down arrows to move to the start and end of the equation you enter each threshold equation the Reader increments to the next equation for example from the positive equation to the double positive equation etc you do not want to use one of the equations select
194. ve if they equal or are greater than the Positive Control well NC 0001 EQN If you enter equal positive and negative cut off values the Reader asks if you want to designate the assay as inverse If you specify inverse assay a well is marked as positive if the result of the threshold equation is less than or equal to the positive cut off value well 1 marked as negative if the result of the threshold equation is greater than the negative cut off INVERSE ASSAY 4 45 30 06 94 YES NO CE Select YES to designate the assay as inverse Select NO for a standard assay Ratio Matrix Output Option The ratio matrix is a table of results obtained by converting the ODs into a different scale than they were read in This is accomplished by multiplying all the ODs on the plate by a ratio equation The ratio equation 1s calculated once for every well on the plate and the result replaces the OD value for subsequent calculations You can also use an International Units IU equation to convert the results to different units which will appear in the ratio matrix as an extra set of IU conversions typical ratio matrix is shown in Appendix B To include a ratio matrix select RATIO at the output options prompt The Reader asks you to enter the ratio equation RATIO _ 4 45 30 06 94 WELL OPTIONS ENTER WELL Inserts well type identifiers Blank Standard Test Control or User well into the equ
195. ve specified calculate percentage for use with this facility either do not response values exist or have not been included in the Curve Fit calculations Create or include the Standards or change the Percent Response samples to ones which are already included in the calculations Troubleshooting Guide 87125 13 Section 1 Error Messages 14 Warning Unable to contract template Warning QC values are 0 000 Check Data Matrix The software was unable to reduce the template in the way you specified Templates cannot be reduced if the original plate contained any empty wells reducing the template means removing all the Test samples the templates combined onto the plate had different row and column orientations Rectify the problem and try again There is a zero in the QC equation Verify if the OD value in the Data Matrix is a result of 0 000 OD or an OVER Ihe Endpoint program will convert an OVER value to 0 000 OD in the QC equation OVER readings result when well OD s exceed the dynamic range of the Reader Troubleshooting Guide 87125 Section 2 Solving Problems Section 2 Solving Problems This section describes hardware printing and general problems and provides the recommended actions to solve them Hardware Hardware Problem Recommended Action roblems The Reader keypad The Reader is operating under the control of will not operate an external computer R
196. wavelength of the reference filter Select the reference filter in the same way as you selected the test filter wavelength Reading a Plate When the filters have been chosen the plate is read The Reader then displays the results starting at Al The left and nght arrow keys can be used to scroll through the readings for each well Al 0 000 4 45P 30 06 94 BLANK CLEAR PRINT MATRIX BLANK Zeros the displayed reading and subtracts this value from measurements of subsequent wells CLEAR Changes a blanked reading back to the origina value All subsequently viewed wells will use air blanking PRINT Outputs the reading displayed for each well location to a connected printer MATRIX Prnts out an OD matrix Returns the display to the Main menu Menus The Menus option lets you choose between jong or short menus Long Menus are the normal Endpoint menus Short Menus invoive the use of eight short cut keys which can be used to access tests for processing in Start mode Press CE to change the current menu MENUS 4 45P 30 06 94 SHORT LONG CE Select LONG or SHORT to specify the menus option Short Menus If you select short menus the Reader will ask which functions keys are to be assigned to which tests For example Endpoint Program User Manual 87125 89 Chapter 6 Utilties 90 1 01 Ali 4 45P 30 06 94 DIR ENTER Use the keypad to enter the test number to be assigned to the first functio
197. wavelength mode can reduce errors caused by dirt and scratches on the bottom of the wells but single wavelength mode is sufficient for most applications The choice of test and reference filter wavelengths depends on the particular enzyme substrate system being tested However the following rules should usually be followed 1 The test filter wavelength should be at or near the maximum absorbance of the reaction product 2 The reference filter wavelength should lie outside the absorbance band of the system but not far removed At Test wavelength Ar Reference wavelength ABSORBANCE 340 mm At 850 FILTER WAVELENGTH Figure 2 Dual Wavelength Selection Endpoint Program User Manua 87125 7 Chapter 2 Understanding the Endpoint Program The Reader subtracts the absorbance at the reference wavelength Ar from the absorbance at the test wavelength At to minimize the effect of systematic errors Aris the wavelength lying outside the major absorbance band of the sample but not far removed from At Atis the wavelength at or close to the peak absorbance of the reaction product If a test requires particular accuracy you may specify test and reference filters of the same wavelength The Reader will average the ODs produced using each filter giving a more accurate result Note If you have problems choosing filters use the Spectrum option to recommend wavelength Refer to the Spectrum section in Chapter 6
198. well type orientation and the next available well location working down the columns 1s B1 Bl 4 45P 30 06 94 Bl 51 T2 Endpoint Program User Manual 87125 Chapter 4 Creating and Editing Tests Select T2 to position the next group of Test well replicates the vanables of test wells have now been set so the Reader will not ask for replicates or orientations The display will return again to the B S T C menu displaying as the next available well location Continue to select Test wells until weli location 1 and Test well T7 are displayed User Wells Select USER from the Manual Tempiate menu to create new well types and assign these to wells Al 4 45P 30 06 94 NCI PC PRI CE The four well labels displayed correspond to User weil types one to four The default names for these are NC Negative Control PC Positive Control CO Cut off Control PR Positive Reference These names can all be changed to match your specific requirements To change the name of one of the well labels 1 Select NC1 to change the label of the first user well The Reader will display the number and label of the wel type USER WELL 1 NC 4 45P 30 06 94 ENIER CE 2 Select ENTER to confirm the name displaved or CE to change it The Reader asks you to enter a new label USER WELL 1 NC 4 49P 30 06 94 YZ ABCD ENTER 3 Use the left and right cursor keys to scroll through the characters Press the function key t
199. will return to the Setup menu Clock Menu Time Select CLOCK from the Setup menu to access the Clock menu and view the time and date settings SETUP 4 45 30 06 94 TIME DATE CE Select TIME to set the clock mode and time The Reader will display the current setting Select ENTER to confirm the mode shown or select CE to display the altematives CLOCK MODE 4 45 30 06 94 12 HOUR 24 HOUR CE Select 12 HOUR or 24 HOUR mode The Reader will allow you to change the time display TIME 4 45 30 06 94 ENTER CE Select ENTER to confirm the time shown or enter the correct time using the keypad Microplate Reader User Manual 87125 Chapter 2 installation and Setup a If you selected the 24 hour mode enter the time and press ENTER If you selected the 12 hour mode enter the time and then select A M or Date Select DATE to display the date mode The Reader wiil display the current setting Select ENTER twice to confirm the mode shown or select CE to display the alternatives Select dd mm yy or mm dd yy The Reader will allow you to change the date display DATE 30 06 94 Select ENTER to confirm the date shown or type in a new date To edit the date entered select CE use the keypad to enter a new date and then select ENTER System Menu Select SYSTEM from the Setup menu to access the System menu and view the printer and user interface settings SETUP 4 45
200. xx numbers you need to disconnect the optics assembly s 10 connector and then slide the assembly out of the instrument 4 Detach the lamp from the assembly and replace with a new one Make sure that the lamp is seated correctly refer to Fit ng the Lamp and Optical Filters in Section 2 1 5 Slide the optics assembly back in if you have an older instrument you must also reconnect the 10 way connector Microplate Reader User Manual 87125 35 Chapter 4 Maintenance 6 Replace the optics door and reconnect the power supply Figure 10 Replacing the Lamp 4 5 Changing the Optical Filters Warning If the Reader has been used recently the optics door and the lamp in the optics assembly may still be hot Allow time for the Reader to cool before touching it Take care when removing the optics door as there may be broken glass in the optics assembly Figure 11 summarizes these instructions Note DO NOT touch the filters bulb or reflector directly 1 Switch off the power supply and disconnect the mains cable 2 Usinga No Posi driver remove the optics door 3 Slide the optics assembly out of the instrument If you have an older instrument check your serial number panel newer Readers have or 2 numbers you need to disconnect the optics assembly s 10 connector and then slide the assembly out of the instrument 4 Remove the relevant filter from its socket in the filter
201. z Maximum 20 Hz Example To set the frequency to 14Hz STX 19 14 ETX Custom Shake Mode Amplitude Command This command sets the amplitude of the Custom Shake operation STX 1 ETX nnnn is a decimal number denoting the amplitude Minimum 1 0 mm Maximum 10 0mm Example To set the amplitude to 2 0mm STX 1 2 0 ETX Plate Retraction Command This command returns the plate to the In position STX 1 B ETX Endpoint Program User Manual 87125 105 Chapter 7 Computer Control 2 Read Mode STX 2 ETX Ais an ASCI number 0 1 2 3 1 Normal read mode One OD value 1s transmitted for each well Five filter read mode ODs for each of the five filters are transmitted for each weH Transmit result for single well providing normal read mode has been set A 0 In normal operation the whole plate is read and all results are transmitted to the computer Setting 2 will allow data from a single well to be transmitted providing the five filter mode has not been previously set Transmut data as percent transmission rather than optical density Transmission data is sent to five decimal places The lamp remains on following the read and must be switched off using the STX 1 6 ETX command Using this command data from a complete plate can be transmitted in dual wavelength mode in under 10 seconds This is useful for Endpoint tests This command sets the repeatability mode Using the repeatability mode you can

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