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Thermo BioMate 3 series Operator's Manual

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Operator's Manual

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Summary of Contents for Thermo BioMate 3 series

  • Page 1 BioMate™ 3 Series Spectrophotometers Operator’s Manual...
  • Page 3 Figure 1 BioMate 3 spectrophotometer Key/ A/C power connector RS232C port Figure 2 Back panel of the spectrophotometer...
  • Page 4 Key/ Paper roll holder Icon for paper direction Paper entry slot Finger tab Figure 3 Installing the paper roll holders for the internal printer (335988) Cell position keys Function keys Figure 4 Keypad of the BioMate 3 spectrophotometer...
  • Page 5 Figure 5 Installing the Single-Position Cell Holder (335916) Key/ Captive screw on lamp door Removing door from hinge Hinge Connecting wires to printer Figure 6 Installing the printer (335988)
  • Page 6 Figure 7 Removing the cover of the fuse compartment Figure 8 Removing the fuse holder Figure 9 Removing and replacing the fuses...
  • Page 7 United Kingdom Plug (BS 1363/A) Add a –04 suffix Thermo Electron Scientific Instrument Corporation certifies that the GENESYS 10, GENESYS 6, and BioMate 3 Spectrophotometers have been tested according to the instrumentation standards listed in this section in compliance with IEC directives and other regulatory requirements. The equipment under test (EUT) consisted of a sample instrument and applicable accessories, which are manufactured by Thermo Electron Scientific Instrument Corporation.
  • Page 9 The information in this publication is provided for reference only. All information contained in this publica- tion is believed to be correct and complete. Thermo Electron Scientific Instruments Corporation shall not be liable for errors contained herein nor for incidental or consequential damages in connection with the fur- nishing, performance or use of this material.
  • Page 10 (1) year from the date of delivery. This warranty is provided only if the warranty registration card is returned to Thermo Electron Scientific Instruments Corporation within fifteen (15) days after delivery.
  • Page 11 SOFTWARE PASSWORD This password allows you to enter the security section of the software used on the Thermo Electron Corporation spectrophotometer. Through the security section, you can "lock" test setups (test parameters) so that they may not be altered. The password also allows you to remove the security so that you may edit the test parameters.
  • Page 12 Thermo Electron Corporation...

  • Page 13: Table Of Contents

    Table of Contents CHAPTER 1 - Setting Up the Instrument Setting up the instrument.........................1-1 Setting utility parameters ......................1-1 Selecting the language ......................1-1 Setting the date and time ......................1-2 Selecting standby settings......................1-2 Setting baseline expiration time ....................1-2 Setting the screen contrast......................1-2 Loading paper in the internal printer..................1-2 Setting the utility parameters for the printer ................1-3 Selecting and positioning glassware....................1-3...
  • Page 14 Rescaling & recalculating tabular kinetics results..............3-19 Survey Scan/Scanning ........................3-20 Recalling a test.........................3-20 Setting up test parameters ......................3-20 Collecting a baseline scan.......................3-20 Scanning an unknown......................3-21 Viewing & manipulating scan data..................3-21 3-Point Net............................3-24 Recalling a test.........................3-24 Setting up test parameters ......................3-24 Thermo Electron Corporation...
  • Page 15 Table of Contents Taking measurements ......................3-24 Multiple Wavelengths........................3-25 Recalling a test.........................3-25 Setting up test parameters ......................3-26 Taking measurements ......................3-26 CHAPTER 4 - Using the Performance Validation Program Overview ............................4-1 Accessing the Performance Validation tests ..................4-1 Troubleshooting checklist.........................4-1 Wavelength Accuracy - Internal.......................4-1 Wavelength Accuracy - Standards ....................4-2 Adding wavelengths........................4-2 Deleting wavelengths.........................4-3...
  • Page 16 Table of Contents Appendix A - Specifications Appendix B - Parameters Appendix C - Calculations Index Thermo Electron Corporation viii...

  • Page 17: Chapter 1 - Setting Up The Instrument

    Setting Up the Instrument Setting up the instrument b) Initializing c) Calibrating filter wheel 1. Carefully unpack the shipping carton and verify that you have received all the items listed d) Finding zero order below. e) Finding energy peak • BioMate 3 spectrophotometer Calibrating grating •...

  • Page 18: Setting The Date And Time

    Note: Arrows on the paper roll holders indicate To prolong xenon lamp life, your the direction of the paper feed (see spectrophotometer has been pre-set at the factory Figure 3). to automatically go into standby mode after 15 minutes. To change Standby Mode time: Thermo Electron Corporation...

  • Page 19: Setting The Utility Parameters For The Printer

    Setting Up the Instrument Selecting and positioning glassware • Feed the paper straight into the paper entry slot. The printer grabs the end of the paper and The wavelength range for different types of cells pulls it in. varies depending on the manufacturer: •...

  • Page 20: Z-Dimensions

    The figure below illustrates the position of the light beam in the spectrophotometer. The specifications for the sample compartment, including the dimensions of the beam are: • Z-dimension • Square cuvettes/Test tubes 8.5mm • Beam size 2mm (wide) x 7mm (high) Thermo Electron Corporation...

  • Page 21: Chapter 2 - Using "Biotests" Software

    Using “Biotests” Software Overview notice the following types of entries for parameters: • Type-in entries are numeric values that you The BioMate instrument allows you to run an can enter using the numeric keypad. assortment of tests used to characterize biological and biochemical substances.

  • Page 22: Smartstart Feature

    Note: At this point, you can power down the or calculates concentration based on instrument and then power it back up. absorbance and concentration factor When it starts up again, the parameter determined by oligo calculator. screen for the selected test will be displayed. Thermo Electron Corporation...

  • Page 23: Dna (260/280 And Dna 260/230)

    Using “Biotests” Software Several of these categories include multiple tests Setting up test parameters that are similar, so the section may not include 1. With the DNA (260/280) or DNA (260/230) screen samples for each test. For example, the screen displayed, use the arrow keys to parameters are the same for the Direct UV highlight the name of the parameter you want measurement of ssDNA and RNA tests, but the...

  • Page 24: Dna With Scan (260/280) And Dna With Scan (260/230)

    Appendix B for a description of the parameters and Appendix C for the default values. To get started, with the BioMate Tests screen displayed, move the arrow keys to highlight Nucleic Acid Tests and press ENTER. A list of Thermo Electron Corporation...

  • Page 25: Dsdna, Ssdna, Rna And Oligos (Entered Factor) Direct Or Uv Measurements

    Using “Biotests” Software 2. Place the blank in the B position. dsDNA, ssDNA, RNA and Oligos (entered factor) Direct or UV Measurements 3. Press Measure Blank to collect the baseline. When the instrument is finished measuring the These test measurements are all set up and run blank, the message disappears.
  • Page 26 This conversion factor is used to calculate the concentration of oligos in your sample from the absorbance measurement. Refer to Appendix B for a description of the parameters and Appendix C for the default values. Thermo Electron Corporation...
  • Page 27 Using “Biotests” Software To get started, with the BioMate Tests screen 1. Place the blank and unknowns in the correct displayed, move the arrow keys to highlight cell positions. Nucleic Acid Tests and press ENTER. A list of 2. Press ENTER to start the measurements. The nucleic acid test appears.

  • Page 28: Protein Measurements

    Measure Standards to set up and run the standards. The instrument automatically measures the blank first, then measures the standards. When the instrument has measured all the standards, the Standards screen appears, showing the absorbance of each Thermo Electron Corporation...

  • Page 29: Direct Uv (280) And Direct Uv (205)

    Using “Biotests” Software standards, along with the slope, intercept and Measuring protein samples correlation coefficient of the standard curve. Measuring unknowns automatically (using Auto 6 or Auto 3) 1. With the Standards screen displayed, place the blank and unknowns in the correct cell positions.

  • Page 30: Warburg-Christian

    Save Test to save the test or Run Test to 3. Press Measure Blank to measure the blank. If measure the blank and unknowns. your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B Thermo Electron Corporation 2-10...

  • Page 31: Cell Growth

    Using “Biotests” Software Measuring the sample Measuring unknowns automatically (using Manual 6 or Single Cell Positioner) 1. With the Warburg-Christian screen displayed, place the blank and unknowns in the correct cell positions. 2. Press ENTER to start the measurements. The instrument automatically measures the blank first, then measures the unknowns and displays the absorbance and concentration of...

  • Page 32: Oligo Calculator

    BioMate Tests screen to highlight Oligo Calculator and press ENTER. The Oligos screen appears. 5. Enter the % formamide and % mismatch (if known) that will be used to calculate the Tm. The calculated Tm values are shown on the screen. Thermo Electron Corporation 2-12...

  • Page 33: Chapter 3 - Using "General Tests" Software

    Using “General Tests” Software General information Editing and Loading Saved Tests When you save a test, it is stored in the Utility Test Directory. Within this directory, these tests can be loaded, deleted or locked/unlocked. To load, delete or lock/unlock tests: 1.

  • Page 34: Using The Smartstart Feature

    4. When the appropriate test is highlighted, press Select Test to add the selected test to the SmartStart menu. An arrow sign “>” will indicate the test has been selected. 5. Press Load Test. Thermo Electron Corporation...

  • Page 35: Running The Cell Correction Program

    Using “General Tests” Software 6. The parameter screen of the test you selected • Fill the cells with distilled water (or other will be displayed. blank solution), and place them in the sample compartment (see “Selecting and Note: At this point, you can power down the positioning glassware”...
  • Page 36 Cell Correction program will be run. A list of wavelengths appears. 5. If you selected Scan mode in the preceding step, press Run Corr. to start the Cell Correction program. If you selected Discrete nms mode, first specify the wavelengths using Thermo Electron Corporation...

  • Page 37: Taking Measurements

    Using “General Tests” Software Note: Cells should be matched at all analytical cell position buttons on the keypad do not wavelengths because matching at one function when you select Single Cell Platform wavelength does not guarantee matching even if you have a 6-Position Cell Holder at others.

  • Page 38: Basic Absorbance/%T Measurements

    %T and you use the Change Mode function key to switch to concentration measurements. The spectrophotometer allows you to measure concentration using either a factor or a standard to convert absorbance readings to concentration units. Thermo Electron Corporation...

  • Page 39: Setting The Wavelength & Mode

    Using “General Tests” Software • When you use a factor, you need to specify the factor and the concentration units. • When you use a standard, you need to specify the concentration of the standard and measure its absorbance. When you use the Basic Concentration program, you can perform these tasks: •...

  • Page 40: Entering A Factor

    The parameters for the selected test appear on 1. If your instrument is equipped with the the screen. 6-Position Cell Holder, place the unknown you want to measure in one of the cell positions and press the corresponding cell position Thermo Electron Corporation...

  • Page 41: Setting Up Test Parameters

    Using “General Tests” Software From this screen, you can: Taking measurements manually (using Manual 6 or Single Cell Platform) • Set up test parameters 1. With the Advanced A/%T/C screen displayed • Run Cell Correction program and the parameters set, press Measure •...

  • Page 42: Recalling A Test

    Measurement Mode set to Conc/Std, press Run Standard. The Measure Standard screen appears. 2. Use the number keys to enter the concentration value of the standard and press ENTER. 3. Place the blank and standard in the correct cell positions. Thermo Electron Corporation 3-10...

  • Page 43: Entering A Factor

    Using “General Tests” Software 4. Press Measure Blank to measure the blank. If 6-Position Cell Holder, you can place up to five your instrument is equipped with a 6-Position samples in the cell holder. Cell Holder, it automatically moves to the B 3.

  • Page 44: Recalling A Standard Curve

    6. Press Measure Standards to measure the standards. If your instrument is equipped with a 6-Position Cell Holder, press the cell position buttons on the keypad to re-position the cell Thermo Electron Corporation 3-12...

  • Page 45: Measuring Unknowns

    Using “General Tests” Software holder and measure the rest of the standards 2. Place the blank and unknowns in the correct manually. cell positions. When the instrument has measured all the 3. Press ENTER to measure. The instrument standards, the Standards screen appears, automatically measures the blank first, then showing the absorbance of each standard, measures the unknowns.

  • Page 46: Absorbance Ratio

    To reset standards 1. With the standard curve displayed on your screen, press Reset Standards and press ENTER. 2. Use the arrow keys to highlight Reset Standards and press ENTER. All the standards and measurements will be removed. Thermo Electron Corporation 3-14...

  • Page 47: Recalling A Test

    Using “General Tests” Software Recalling a test Measuring unknowns Measuring unknowns automatically (using Auto 6 or Auto 3) 1. With the Absorbance Ratio screen displayed, press Stored Tests. A list of stored tests appears. 1. Place the blank and unknowns in the correct 2.

  • Page 48: Absorbance Difference

    Set up Cell Correction program 3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position • Save a test Cell Holder, it automatically moves to the B • View the list of stored tests Thermo Electron Corporation 3-16...

  • Page 49: Kinetics

    Using “General Tests” Software position to measure the blank. When it When the Test Types screen appears, highlight completes the measurement, it returns to its Kinetics and press ENTER. previous cell position. Recalling a test 1. With the Kinetics screen displayed, press Stored Tests.

  • Page 50: Rescaling & Recalculating Kinetics Results

    1. With your kinetics data displayed on the edit recalculates the reaction rate. screen, press Manual Scale. The manual scale options appear. When you are working with graphical kinetics results, you need to press Edit Graph before you can rescale and recalculate. Thermo Electron Corporation 3-18...

  • Page 51: Rescaling & Recalculating Tabular Kinetics Results

    Using “General Tests” Software have selected and displays the recalculated rate and result. Rescaling & recalculating tabular kinetics results When you are working with tabular kinetics results, you need to press Edit Data before you can rescale and recalculate. After collecting your kinetics data, you can use all the data for the rate calculation or you can select specific start and end times.

  • Page 52: Survey Scan/Scanning

    Set up Cell Correction program • Save a test • View the list of stored tests • Collect a baseline • Scan unknowns Note: If you want to switch between tabular and graphical displays, press Graph/Tabular. Thermo Electron Corporation 3-20...

  • Page 53: Scanning An Unknown

    Using “General Tests” Software Scanning an unknown Note: If your instrument is equipped with a 6-Position Cell Holder, be sure to place the unknown in cell position #1. The instrument always uses cell position #1 to scan the unknown. 1. With the Survey Scan test parameters displayed on the screen, press Run Test.
  • Page 54 (designated for the left, center and right wavelengths) appears. 2. To set the minimum or maximum value for the X- or Y-axis, press Min Y, Max Y, Min X Max X. A screen appears prompting you to enter the appropriate value. Thermo Electron Corporation 3-22...
  • Page 55 Using “General Tests” Software 3. Use Cursor → → and Cursor ← ← to position the left cursor line to the desired wavelength value. The instrument calculates the area under the curve for the selected wavelengths. 4. Continue selecting the other wavelengths by pressing Next Cursor to activate the next cursor line.

  • Page 56: 3-Point Net

    To get started, press the TEST key on the keypad. 1. With the 3-Point Net screen displayed and the When the Test Types screen appears, highlight parameters set, press Run Test. The 3-Point Net and press ENTER. 3-Point Net measurement screen appears. Thermo Electron Corporation 3-24...
  • Page 57 Using “General Tests” Software completes the measurement, it returns to its previous cell position. 4. Press Measure Sample to measure the unknowns. The sample measurement appears on the screen. If your instrument is equipped with a 6-Position Cell Holder, press the cell position buttons on the keypad to reposition the cell holder and measure the rest of the unknowns manually.

  • Page 58: Taking Measurements

    3. Press Add nm. 4. Enter the values for the wavelength and factor and press ENTER. 5. When the values are correct, press Add nm. Thermo Electron Corporation 3-26...
  • Page 59 Using “General Tests” Software Taking measurements manually (using Manual 6 or Single Cell Platform) 1. With the Multiple Wavelength screen displayed and the parameters set, press Run Test. The Multiple Wavelength measurement screen appears. 2. Place the blank and unknowns in the cell holder.
  • Page 60 Using “General Tests” Software Thermo Electron Corporation 3-28...

  • Page 61: Chapter 4 - Using The Performance Validation Program

    Using the Performance Validation Program Overview Troubleshooting checklist The Performance Validation program allows you to If a Performance Validation test fails, follow the run tests to check the performance of your instructions below to help you diagnose common instrument. Available tests include: problems that may cause a test to fail.

  • Page 62: Wavelength Accuracy - Standards

    The wavelength accuracy 4. When the value is correct, press Add test passes or fails based on this wavelength Tolerance to add the tolerance. alone. The other two wavelengths may be used for long-term repeatability testing. The Thermo Electron Corporation...

  • Page 63: Deleting Wavelengths

    Using the Performance Validation Program Deleting wavelengths Note: You can display the tolerances for this test in either absorbance or %transmittance. 1. If you want to delete a wavelength, use the arrow keys to highlight the appropriate 1. With the Performance Validation screen wavelength.

  • Page 64: Noise Measurement

    Noise Measurement. 2. Press Start Test to run the test. The results of 2. Press ENTER. The Noise Measurement the test appear on the screen, indicating pass screen appears. or fail for each wavelength. Thermo Electron Corporation...

  • Page 65: Internal Printer Test

    Using the Performance Validation Program 1. With the Performance Validation screen displayed, use the arrow keys to highlight Stray Light. 2. Press ENTER. The Stray Light screen appears. 3. Make sure that the Blank position is empty and insert the 2A filter in position #1 if you are measuring at 2A.

  • Page 66: Rs232C Test

    1. Verify that the RS232 Test Plug is securely attached to the RS232C port on the back panel of the instrument. 2. With the Performance Validation screen displayed, use the arrow keys to highlight RS232C Test. Thermo Electron Corporation...

  • Page 67: Chapter 5 - Connecting & Using Accessories

    Connecting & Using Accessories General information Cell holders & cell holder accessories The spectrophotometer supports a variety of If the spectrophotometer includes a 6-Position Cell sample-handling accessories. This section Holder, you can install a single-position cell describes how to connect and use the following platform.

  • Page 68: Changing Cell Holders

    Cell Holder straight down into the sample Note: You can install only three each of some compartment. accessory cell holders. Make sure to place them in positions B, 2 and 4. Thermo Electron Corporation...

  • Page 69: Internal Printer

    Connecting & Using Accessories Internal printer External computers Installing the internal printer To connect an external computer, make sure that the pin-outs on the connectors are set according to the illustration below. WARNING To connect an external computer, connect the computer cable to the 9-pin RS232C port on the back of the instrument (#2, Figure 2).
  • Page 70 Connecting & Using Accessories Thermo Electron Corporation...

  • Page 71: Chapter 6 - Performing Maintenance Procedures

    Performing Maintenance Procedures The spectrophotometer is durable and reliable, so • Always clean up spills to prevent or minimize routine maintenance is minimal. This section damage to the instrument. If concentrated includes complete instructions for: acids or bases, or any hydrocarbon materials, are spilled on the instrument, be sure to clean •...

  • Page 72: Cleaning The Windows Of The Sample Compartment

    • 120VAC, 2.5A, Slo-Blo • 240VAC, 1.25A, Slo-Blo (2 required) See Replacement parts on page 5-3 for a list of replacement part numbers. WARNING The instrument fuse must be replaced with the same type and rating fuse. Thermo Electron Corporation...

  • Page 73: Replacement Parts

    Performing Maintenance Procedures Replacement parts Catalog # Description 335916 Single Cell Platform - with single cuvette holder installed. 336028 Single Cell Holder - Accommodates 10mm test tubes, 10mm square cuvettes, short pathlength cuvettes with spacers, and 10mm ultra-microcell; fits on 335927 6-Position Cell Holder or 335916 Single Cell Holder Platform. 335927 6-Position Cell Holder - with six (6) 336028 single cell holders installed.
  • Page 74 Performing Maintenance Procedures Thermo Electron Corporation...
  • Page 75 Appendix A - Specifications Specifications Table 1 Specifications for BioMate 3 spectrophotometers BioMate 3 Spectral Bandwidth Optical System Split beam, grating-based, dual detectors Lamp Source; Lifetime Xenon; 5 years typical Wavelength Range 190 - 1100nm Accuracy ± 1.0nm Repeatability ± 0.5nm Display 320 x 240 pixel LCD, 3.8"...
  • Page 76 24 hours after taking it out of storage. Temperature should be maintained at ±4° F. Relative humidity should be maintained to ±5%. Altitude From below sea level to 2000 meters (6562 feet) For indoor use only Installation Category II Pollution Degree 2 Thermo Electron Corporation...
  • Page 77 Appendix B - Parameters The following table lists all the parameters used for the BioMate 3 applications and for the general tests available on the instrument and a brief description of each parameter. Parameter Description # of Wavelengths Number of wavelengths set for multiple wavelength analysis # of wavelengths for Used to determine wavelength accuracy of unit wavelength accuracy...
  • Page 78 Internal Reference wavelength; for each reported measurement, measures analytical wavelength & reference wavelength. Reported measurement = abs @ analytical WL - abs @ reference WL Ref. Wavelength Turns internal zeroing on or off Correction Thermo Electron Corporation BioMate 3 Operator’s Manual...
  • Page 79 Appendix B - Parameters Parameter Description Sample Positioner Type of Positioner - 1 Cell Platform = no auto turret Manual = turret moved by buttons Auto 3 = turret auto moved - B, 2, 4 Auto 6 = turret auto moved - B, 1,2,3,4,5 Sample Volume Total volume of sample Scan Speed...
  • Page 80 Appendix B - Parameters Thermo Electron Corporation...
  • Page 81 Appendix C - Calculations Calculations Table 1 Calculations for “Biotest” Software Test Name Calculation(s) Default Displayed Parameters Results µg/mL DNA/Protein Dilution Factor (D ) = diluent vol + sample volume = 260nm (260, 280) sample volume = 280nm = 320nm DNA concentration = [(A –...
  • Page 82 205nm mg/mL Factor = 31 Warburg-Christian Dilution Factor (D ) = diluent vol. + sample vol. = 280nm mg/mL sample volume = 260nm = 1.55 Protein Concentration = [(A – (A = 0.76 Cell growth None 600nm Thermo Electron Corporation...
  • Page 83 Appendix C - Calculations Calculations Table 2 Calculations for BioMate Oligo Calculator Calculation Entry Parameters Formula Displayed Units # of bases Repetitive sequence of Count of total # of bases entered Length = # of A, T (or U), G and C bases %GC content Use AT (U) GC sequence...
  • Page 84 • %form = %formamide in the sample • L = # of base pairs • P = % mismatching Conversion from • µg/mL and molecular pmol/µ = µg/mL x 1000 pmol/µ weight from Oligo (calc DNA Mol. Wt. factor) test Thermo Electron Corporation...
  • Page 85 Appendix C - Calculations Calculations Table 3 Calculations for Software Calculation Calculation(s) Graphs Standard Curves SX = Σ x Partial sums SY = Σ y SXX = Σ x SYY = Σ y SXY = Σ x SQX = Σ (x = N * SXX - SX SQY = Σ...
  • Page 86 − Abs Absλ Absλ Absorbance Ratio − Abs Absλ Absλ Absorbance Difference ∗ factor 2 Result = Absλ * factor 1 - Absλ (Absλ - Absλ ) * factor 1 - (Absλ - Absλ ) * factor 2 Thermo Electron Corporation...
  • Page 87 Appendix C - Calculations Calculation Calculation(s) Graphs Baseline corrected absorbance = 3-Point Net λ  λ   A λ  λ 3-Point Net Absorbance sample curve BioMate 3 Operator’s Manual...
  • Page 88 Appendix C - Calculations Thermo Electron Corporation...
  • Page 89 Index 3-Point Net ....3-24, 3-25, C-7 Concentration measurements ..3-6, 3-10 measurements ....3-20, 3-23 Concentration units .
  • Page 90 RS232C ......4-6 Printer, installing ....5, 5-3 Thermo Electron Corporation...
  • Page 91 Index saving ..3-5, 3-9, 3-10, 3-13, 3-15, 3-16, 3-18, 3-21, 3-25, 3-26 Tm ....2-12, A-1, C-3, C-4 Total run time .
  • Page 92 Index Thermo Electron Corporation...
  • Page 94 Item No.: 335904-10001, Rev G 06/03 Component No.: 335904-10063, Rev G 06/03...

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