Thermo BioMate 3 series, 335904, 335904P, 335905, 335905P Operator's Manual

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BioMate™ 3 Series

Spectrophotometers

Operator’s Manual

Figure 1 BioMate 3 spectrophotometer

Figure 2 Back panel of the spectrophotometer

Key/

c A/C power connector d RS232C port

Figure 3 Installing the paper roll holders for the internal printer (335988)

Figure 4 Keypad of the BioMate 3 spectrophotometer

Key

c Cell position keys

d Function keys

Key/

c Paper roll holder

d Icon for paper direction

e Paper entry slot

f Finger tab

Figure 5 Installing the Single-Position Cell Holder (335916)

Figure 6 Installing the printer (335988)

Key/

c Captive screw on lamp door

d Removing door from hinge

e Hinge

f Connecting wires to printer

Figure 7 Removing the cover of the fuse compartment

Figure 8 Removing the fuse holder

Figure 9 Removing and replacing the fuses

Declaration of Conformity

(For instruments manufactured after July 1, 2001)

Model: GENESYS™ 10 Series Catalog Nos.: 335900, 335900A, 335900P, 335900AP, 335901, 335901A, 335901P, 335901AP 335902, 335902A, 335902P, 335902AP, 335903, 335903A, 335903P, 335903AP 335906, 335906P, 335907, 335907P

Model: BioMate™ 3 Catalog Nos.: 335904, 335904P, 335905, 335905P

Model: GENESYS™ 6 Catalog Nos.: 335908, 335908P

North American Plug (NEMA 5-15) Numbers above European Plug (CEE 7/7 Schuko) Add a –02 suffix 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. The EUT was configured to ensure that both the worst case condition,

and that all of the accessories were tested. This

equipment

has been tested for use in non-residential environments.

IEC Directives

89/336/EEC Electromagnetic Compatibility Directive 73/23/EEC Low Voltage Directive

Electromagnetic Compatibility Test Standards

IEC 61326-1 1998, Electrical Equipment for Measur

ement, Control, and Laboratory use

- EMC Requirements. Class A Limits

IEC 61000-4-2 1999, Electrostatic Discharge Immunity Test (Test level: 4KV Air Discharge and 4 KV Contact Discharge)

IEC 61000-4-3 1998, Radiated, Radio Frequency, Electromagnetic Field Immunity Test (Test level: 3V/m)

IEC 61000-4-4 1995, Electrical Fast Transient/Burst Immunity Test (Test level: 1KV on the supply lines)

IEC 61000-4-5 1995, Surge Immunity Test (Test level: 0.5KV line to line and 1KV line to earth on the supply lines)

IEC 61000-4-6 1996, Immunity to Conducted Disturbances, Induced by Radio-Frequency Fields (Test level: 3V on the supply lines)

IEC 61000-4-11 1994, Voltage Dips, Short Interruptions, and Voltage Variations Test Level: 1 cycle/100%

CISPR 16-2 1999, Specification for Radio Disturbance and

Immunity Measuring Apparatus and Methods

–

Methods of Measurement of Disturbances and Immunity

Safety Test Standards

IEC 61010-1 1990 + A1 1992 +A2 1995. Safety requirements for El

ectrical Equipment for

Measurement, Control and

Laboratory use.

CSA C22.2 No. 1010.1, plus Am 2

IEC 61010-1 1997, Safety requirements for Electrical Equipment for Measuremen

t, Control and Laboratory use;

Part 1: General Requirements Test level: Installation Category II, Pollution Degree 2

Authorized signature:

_______________________________________ ___ Date: ____27May03____ Brenda Wilcox Vice President, Molecular Spectroscopy

i BioMate 3 Operator’s Manual

The information in this publication is provided for reference only. All information contained in this publication 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 furnishing, performance or use of this material. All product specifications, as well as the information contained in this publication, are subject to change without notice.

This publication may contain or reference information and products protected by copyrights or patents and does not convey any license under our patent rights, nor the rights of others. We do not assume any liability arising out of any infringements of patents or other rights of third parties.

We make no warranty of any kind with regard to this material, including but not limited to the implied warranties of merchantability and fitness for a particular purpose.

Copyright © 2003 by Thermo Electron Scientific Instruments Corporation, Madison, WI 53711. Printed in the United States of America. All world rights reserved. No part of this publication may be stored in a retrieval system, transmitted, or reproduced in any way, including but not limited to photocopy, photograph, magnetic, or other record, without the prior written permission of Thermo Electron Scientific Instruments Corporation.

For technical assistance, please contact:

THERMO ELECTRON CORPORATION

(North America, Asia Pacific, Middle East, Africa, India and Latin America) 5225 Verona Road, Madison, WI 53711-4495, USA Telephone: (800) 642-6538 or (608) 276-6373 Fax: (608) 273-5045 E-Mail: careplan.techsupport@thermo.com

THERMO ELECTRON CORPORATION

(Europe) Mercers Row, Cambridge CB5 8HY, UK Telephone: Int +44 (0) 1223 446655 Fax: Int +44 (0) 1223 446644 E-Mail: careplan.techsupport@thermo.com

SPECTRONIC is a registered trademark and BioMate is a trademark of Thermo Electron Scientific Instruments Corporation.

Patent No.: 6414753

Item No.: 335904-10001, Rev. G 06/03 Component No.: 335904-10063, Rev. G 06/03

Thermo Electron Corporation ii

GENERAL SAFETY NOTES USED IN THIS MANUAL

This symbol alerts you to important information about using the instrument. Be sure to read and follow the associated instructions carefully.

This symbol alerts you to potential electrical hazards. Be sure that only qualified personnel perform the related procedures.

This symbol alerts you to hot surfaces. Be sure to read and follow the associated instructions carefully.

This symbol alerts you to potential UV radiation exposure, which can cause eye damage. Wear UV-opaque eye protection..

NEW PRODUCT WARRANTY

Thermo Electron Scientific Instruments Corporation instrumentation and related accessories are warranted against defects in material and workmanship for a period of one (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.

This warranty covers parts (except those specified below) and labor, and applies only to equipment which has been installed and operated in accordance with the operator's reference guide and which has been serviced only by authorized Thermo Electron Scientific Instruments Corporation dealers or service personnel. This warranty does not apply to equipment and accessories that have been modified or tampered with in any way, misused, or damaged by accident, neglect, or conditions beyond Thermo Electron Scientific Instruments Corporation's control.

This warranty does not apply to lamps, glassware, and similar expendable components. However, such parts and components may be warranted by their manufacturer.

Thermo Electron Scientific Instruments Corporation is not responsible under this warranty for loss in operating performance due to environmental conditions.

THIS WARRANTY IS IN LIEU OF ALL WARRANTIES EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF FITNESS FOR A PARTICULAR PURPOSE OR MERCHANTABILITY OR OTHERWISE, and states Thermo Electron Scientific Instruments Corporation's entire and exclusive liability and the Customer's exclusive remedy for any claim in connection with the sale or furnishing of services, goods, or parts, their design, suitability for use, installation, or operations. Thermo Electron Scientific Instruments Corporation will in no event be liable for any direct, indirect, special, or consequential damages, whatsoever, including loss of goodwill, whether grounded in tort (including negligence), strict liability or contract, and Thermo Electron Scientific Instruments Corporation's liability under no circumstances will exceed the contract price for the goods and/or services for which liability is claimed.

iii BioMate 3 Operator’s Manua

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. Please refer to the appropriate section in this Operator's Manual for more information on locking a test.

PASSWORD: 4 3 6 3 7 9 7

Thermo Electron Corporation iv

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

Z-dimensions ....................................................................................................................................1-4

CHAPTER 2 - Using “Biotests” Software

Overview ...........................................................................................................................................2-1

Table of parameters ...................................................................................................................2-1

Entering information & commands..................................................................................................2-1

Types of parameter entries........................................................................................................2-1

Keypad layout.............................................................................................................................2-1

SmartStart feature ............................................................................................................................2-2

Setting up a single-test SmartStart ...........................................................................................2-2

Setting up a multiple-test SmartStart ........................................................................................2-2

Nucleic acid measurements ............................................................................................................2-2

DNA (260/280 and DNA 260/230) ............................................................................................2-3

DNA with Scan (260/280) and DNA with Scan (260/230).......................................................2-4

dsDNA, ssDNA, RNA and Oligos (entered factor) Direct or UV Measurements...................2-5

Protein Measurements.....................................................................................................................2-8

Bradford (standard & micro), Lowry (standard & micro), BCA (standard & micro) and Biuret

measurements ...........................................................................................................................2-8

Direct UV (280) and Direct UV (205)........................................................................................2-9

Warburg-Christian....................................................................................................................2-10

Cell Growth .....................................................................................................................................2-11

Setting test parameters ...........................................................................................................2-11

Measuring the sample .............................................................................................................2-11

Oligo Calculator..............................................................................................................................2-12

Using the oligo calculator ........................................................................................................2-12

CHAPTER 3 - Using “General Tests” Software

General information..........................................................................................................................3-1

Editing and Loading Saved Tests .............................................................................................3-1

Specifying names for tests ........................................................................................................3-1

Specifying concentration units...................................................................................................3-1

Using the SmartStart feature.....................................................................................................3-2

Running the cell correction program.........................................................................................3-3

Taking measurements ...............................................................................................................3-5

Saving tests ................................................................................................................................3-5

Basic Absorbance/%T measurements............................................................................................3-6

Setting the wavelength ..............................................................................................................3-6

Table of Contents

v BioMate 3 Operator’s Manua

Table of Contents

Measuring a blank......................................................................................................................3-6

Measuring unknowns.................................................................................................................3-6

Basic Concentration measurements...............................................................................................3-6

Setting the wavelength & mode................................................................................................3-7

Measuring a blank......................................................................................................................3-7

Measuring a standard................................................................................................................3-7

Entering a factor.........................................................................................................................3-8

Measuring unknowns.................................................................................................................3-8

Advanced A/%T/C - Absorbance & %Transmittance measurements ..........................................3-8

Recalling a test...........................................................................................................................3-8

Setting up test parameters ........................................................................................................3-9

Taking measurements ...............................................................................................................3-9

Advanced A/%T/C - Concentration measurements.......................................................................3-9

Recalling a test.........................................................................................................................3-10

Setting up test parameters ......................................................................................................3-10

Measuring a standard..............................................................................................................3-10

Entering a factor .......................................................................................................................3-11

Measuring unknowns...............................................................................................................3-11

Standard Curve...............................................................................................................................3-11

Recalling a standard curve......................................................................................................3-11

Setting the parameters for a standard curve..........................................................................3-12

Measuring the standards for a standard curve......................................................................3-12

Measuring unknowns...............................................................................................................3-13

Editing a standard curve..........................................................................................................3-13

Absorbance Ratio...........................................................................................................................3-13

Recalling a test.........................................................................................................................3-14

Setting up test parameters ......................................................................................................3-15

Measuring unknowns...............................................................................................................3-15

Absorbance Difference ..................................................................................................................3-16

Recalling a test.........................................................................................................................3-16

Setting up test parameters ......................................................................................................3-16

Measuring unknowns...............................................................................................................3-16

Kinetics............................................................................................................................................3-17

Recalling a test.........................................................................................................................3-17

Setting up test parameters ......................................................................................................3-17

Measuring unknowns...............................................................................................................3-17

Rescaling & recalculating kinetics results ..............................................................................3-18

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 vi

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

Photometric Accuracy ......................................................................................................................4-3

Selecting the mode ....................................................................................................................4-3

Adding standards .......................................................................................................................4-3

Deleting standards .....................................................................................................................4-4

Running the test .........................................................................................................................4-4

Noise Measurement.........................................................................................................................4-4

Stray Light.........................................................................................................................................4-5

Running the test .........................................................................................................................4-5

Internal Printer Test ..........................................................................................................................4-5

RS232C Test ....................................................................................................................................4-6

CHAPTER 5 - Connecting & Using Accessories

General information..........................................................................................................................5-1

Cell holders & cell holder accessories ............................................................................................5-1

Changing cell holders ................................................................................................................5-2

Internal printer...................................................................................................................................5-3

Installing the internal printer.......................................................................................................5-3

Loading paper in the internal printer.........................................................................................5-3

External computers ..........................................................................................................................5-3

CHAPTER 6 - Performing Maintenance Procedures

Routine care .....................................................................................................................................6-1

Cleaning............................................................................................................................................6-1

Cleaning and maintenance of cells...........................................................................................6-1

Cleaning the windows of the sample compartment.................................................................6-2

Changing the fuse ............................................................................................................................6-2

Replacement parts ...........................................................................................................................6-3

Table of Contents

vii BioMate 3 Operator’s Manua

Table of Contents

Appendix A - Specifications

Appendix B - Parameters

Appendix C - Calculations

Index

Thermo Electron Corporation viii

Setting up the instrument

1. Carefully unpack the shipping carton and verify

that you have received all the items listed below.

• BioMate 3 spectrophotometer

• Power cord

• Operator's Manual - BioMate 3

spectrophotometer

• Dust cover

• Single Cell Holder

Models shipped with internal printer installed will also include:

• 1 roll of printer paper

• 1 printer holder set

2. Place the instrument on a flat, even surface that is:

• As far as possible from any strong electric

or magnetic fields and from any electrical device that may generate high-frequency fields

• Free of dust, corrosive gases and strong

vibrations

3. Remove any obstructions or materials that could hinder the flow of air under, behind and around the instrument.

4. Connect the female end of the power cord into the connector labeled A/C power on the back panel of the instrument (see Figure 2).

5. Plug the other end of the power cord into a grounded outlet with the appropriate voltage.

6. Ensure that the sample compartment does not contain any samples, and that the sample compartment door is closed.

7. Snap the paper roll holders (if needed) into place as shown in Figure 3. They will fit flush with the top of the instrument.

8. Turn on the instrument by pressing the power switch to ON (1=ON, 0=OFF). The power-on sequence will appear on the display and the instrument will go through its self-diagnostics. The instrument performs these diagnostics in the sequence shown:

a) Logo

b) Initializing

c) Calibrating filter wheel

d) Finding zero order e) Finding energy peak

f) Calibrating grating

Setting utility parameters

You should set up some of the utility parameters after the instrument is first powered up. These parameters include the date and time, standby setting, language, screen contrast settings and parameters needed to set up the printer.

You can set up the other utility parameters, or change the utility settings, at any time except when an entry screen is displayed or when the instrument is carrying out a task (such as setting the blank).

• Press the UTILITY key. The Utility screen appears on the display.

From this screen, you can set the date and time, select the standby settings, select the language, reset the lamp hours, select the contrast settings and select the parameters for a printer.

Selecting the language

The instrument supports English, Spanish, French, German and Italian as the language options.

• With the Utility screen displayed, press the arrow keys to highlight Language and press ENTER.

• Press the arrow keys to highlight the language you want to select and press ENTER.

Setting Up the Instrument

1-1 BioMate 3 Operator’s Manual

Setting the date and time

To access the date and time settings:

• With the Utility screen displayed, press the arrow keys to highlight Date/Time Setup and press ENTER. The screen displays the three date/time options that you can modify - date, time format and time.

To set the date:

• Press the arrow keys to highlight Set Date and press ENTER.

• Press Set Day, type the date, then press ENTER.

• Press Set Month, highlight the correct month, then press ENTER.

• Press Set Year, type the year, then press ENTER.

• When the date is correct, press ESC to save the settings and return to the Utility screen.

To select the time format:

You can set up the spectrophotometer to display the time in either am/pm format or in 24-hour format.

• To change the display format for the time, press the arrow keys to highlight Time Format and press ENTER until the format that you want to use (AM/PM or 24 hour) appears.

To set the time:

• Press the arrow keys to highlight Set Time and press ENTER.

• To set the hour, press Set Hour, type in the hour and press ENTER.

• To set the minutes, press Set Minute, type in the minute and press ENTER.

• To select between AM and PM, press Set

AM/PM until the appropriate setting appears.

Note: Any changes you make are saved

automatically (even during power down) by battery backup.

Selecting standby settings

To prolong xenon lamp life, your spectrophotometer has been pre-set at the factory to automatically go into standby mode after 15 minutes. To change Standby Mode time:

• With the Utility screen displayed, press the arrow keys to highlight Standby and press ENTER.

• Press the arrow keys to highlight the length of time you want the instrument will wait before entering standby mode and press ENTER.

Setting baseline expiration time

If you will be performing scans on your samples, you can set a time limit for a collected baseline.

To set the baseline expiration time:

• With the Utility screen displayed, press the arrow keys to highlight Baseline Expiration (hr:min) and press ENTER.

• Enter the desired time into the Entry baseline expiration time field. Press ENTER.

Setting the screen contrast

To make it easier to read the display, you can adjust the screen contrast on the spectrophotometer.

• With the Utility screen displayed, press the arrow keys to highlight Screen Contrast and press ENTER.

• Press the arrow keys to adjust the screen contrast.

• When the screen contrast is correct, press ESC.

Setting up the internal printer

To set up the printer properly, you need to load the paper and set the utility parameters for the printer. Before setting up the parameters for the printer, be sure that the printer is installed. If you have ordered the internal printer as a separate item, you will need to install it. Refer to the section Connecting & using accessories for instructions on installing the printer.

Loading paper in the internal printer

Note: Make sure that the paper roll holders are in

place as shown in Figure 3. When installed correctly, they will fit flush with the top of the instrument.

• Cut the paper so the edge is even.

Note: Arrows on the paper roll holders indicate

the direction of the paper feed (see Figure 3).

Setting Up the Instrument

Thermo Electron Corporation 1-2

• Feed the paper straight into the paper entry slot. The printer grabs the end of the paper and pulls it in.

• In Basic Absorbance/%Transmittance (%T), when the paper stops, press ENTER to continue advancing the paper until the paper comes out of the paper exit slot.

• Pull out on the finger tabs on the paper roll holders and secure the roll of paper onto the paper roll holder.

Setting the utility parameters for the printer

If you wish to use a printer you can output to:

• Internal printer.

• External RS232 printer.

To ensure that the spectrophotometer can output information correctly to the printer, you need to select the appropriate device.

• Press the UTILITY key. The Utility screen appears on the display.

• Press the arrow keys to highlight Printer and press ENTER.

• Select the printer that you want to use and press ENTER until On appears.

• Press ESC to save the settings and return to the Utility screen.

Selecting and positioning glassware

The wavelength range for different types of cells varies depending on the manufacturer:

• Glass - From 320 to 360nm, up to 1100nm.

• Quartz - From 190 to 230nm, up to 1100nm.

• Disposable - Refer to manufacturer's specifications and ensure that you work within the recommended range.

Test tubes vs. cuvettes

• Square cuvettes that are carefully matched (see “Correcting for cell variability” below) yield very precise results. Matched test tubes, when properly handled, can show as little as 1-2% deviation between readings.

• The pathlength of test tubes is not as well defined as in square cuvettes. However, constructing a standard curve eliminates the need for great accuracy in knowing the pathlength, provided that the same pathlength cell is used for all blanks, standards and samples.

Other guidelines

• Be sure to position cuvettes and test tubes so that the clear sides face the light beam. This means that one clear side should face the front of the instrument and the other clear side should face the back of the instrument.

Note: Test tubes should always be placed in the

instrument in exactly the same orientation in the light beam. A fiducial mark on the test tube helps you orient the test tubes consistently and correctly.

• When using small aperture cells:

• Always use masked cells.

• Use the same cell (or cuvette) for your

blank and your samples.

Setting Up the Instrument

1-3 BioMate 3 Operator’s Manual

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)

Setting Up the Instrument

Thermo Electron Corporation 1-4

Overview

The BioMate instrument allows you to run an assortment of tests used to characterize biological and biochemical substances. These tests fall into the following categories:

• Nucleic acid measurements

• Protein measurements

• Cell growth analysis

• Oligonucleotide calculations

All of the parameters for the BioMate applications described in this chapter are factory-set. This means that if you want to change the parameters, you will need to specify a different name to save the new test parameters.

Turn on your spectrophotometer. After the poweron sequence is completed, the list of BioMate test categories appears.

Table of parameters

Parameters used in the spectrophotometer are located in Appendix B.

You can use this list as a reference when you are setting up tests.

Entering information & commands

The keypad on the spectrophotometer includes a numeric keypad as well as certain special keys that you can use to enter information and commands.

Types of parameter entries

Different parameters require different types of entries - you can select from a list for some parameters, while you need to enter a value for others. While using the spectrophotometer, you will

notice the following types of entries for parameters:

• Type-in entries are numeric values that you can enter using the numeric keypad.

• Toggle entries offer two options for a parameter. You can press ENTER to switch between the two options, then press one of the arrow keys to move to another parameter.

• Pop-up windows list multiple options for a parameter or display messages. You can press the arrow keys to select the value you want, then press ENTER to select it and move to another parameter.

• Cursor selections are used on graphical displays and the character list you use to name tests and files. On graphical displays, the cursor appears as a vertical line; on the character list, the cursor highlights the character where it is positioned. You use the cursor control keys to move the cursor to the character or position on the graph you want to select.

Keypad layout

The keypad on the spectrophotometer (shown in Figure 4) includes a numeric keypad as well as the following special keys:

• Function keys - These four keys allow you to select a particular task you want to perform. The tasks you can perform appear on the display screen above each key and vary from one screen to another. On some screens, all four keys will function, while on other screens only some of the function keys will work.

• Esc - In general, when you press ESC, the program clears the current entry but does not change any values you have already accepted. The program may also return you to the previous screen when you press ESC.

• Clear - When you press CLEAR, the program deletes any entry you have made but does not change any values you have already accepted. The program does not return you to the previous screen when you press CLEAR.

• Enter - Typically, when you press ENTER, the program accepts any highlighted or selected values and advances to the next parameter or screen. Specific instructions later in this guide indicate any special instructions about using

ENTER.

Using “Biotests” Software

2-1 BioMate 3 Operator’s Manua

• Arrow keys - These keys allow you to control the position of the cursor so you can select values from lists or select an option from a screen.

• Cell position keys - These keys allow you to select which cell position the instrument will use for a measurement. If you have the optional turret installed, one position is reserved for your blank and you can select from five cell positions for your samples.

• Utility - When you press UTILITY, the Utility screen appears on the display.

• Test - When you press TEST, the Test Types screen appears on the display.

• Print - When you press PRINT, the instrument prints the information that appears on the display.

SmartS

tart feature

BioMate’s SmartStart feature enables you to select the test methods you use most frequently and have them appear when you start up your instrument. If your laboratory runs only a single test, you can use the SmartStart feature to select it and it will appear each time you start up your instrument. Similarly, if you have a set of tests you run, you can use SmartStart to select them so the list appears when you start up the instrument.

Setting up a single-test SmartStart

1. With the BioMate Tests Screen displayed,

press the Stored Tests key on the spectrophotometer keypad. A list of all the tests on the instrument appears on the screen.

2. Scroll down through the list until the appropriate test is highlighted.

3. 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

4. Press Load Test.

5. The parameter screen of the test you selected

will be displayed.

Note: At this point, you can power down the

instrument and then power it back up. When it starts up again, the parameter screen for the selected test will be displayed.

Setting up a multiple-test SmartStart

1. Press the Stored Tests key on the

spectrophotometer keypad.

2. Scroll down through the list until the first appropriate test is highlighted.

3. Press Select Tests to add the selected test to the SmartStart menu.

4. Continue scrolling through the list and adding tests until you’ve made all the appropriate selections.

5. Press ESC until you return to the BioMate Tests screen.

Note: At this point, you can power down the

instrument and then power it back up. When it starts up again, the list of tests you’ve selected will be displayed.

Nucleic acid measurement

You can use these tests to determine the concentration and purity of nucleic acid in a given sample.

• DNA - measures absorbance at 260 and 280nm; determines concentration and purity based on absorbance ratio and absorbance difference; also calculates protein concentration.

• DNA with scan - records absorbance scan between 260 and 280nm or between 260 and 230nm; determines concentration and purity based on absorbance ratio and absorbance concentration; also calculates protein concentration.

• dsDNA - measures absorbance at 260nm; calculates concentration based on absorbance and concentration factor.

• ssDNA, RNA - measures absorbance at 260nm; calculates concentration based on absorbance and concentration factor.

• Oligonucleotides ("Oligos") - measures absorbance at 260nm; calculates concentration based on absorbance and concentration factor or calculates concentration based on absorbance and concentration factor determined by oligo calculator.

Using “Biotests” Software

Thermo Electron Corporation 2-2

Several of these categories include multiple tests that are similar, so the section may not include screen samples for each test. For example, the parameters are the same for the Direct UV measurement of ssDNA and RNA tests, but the factor used to convert absorbance to concentration is different. Similarly, for the Direct UV measurement of oligonucleotides tests, the parameters are also the same, but the factors used to convert absorbance to concentration are different. For a complete list of all parameters and calculations for each test, refer to Appendices B and C.

DNA (260/280) and DNA (260/230)

These tests function almost identically - the only difference is the wavelengths used for the measurements. One test measures absorbance at 260 and 280nm, while the other measures absorbance at 260 and 230nm. Refer to 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 nucleic acid test appears. Move the arrow keys to highlight DNA (260/280). The DNA (260/280) parameter screen appears.

Note: The following screens show the

parameters for the DNA (260/280) test. For the DNA (260/230) test, Wavelength 2 is set to 230nm.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

Setting up test parameters

1. With the DNA (260/280) or DNA (260/230) screen displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure the blank and unknowns.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. 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 sample measurements on the screen.

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Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the DNA setup screen displayed, press

Run Test.

2. Place the blank and unknown in the correct cell

positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B position to measure the blank. When it completes the measurement, it returns to its previous cell position.

4. Press Measure Sample to start the measurement. If your instrument is equipped with a 6-Position Cell Holder, press the cell position buttons on the keypad to re-position the cell holder and measure the rest of the unknowns manually.

DNA with Scan (260/280) and DNA with Scan (260/230)

The DNA measurement with scan tests include two test that function almost identically - the only difference is in the wavelengths used for the measurements. In both cases the scan is measured from 225 to 325nm. One test measures absorbance at 260 and 280nm, while the other measures absorbance at 260 and 230nm. Refer to 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

nucleic acid test appears. Move the arrow keys to highlight DNA with Scan (260/280). The DNA with

Scan (260/280) parameter screen appears.

Note: The following screens show the

parameters for the DNA (260/280) test. For the DNA (260/230) test, Wavelength 2 is set to 230nm.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

Setting up test parameters

1. With the DNA with Scan (260/280) or DNA with Scan (260/230) screen displayed, use the

arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure the blank and unknowns.

Collecting a baseline scan

Note: If your instrument is equipped with a 6-

Position Cell Holder, be sure to place the blank in the B position. The instrument always uses the B position to collect the baseline.

1. With the DNA with Scan (260/280) or DNA with Scan (260/230) screen displayed, press Run Test. The DNA with Scan measurement

screen appears.

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2. Place the blank in the B position.

3. Press Measure Blank to collect the baseline.

When the instrument is finished measuring the blank, the message disappears.

Note: If you want to switch between tabular and

graphical displays, press Graph or

Tabular.

Measuring the sample

1. If your instrument is equipped with a 6-Position Cell Holder, be sure to place the unknown in cell position #1.

Note: The instrument always uses cell position

#1 to measure the sample.

2. With the DNA with Scan measurement screen displayed, press Measure Sample to measure the sample. When the instrument is finished measuring the absorbance scan, it displays a graph of the scan along with the sample ID#, DNA ratio, DNA concentration and protein concentration.

Note: If you want to switch between tabular and

graphical displays, press Graph or

Tabular.

Note: You may need to use the up and down

arrow keys to view all the data for the screen.

dsDNA, ssDNA, RNA and Oligos (entered factor) Direct or UV Measurements

These test measurements are all set up and run using the same types of test parameters. Refer to 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 nucleic acid test appears. Move the arrow keys to highlight the desired test and press ENTER. The dsDNA, ssDNA, RNA or Oligos (entered factor) parameter screen appears.

Note: The following screens show the

parameters for the dsDNA test.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

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Setting up test parameters

1. With the dsDNA, ssDNA, RNA or Oligos setup screen displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure the blank and unknowns.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. 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 sample measurements on the screen.

Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the dsDNA setup screen displayed, press

Run Test.

2. Place the blank and unknown in the correct cell

positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

Oligos (calculated factor)

The Oligos (calculated factor) measurement calculates molecular weight, extinction coefficient and a conversion factor for a base sequence that you enter. 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.

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Oligos (calc factor) parameter screen appears.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure

Samples keys.

Setting up test parameters

1. With the Oligos (calc factor) setup screen displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure the blank and unknowns.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. 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 absorbance, oligo concentration in µg/mL and pmol/µL.

Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the Oligos (calc factor) screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

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Protein Measurements

Bradford (standard & micro), Lowry (standard & micro), BCA (standard & micro) and Biuret measurements

You can use these tests to determine the concentration of protein in a given sample, using the following analytical methods:

Bradford - measures absorbance at 595nm; determines concentration for either standard or micro sample concentrations.

Lowry - measures absorbance at 550nm for standard and 770nm for micro; determines concentration for either standard or micro sample concentrations.

Bicinchoninic Acid (BCA) - measures absorbance at 562nm; determines concentration for either standard or micro sample concentrations.

Biuret - measures absorbance at 540nm.

Several of these categories include multiple tests that are similar, so this section includes screen samples for the standard Bradford test only. For a complete list of all parameters for each test, refer to Appendix B; for a list of calculations used for the tests, refer to Appendix C.

To get started, with the BioMate Tests screen displayed, move the arrow keys to highlight Protein Tests and press ENTER. A list of protein tests appears. Move the arrow keys to highlight the desired test and press ENTER. The Bradford-

Standard parameter screen appears.

Note: The following screens show the

parameters for the Bradford-Standard test. All the other protein standard curve methods work in a similar fashion.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

Setting up test parameters for a standard curve

1. With the Bradford-Standard setup screen displayed, use the arrow keys to highlight the name of the parameter you want to set. Set the parameters for measuring the standards. Refer to the list of parameters in Appendix B for a description of the parameters and Appendix C for the default values.

2. When the parameters are set, you can press Save Test to save the test or Run Standards

to measure the blank and standards. The

Standard Measurement screen appears.

3. If you need to edit concentration values, use

the arrow keys to select the standard you want to edit and press Edit Standards. From the Edit Standards window you can edit, add or delete one or all standards.

Measuring the standards for a standard curve

Measuring standards automatically (using Auto 6 or Auto 3)

1. Place the blank and standards in the correct cell positions.

2. When all the standards are correct, press 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

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standards, along with the slope, intercept and correlation coefficient of the standard curve.

Measuring standards automatically (using Auto 6 or Auto 3)

1. Place the blank and standards in the correct cell positions.

2. When all the standards are correct, press Measure Standards to set up and run the

standards.

4. 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 holder and measure the rest of the standards manually.

When the instrument has measured all the standards, the Standards screen appears, showing the absorbance of each standards, along with the slope, intercept and correlation coefficient of the standard curve.

You can use this screen to:

• Edit the standards (press Edit Standards)

• Display a graph of the standard curve data (press View Graph)

• Save the standard curve (press Save Test)

• Measure your samples (press Run Test)

Measuring protein samples

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.

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 each unknown.

Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the Standards screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell

positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

Direct UV (280) and Direct UV (205)

The Direct UV methods determine protein concentration based on absorbance at either 280 or 205nm. Refer to Appendix B for a description of the parameters and Appendix C for the default values.

To get started, move the arrow keys on the BioMate tests screen to highlight Protein Tests and press ENTER. Then the move the arrow keys to highlight Direct UV (280) and press ENTER. The Direct UV (280) parameter screen appears.

Note: The following screens show the

parameters for the Direct UV tests at 280nm. For the Direct UV test at 205nm, the wavelength is set to 205nm.

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Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

Setting up test parameters

1. With the Direct UV (280) setup screen displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or to measure the

blank and unknowns.

Measuring the sample

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. With the Direct UV (280) 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 each unknown.

Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the Direct UV (280) screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B

position to measure the blank. When it completes the measurement, it returns to its previous cell position.

Warburg-Christian

The Warburg-Christian analysis uses an absorbance difference measurement at 280 and 260nm to determine the protein concentration of an unknown. Refer to Appendix B for a description of the parameters and Appendix C for the default values.

To get started, move the arrow keys on the BioMate tests screen to highlight Protein Tests and press ENTER. Then the move the arrow keys to highlight Warburg-Christian and press ENTER. The Warburg-Christian parameter screen appears.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

Setting up test parameters

1. With the Warburg-Christian setup screen displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to measure the blank and unknowns.

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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 each unknown.

Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the Warburg-Christian screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

5. When the instrument has measured all the unknowns, it displays the absorbance and concentration.

Cell Growth

The cell growth measurement uses absorbance at 600nm to indicate the progress of cell growth in a sample. The instrument does not perform any calculations or graphing for the data.

To get started, move the arrow keys on the BioMate Tests screen to highlight Cell Growth and press ENTER. The Cell Growth setup screen appears.

Note: If Cell Correction is ON, you must run the

Setup Correction program before you can access the Run Test or Measure Samples keys.

Setting up test parameters

1. With the Cell Growth setup screen displayed,

use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure the blank and unknowns.

Measuring the sample

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. With the Cell Growth measurement 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 of each unknown

Measuring unknowns manually (using Manual 6 or Single Cell Positioner)

1. With the Cell Growth measurement screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell positions. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B position to measure the blank. When it

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completes the measurement, it returns to its previous cell position.

5. When the instrument has measured all the unknowns, it displays the absorbance and concentration.

Oligo Calculator

The oligonucleotide calculator determines the following data for a base sequence that you enter:

• Number of bases

• Percent GC content

• Molecular weight

• Absorptivity (ε)

• Conversion factor to convert nucleotide absorbance to concentration

• Tm for oligos of up to 20 bases

• Tm for oligos of up to 40 bases for DNA-DNA, DNA-RNA and RNA-RNA hybrids

Refer to Appendix B for a description of the parameters and Appendix C for the default values.

To get started, move the arrow keys on the

BioMate Tests screen to highlight Oligo Calculator and press ENTER. The Oligos screen

appears.

Using the oligo calculator

1. With the Oligos screen displayed, press Base Sequence. The Base Sequence identification

screen appears.

2. Use the arrow keys to select the appropriate character for the base you want to enter. Press

Add Base to add the base to the sequence.

3. When the base sequence is correct, press Accept Sequence to accept it. The instrument

calculates and displays the results

4. To determine the theoretical Tm of the sequence, press Tm Calc. The Tm calculation 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.

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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. Press the UTILITY key on the keyboard. The Utility screen appears.

2. Using the arrow keys, highlight Stored Tests Directory and press ENTER. A list of all the

stored tests appears.

3. To load a test, use the arrow keys to highlight the name of the test you want to recall and press ENTER. The test will be loaded and the parameters for the selected test appear on the screen.

4. To lock or unlock a test, use the arrow keys to highlight the name of the test you want to lock or unlock and press Lock/Unlock. Enter the password (found on page iii of this manual) and press ENTER. The test is either locked or unlocked.

5. To delete a test, use the arrow keys to highlight the name of the test you want to delete. Press

ENTER. The test is deleted.

Specifying names for tests

When you save tests, you need to specify the name you want to use for the file. The spectrophotometer does not have a full keypad, so you need to select the characters for the filename from a character list.

1. After setting up the values for the test parameters, press Save Test. The Create Test Name screen appears.

You can use this screen to:

• Delete the name of a test

• Delete a character in the name of a test

• Add a character to the name of a test

• Accept the name of a test

2. Use the arrow keys to highlight the first character you want to use for the name of your test and press Add Character to add the selected character to the name.

3. Continue selecting and adding characters until you have selected all the characters for the name.

4. Press Accept Name to accept the name and return to the previous screen. The name of the test appears at the top of the screen showing the test parameters.

Specifying concentration units

When you run concentration tests, you need to specify the units you want to use when reporting concentrations. The spectrophotometer includes a set of basic concentration units and you can also enter custom units if you wish.

All programs in the spectrophotometer use the same list of basic units:

• Concentration • mg/mL

• ppm • µg/L

• ppb • M/L

• g/L • mM/L

• mg/L • IU

In addition to these units, you can create your own custom unit, using a character list like the one described in Specifying names for tests. Once

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you create a custom unit, it will appear in the list that you use to select the units.

To select the units

1. Highlight the Units parameter on the screen and press ENTER.

2. Use the arrow keys to highlight the unit you want to select and press ENTER.

To create custom units

In addition to the basic concentration units, you can create one other custom concentration unit and add it to the list.

1. With the list of basic units displayed, use the arrow keys to highlight [Unit] and press ENTER.

Press Edit [Unit] on a test set-up screen for a test with units.

The character list appears. You can use this screen to:

• Delete the name of a unit

• Delete a character in the name of a unit

• Add a character to the name of a unit

• Accept the name of a unit

2. Use the arrow keys to highlight the first character you want to use for the name of your custom unit and press Add Character to add the selected character to the name.

3. Continue selecting and adding characters until you have selected all the characters for the name.

4. Press Accept Name to accept the name and return to the previous screen. The name of the new custom unit appears on the list of basic units.

Using the SmartStart feature

The SmartStart feature enables you to select the test methods you use most frequently and have them appear when you start up your instrument. If your laboratory runs only a single test, you can use the SmartStart feature to select it and it will appear each time you start up your instrument. Similarly, if you have a set of tests you run, you can use SmartStart to select them so the list appears when you start up the instrument.

Setting up a single-test SmartStart

1. Press the UTILITY key on the keypad to display the Utility screen.

2. Highlight the Stored Tests Directory and press ENTER. A list of all the tests on the instrument appears on the screen.

3. Scroll down through the list until the appropriate test is highlighted.

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.

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6. The parameter screen of the test you selected will be displayed.

Note: At this point, you can power down the

instrument and then power it back up. When it starts up again, the parameter screen for the selected test will be displayed.

Setting up a multiple-test SmartStart

1. Press the UTILITY key on the keypad to display the Utility screen.

2. Highlight the Stored Tests Directory and press ENTER. A list of all the tests on the instrument appears on the screen.

3. Scroll down through the list until the first appropriate test is highlighted.

4. Press Select Tests to add the selected test to the SmartStart menu.

5. Continue scrolling through the list and adding tests until you’ve made all the appropriate selections.

6. Press ESC until you return to the Tests screen.

Note: At this point, you can power down the

instrument and then power it back up. When it starts up again, the list of tests you’ve selected will be displayed.

Running the cell correction program

Note: The Cell Correction program is not active

in the Main (Basic Absorbance/%T/Basic Concentration) screen.

Note: The Cell Correction feature is active only

when the 6-Position Sample Holder is set to either Auto 6 or Auto 3. The feature is not active when the cell holder is set to 1- Cell Platform or Manual 6, nor when the Single Cell Holder is installed.

Every test setup screen provides access to the cell correction program. Before running the cell correction program:

• Clean the inside and outside of all the cells

to be matched.

• Fill the cells with distilled water (or other blank solution), and place them in the sample compartment (see “Selecting and positioning glassware” in the preceding section). Be sure to place the blank cuvette in Cell “B” of the sample compartment.

TIP: If one cell has lower absorbance

than the others, make it the blank.

To run the Cell Correction program:

1. Press the TEST key on the keypad. When the Test Types screen appears, highlight the test you want to run and press ENTER.

2. Highlight Cell Correction and press ENTER.

The Cell Correction function is now activated, as indicated by the word On across from Cell Correction on the test setup screen.

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Note: When Cell Correction is activated,

additional parameter lines are added to the screen above the Cell Correction line. If the Cell Correction line is no longer visible on the screen, highlight More parameters... and press ENTER.

3. Highlight Set Up Correction and press ENTER. The Cell Correction screen appears.

4. Highlight Correction Mode and press ENTER

to set the mode to either:

• Scan - Cell Correction is run on a blank and one sample cell for the range of wavelengths you specify in Scanning mode.

• Discrete nms - The Cell Correction program is run on a blank and up to five sample cells for up to 31 user-specified, discrete wavelengths.

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

the procedures which follow, and then the Cell Correction program.

The Cell Correction program will measure the other cells against the blank and will record, store and date the measurements. From these measurements the Cell Correction program establishes the required correction factors, which then are automatically applied during all subsequent tests (if Cell Correction is activated).

Specifying wavelengths for Discrete nms mode:

1. Highlight Sample Positioner and press ENTER to set this parameter to either Auto 3 (when using three, large cell holders) or Auto 6 (when using six, small cell holders).

2. Highlight Number of Matched Cuvettes and

press ENTER. Then use the keypad to specify the number of cells you are matching. Press

ENTER.

3. Press Set nms to select the wavelengths for

which the Cell Correction program will be run. A list of wavelengths appears.

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Note: Cells should be matched at all analytical

wavelengths because matching at one wavelength does not guarantee matching at others.

4. Use the arrow keys to highlight the position where you want to enter the first wavelength.

5. Press Add nm.

6. Enter the value for the wavelength and press ENTER.

7. Continue until you have entered all the

wavelengths.

After all the wavelengths have been entered, press Run Corr. to start the Cell Correction program. The Cell Correction program will measure the other cells against the blank and will record, store and date the measurements. From these measurements the Cell Correction program establishes the required correction factors, which then are automatically applied during all subsequent tests (if Cell Correction is activated).

Taking measurements

The spectrophotometer lets you use different cell holders and cell holder accessories to take measurements. When you set up your test parameters, you will select the type of measurement you want to use and indicate how many samples you have. You can choose from the following options:

• Auto 6 - You can take one blank measurement and up to five sample measurements without changing the samples in the cell holder. The instrument automatically measures the blank (in the blank position), then automatically advances the cell holder to the appropriate position for the next measurement. This option is available only with the 6-Position Cell Holder.

• Auto 3 - You can take up to three measurements without changing the samples in the cell holder. The instrument automatically measures the blank (in the blank position), then automatically advances the cell holder to the appropriate position for the next measurement. This option is available only with the 6-Position Cell Holder.

• Single Cell Platform - You place the blank in the cell holder, measure it, place a sample in the cell holder, then measure your sample. This process is completely manual. In fact, the

cell position buttons on the keypad do not function when you select Single Cell Platform even if you have a 6-Position Cell Holder installed in the sample compartment.

• Manual 6 - You can take up to six measurements without changing the samples in the cell holder, using the cell position buttons on the keypad to advance the cell holder to the appropriate position for the next measurement. You place the blank in the blank position and your samples in the other cell positions. Regardless of where the cell holder is positioned, when you press Measure Blank the cell holder automatically goes to the blank position and measures the blank. However, you can use the cell position buttons to select a different position for the measurement. This option is available only with the 6-Position Cell Holder .

Note: When you have the 6-Position Cell Holder

installed, the instrument always considers the material in the B position as a blank. This means that even after measuring your blank the first time, you can place unknowns only in positions 1 through 5.

The two automatic measurements (Auto 6 and Auto 3) are available only for instruments with the 6-Position Cell Holder. However, if you have one of these models, you can also choose to take measurements manually. Each test section later in this chapter includes specific instructions on how to take measurements automatically and manually.

Saving tests

When you power-down the instrument, the current test is maintained by battery back-up. This means that when you turn the instrument on again, the cell holder alignment and values for all parameters will be the same as they were when the instrument was last used. When you load a test that has been saved, the values for all parameters stored with that test will replace the current values for the test parameters.

As you create customized tests and collect data, you will be saving tests for later use. The spectrophotometer uses test files to contain the values for all the parameters needed to run a test, including the alignment of the cell holder and the other parameters for the accessories installed. Once you select the values for the parameters, you

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can assign a test name and save the test. You can then restore the test and run it without having to set up the parameters again.

Basic Absorbance/%T measurements

The Absorbance/%Transmittance (%T) program takes measurements and displays them as either absorbance or %T. For each measurement taken, the absorbance (or %T) appear on the screen, along with the type of measurement, the date and time, the wavelength and the cell position used for the measurement. All the steps for taking measurements in the two modes are the same - the only difference will be the units used to display the results.

When you use the Basic Absorbance/%T program, you can perform these tasks:

• Set the wavelength

• Measure a blank

• Measure unknowns

If you want to work with %T instead of absorbance, simply press Change Mode until you see the %T mode. You can switch from one mode to another whenever you see the Change Mode function key.

Setting the wavelength

1. Press Set nm or any number key to set the

wavelength.

2. Enter the wavelength where you want the measurements taken, then press Set nm again.

Measuring a blank

1. Place the blank in the cell holder. If your

instrument has a 6-Position Cell Holder, be sure to place the blank in the B position.

2. If you want to enter an absorbance or transmittance value for the blank, press a number key and enter the concentration in the

Entry field.

3. Press Measure Blank to measure the blank.

When the instrument is finished measuring the absorbance of the blank, the message disappears.

Measuring unknowns

1. If your instrument is equipped with the 6-Position

Cell Holder, place the unknown you want to measure in one of the cell positions and press the corresponding cell position button on the keypad to move the cell holder to the measuring position. The absorbance (ABS) or %transmittance (%T) measurement appears on the display.

If your instrument is equipped with the Single Cell Holder Platform, remove the blank and place the unknown in the cell holder. The absorbance or %transmittance measurement appears on the display.

Basic Concentration measurements

Measuring concentration is similar to measuring absorbance or %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.

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• 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:

• Set the wavelength

• Measure a blank

• Measure a standard OR enter a factor

• Measure unknowns

The steps for taking measurements in the two modes are similar - the only difference will be whether you measure a standard or enter a factor.

Setting the wavelength & mode

1. Press Set nm or any number key to set the

wavelength.

2. Enter the wavelength where you want the measurements taken, then press Set nm again.

3. Press Change Mode until the appropriate measurement mode (Concentration with Standard or Concentration with Factor) appears.

Measuring a blank

1. Place the blank in the cell holder. If your

instrument has a 6-Position Cell Holder, be sure to place the blank in the B position.

2. If you want to enter a concentration for the blank, press a number key and enter the concentration in the Entry field.

3. Press Measure Blank to measure the blank. When the instrument is finished measuring the absorbance of the blank, the message disappears.

Measuring a standard

1. If necessary, press Change Mode to switch to the Concentration with Standard mode.

2. If your instrument is equipped with the

6-Position Cell Holder, place the standard in one of the cell positions and press the corresponding cell position key on the keypad.

If your instrument is equipped with the Single Cell Holder Platform, remove the blank and place the standard in the cell holder.

3. Press Units/Standard to set the units and measure the standard.

4. Enter Conc, use the number keys to enter the concentration value of the standard and then press ENTER.

5. Press Select Units, use the arrow keys to highlight the entry in the Units field and then press ENTER to select the units for the concentration.

6. Press Measure Standard to measure the standard. When the instrument is finished measuring the absorbance of the standard, it displays the absorbance and calculated factor.

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Entering a factor

1. If necessary, press Change Mode to switch to the Concentration with Factor mode.

2. Press Units/Factor to set the factor and select

the units.

3. Use the arrow keys to highlight the entry in the Factor field and press Enter Factor to enter

the factor.

4. Use the number keys to enter the factor.

5. Press Enter Factor to accept the factor and

return to the screen displaying the factor and units. The factor you just entered appears on the display.

6. Press ESC to return to the Concentration with Factor screen.

Measuring unknowns

1. If your instrument is equipped with the

6-Position Cell Holder, place the unknown you want to measure in one of the cell positions and press the corresponding cell position

button on the keypad to move the cell holder to the measuring position. The measurement appears on the display.

If your instrument is equipped with the Single Cell Holder Platform, remove the blank and place the unknown in the cell holder. The measurement appears on the display.

Advanced A/%T/C - Absorbance & %Transmittance measurements

When you use the Advanced A/%T/C program for absorbance or %transmittance measurements, you can perform these tasks:

• Select the measurement mode you want to use (Absorbance or %Transmittance)

• Run Cell Correction program

• Recall a test OR set up your test parameters

• Measure a blank

• Measure unknowns

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight

Advanced A/%T/C and press ENTER.

Recalling a test

1. With the Advanced A/%T/C screen displayed,

press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

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Thermo Electron Corporation 3-8

From this screen, you can:

• Set up test parameters

• Run Cell Correction program

• Save a test

• View the list of stored tests

• Measure a blank and unknowns

Setting up test parameters

1. With the Advanced A/%T/C screen displayed,

use the arrow keys to highlight the name of the parameter you want to set.

Some parameters appear only if you select one of the concentration modes, while others appear regardless of the measurement mode you select. A complete list of the parameters are located in Appendix B.

2. When the parameters are set, you can press Save Test to save the test or Measure Sample to measure a blank or unknowns.

Taking measurements

Taking measurements automatically (using Auto 6 or Auto 3)

1. With the Advanced A/%T/C screen displayed and the parameters set, press Run Sample. The Advanced A/%T/C measurement screen appears.

2. Place the blank and the unknowns in the correct cell positions.

3. Press Measure Sample to measure the unknowns. The instrument automatically measures the blank first, then measures the unknowns and displays the sample measurements on the screen.

Taking measurements manually (using Manual 6 or Single Cell Platform)

1. With the Advanced A/%T/C screen displayed and the parameters set, press Measure Sample. The Advanced A/%T/C measurement screen appears, prompting you to place your samples in the cell holder.

2. Place the blank and unknowns in the cell holder. If your instrument is equipped with a 6-Position Cell Holder, be sure to place the blank in the B position. You can place up to five samples in the cell holder.

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.

Advanced A/%T/C - Concentration measurements

When you use the Advanced A/%T/C program for concentration measurements, you can perform these tasks:

• Select the measurement mode you want to use (concentration with one standard or concentration with a factor)

• Recall a test OR set up your test parameters

• Measure a standard OR enter a factor (only if you select either concentration with one standard or concentration with a factor)

• Measure a blank and unknowns

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight Advanced A/%T/C and press ENTER.

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Recalling a test

1. With the Advanced A/%T/C screen displayed,

press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

Setting up test parameters

1. With the Advanced A/%T/C screen displayed,

use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test or Run Standard to measure a standard.

Measuring a standard

Measuring a standard automatically (using Auto 6 or Auto 3)

1. With the Advanced A/%T/C screen displayed and the 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 Press Measure Standard.

4. Place the blank and standard in the correct cell

positions.

5. Press ENTER to measure the blank and the standard. The instrument automatically measures the blank first, then measures the unknowns and displays the absorbance and calculated factor.

Measuring a standard manually (using Manual 6 or Single Cell Platform)

1. With the Advanced A/%T/C screen displayed and the 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.

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Thermo Electron Corporation 3-10

4. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B position to measure the blank. When it completes the measurement, it returns to its previous cell position.

5. Press Measure Standard to measure the standard. When the instrument is finished measuring the absorbance of the standard, it displays the absorbance and calculated factor.

Entering a factor

1. With the Advanced A/%T/C screen displayed and the Measurement Mode set to Conc/Factor, use the arrow keys to highlight Factor.

2. If you need to change the factor, use the

number keys to enter the correct factor.

3. If you need to change the units, use the arrow keys to highlight Units and select the correct units.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. With the Advanced A/%T/C screen displayed and the Measurement Mode set to Conc/Std or Conc/Factor, press Run Test. The Advanced A/%T/C measurement screen appears, prompting you to place your samples in the cell holder.

2. Place the blank and unknowns in the correct cell positions. Press ENTER. The instrument automatically measures the blank first, then measures the unknowns and displays the sample measurements on the screen.

3. Press Measure Sample to measure additional unknowns.

Measuring unknowns manually (using Manual 6 or Single Cell Platform)

1. With the Advanced A/%T/C screen displayed and the Measurement Mode set to Conc/Std or Conc/Factor, press Run Test. The Advanced A/%T/C measurement screen appears.

2. Place the blank and unknown in the correct cell position. If your instrument is equipped with a

6-Position Cell Holder, you can place up to five samples in the cell holder.

4. Press Measure Sample to start the measurement. 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.

tandard Curve

When you use the Standard Curve program, you can perform these tasks:

• Recall a standard curve OR create a standard curve (set up the parameters and then measure the standards for the curve)

• Run the Cell Correction program (BioMate 3 UVscanning model only)

• Measure unknowns

• View the data - select between graphical and tabular displays

• Edit a standard curve - change the number of standards, select a different curve fit or delete points from the curve

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight

Standard Curve and press ENTER. The Standard Curve screen appears.

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3-11 BioMate 3 Operator’s Manual

Recalling a standard curve

1. Press Stored Tests to display a list of stored

tests.

2. Highlight the standard curve you want to recall.

3. Press ENTER to load the selected standard

curve.

Setting the parameters for a standard curve

1. Place the standards in the correct cell positions.

2. Set the parameters for measuring the

standards. Refer to the list of parameters in Appendix B for a description of each.

• Enter the Test Name, Wavelength, Reference Wavelength Correction and Reference Wavelength.

• Select the Curve Fit, Units and Sample Positioner.

• Set the Number of Standards and Number of Samples.

• Enter the low and high limits.

• Select the settings for the Statistics and AutoPrint functions.

• Run the Cell Correction program

Measuring the standards for a standard curve

Measuring standards automatically (using Auto 6 or Auto 3)

1. Place the blank and standards in the correct cell positions.

2. When all the parameters are correct, press Run Standards to set up and run the

standards.

3. Enter the concentration value into the Entry concentration field and press ENTER. When you've entered all the concentration values, the

Standards screen appears.

4. Press Measure Standards to measure the

blank and 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 standard, along with the slope, intercept and correlation coefficient of the standard curve.

Measuring standards manually (using Manual 6 or Single Cell Platform)

1. Place the blank and standards in the correct cell positions.

2. When all the parameters are correct, press Run Standards to set up and run the

standards.

3. Enter the concentration value into the Entry concentration field. Press ENTER

4. When you have entered all the concentration values, the Standards screen appears.

5. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B position to measure the blank. When it completes the measurement, it returns to its previous cell position.

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

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Thermo Electron Corporation 3-12

holder and measure the rest of the standards manually.

When the instrument has measured all the standards, the Standards screen appears, showing the absorbance of each standard, along with the slope, intercept and correlation coefficient of the standard curve.

You can use this screen to:

• Edit the standards press (Edit Standards)

• Display a graph of the standard curve data (press View Graph)

• Save the standard curve (press Save Test)

• Measure your samples (press Run Test)

If you want to switch between tabular and graphical displays, press View Graph/Tabular.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. With the Standards screen displayed, press Run Test. The Samples screen appears.

2. Place the blank and unknowns in the correct

cell positions.

3. Press ENTER to measure. The instrument automatically measures the blank first, then measures the unknowns. When the instrument has measured all the unknowns, the Standard Curve screen appears, showing the absorbance and concentration of each unknown.

Measuring unknowns manually (using Manual 6 or Single Cell Platform)

1. With the Standards screen displayed, press Run Test. The Samples screen appears.

2. Place the blank and unknowns in the correct

cell positions.

4. Press Measure Samples to measure the unknowns. If your instrument is equipped with a 6-Position Cell Holder, press the cell position buttons on the keypad to re-position the cell holder and measure the rest of the unknowns manually. When the instrument has measured all the unknowns, the Standards screen appears, showing the absorbance and concentration of each unknown.

Editing a standard curve

You may edit the concentration of any standard on a standard curve. In addition, you may change the number of standards, select a different curve fit or delete points from the curve.

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3-13 BioMate 3 Operator’s Manual

To edit the concentration of a standard

1. With the standard curve displayed on your screen, use the arrow keys to highlight the standard you want to edit. Press Edit

Standards.

2. With the Edit Concentration highlighted, Press ENTER.

3. Press Edit Conc or a number key.

4. Enter the concentration value in the Entry

field.

5. When the concentration value is correct, press ENTER to accept the value.

To add a standard

1. With the standard curve displayed on your screen, press Edit Standards.

2. Use the arrow keys to highlight Add Standard.

3. Enter the concentration value of the additional standard in the Entry field.

4. When the concentration value is correct, press ENTER to accept the value.

5. Press Measure Standards to remeasure all

the standards.

To delete a standard

1. With the standard curve displayed on your screen, use the arrow keys to highlight the standard you want to delete. Press Edit

Standards.

2. Use the arrow keys to highlight Delete Standard. Press ENTER to delete the

standard.

To clear measurements

1. With the standard curve displayed on your screen, press Edit Standards.

2. Use the arrow keys to highlight Clear Measurements and press ENTER. All the

absorbance measurements will be removed from the screen.

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.

To select a different curve fit for a standard curve

Note: To change the curve fit for a standard

curve, you must display the standard curve as a graph, not as a table.

1. With the standard curve you want to edit displayed as a graph on your screen, press

Change Fit.

2. Use the arrow keys to highlight the curve fit

you want to use for the standard curve and press ENTER. The instrument applies the selected curve fit to the data and displays the new graph.

Absorbance Ratio

When you use the Absorbance Ratio program, you can perform these tasks:

• Recall a test OR set up your test parameters

• Run the Cell Correction program

• Measure a blank

• Measure unknowns

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight Absorbance Ratio and press ENTER.

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Thermo Electron Corporation 3-14

Recalling a test

1. With the Absorbance Ratio screen displayed,

press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

From this screen, you can:

• Set up test parameters

• Run the Cell Correction program

• Save a test

• View the list of stored tests

• Measure a blank

• Measure unknowns

Setting up test parameters

1. With the Absorbance Ratio screen displayed,

use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure a blank or unknowns.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. Place the blank and unknowns in the correct cell positions.

2. Press ENTER to start the measurement. The instrument automatically measures the blank first, then measures the unknowns and displays the sample measurements on the screen.

Measuring unknowns manually (using Manual 6 or Single Cell Platform)

1. With the Absorbance Ratio screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell position. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B

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3-15 BioMate 3 Operator’s Manual

position to measure the blank. When it completes the measurement, it returns to its previous cell position.

Absorbance Difference

When you use the Absorbance Difference program, you can perform these tasks:

• Recall a test OR set up your test parameters

• Run the Cell Correction program

• Measure a blank

• Measure unknowns

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight

Absorbance Difference and press ENTER.

Recalling a test

1. With the Absorbance Difference screen

displayed, press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

From this screen, you can:

• Set up test parameters

• Set up Cell Correction program

• Save a test

• View the list of stored tests

• Measure a blank

• Measure unknowns

Setting up test parameters

1. With the Absorbance Difference screen

displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure a blank or unknowns.

Measuring unknowns

Measuring unknowns automatically (using Auto 6 or Auto 3)

1. With the Absorbance Difference screen displayed, press Run Test.

2. Place the blank and unknowns in the correct cell positions.

3. Press ENTER to start the measurement. The instrument automatically measures the blank first, then measures the unknowns and displays the sample measurements on the screen.

Measuring unknowns manually (using Manual 6 or Single Cell Platform)

1. With the Absorbance Difference screen displayed, press Run Test.

2. Place the blank and unknown in the correct cell position. If your instrument is equipped with a 6-Position Cell Holder, you can place up to five samples in the cell holder.

3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B

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Thermo Electron Corporation 3-16

position to measure the blank. When it completes the measurement, it returns to its previous cell position.

Kinetics

When you use the Kinetics program, you can perform these tasks:

• Recall a test OR set up your test parameters

• Run the Cell Correction program

• Measure a blank

• Measure an unknown

• Recalculate reaction rates

• Modify the scale of the plot

When you use the Kinetics program, you can choose to work with either graphical data or with tabular data. You can perform the same functions regardless of the type of display you select. However, the location of function keys varies depending on the type of display you choose.

Note: The Kinetics program allows you to

measure only one unknown at a time.

Note: The Kinetics program allows you to collect

up to 400 data points per run. When you set up your test parameters, be sure to select the interval time and total run time accordingly.

To get started, press the TEST key on the keypad.

When the Test Types screen appears, highlight

Kinetics and press ENTER.

Recalling a test

1. With the Kinetics screen displayed, press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of

the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

From this screen, you can:

• Set up test parameters

• Run the Cell Correction program

• Save a test

• View the list of stored tests

• Measure a blank

• Measure unknowns

• Set up your analog recorder

Setting up test parameters

1. With the Kinetics screen displayed, use the

arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure a blank or an unknown.

Measuring unknowns

Note: If your instrument is equipped with a 6-

position cell holder, be sure to place the blank in position B and the unknown in cell position #1. The instrument always uses cell position #1 to scan the unknown.

3-17 BioMate 3 Operator’s Manual

Using “General Tests” Software

1. With the Kinetics test parameters displayed on the screen, press Run Test.

2. If you have a 6-position cell holder, place the blank in position B and the unknown in position #1. Press Measure Sample to measure the blank and the unknown. When the instrument completes the measurement, the kinetics data and rate appear on the screen.

3. If you have 1-position cell holder, press Measure Blank to measure the blank, then insert your unknown and press Measure Sample. When the instrument completes the

measurement, the kinetics data and rate appear on the screen.

If you want to switch between tabular and graphical displays, press Graph/Tabular.

When you have a graphical display, you can press Edit Graph, then press Cursor to move the cursor line from one position to another on the plot. As the cursor moves the rate and result values indicate the values for the point on the plot where the cursor is located.

Rescaling & recalculating graphical kinetics results

Within the Kinetics program, you can view and manipulate your results either in graphical form or in tabular form. When your results are displayed on the screen, you can modify the range (start and

stop time) and the instrument automatically recalculates the reaction rate.

When you are working with graphical kinetics results, you need to press Edit Graph before you can rescale and recalculate.

You can modify the scale of your kinetics data plot in two ways - automatically or manually. When you select Auto Scale, the instrument automatically scales the X- and Y-axes so all the data appears on the plot. When you select Manual Scale, you select specific minimum and maximum values for the Xand Y-axes. Whenever you modify the scale, the instrument also automatically recalculates and displays the new reaction rate and result.

When the edit screen appears, you can:

• Use the Auto Scale function to change the scale, display the new graph and recalculate the results

• Use the Manual Scale function to change the scale, display the new graph and recalculate the results

• Use the cursor to select new minimum or maximum values for the X-axis and recalculate the results.

To use the Auto Scale function

1. With your kinetics data displayed on the Edit Graph screen, press Auto Scale. The

instrument automatically adjusts the minimum and maximum values for the X- and Y-axes so all the data appears on the plot. The instrument also recalculates the results, using all the data, and displays it on the screen.

To use the Manual Scale function

1. With your kinetics data displayed on the edit screen, press Manual Scale. The manual scale options appear.

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Thermo Electron Corporation 3-18

2. Use the number keys to enter the appropriate minimum or maximum value for the X- or Yaxis, then press the appropriate function key (Min Y, Max Y, Min X, Max X) to accept it. The instrument redraws the plot using the minimum and maximum value you have entered and displays the recalculated rate and result.

3. Continue until you have entered all the values you want to change.

To use the cursor

1. With your kinetics data displayed on the edit screen, press Cursor. The cursor options appear.

2. Press Cursor ←←or Cursor →→to position the cursor line on the appropriate point on the graph. The instrument displays the data for the selected point.

3. When the cursor line is in the correct position, press Set Min X or Set Max X to accept the selected point. The instrument redraws the plot using the minimum and maximum value you

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. Whenever you modify the start and end times or select all the data, the instrument automatically recalculates and displays the new reaction rate and result.

When the edit screen appears, you can:

• Use all the data to recalculate the results

• Select specific start and end times for the rate calculation and recalculate the results.

To use all the data to calculate the reaction rate

1. With your table of kinetics data displayed on the edit screen, press Use all data. The instrument calculates the rate and displays it on the screen.

To select specific start and end times for the rate calculation

1. With your table of kinetics data displayed on the edit screen, use the arrow keys on the keypad to move the highlight symbol (→→) to the appropriate data point in the table.

2. Press Start Time or End Time. The instrument displays the recalculated rate and result.

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Using “General Tests” Software

Survey Scan/

Scanning

The Survey Scan program allows you to scan a wavelength range. When you use the Survey Scan program, you can perform these tasks:

• Recall a test OR set up your test parameters

• Run the Cell Correction program

• Collect a baseline scan

• Scan an unknown

• View scan data

• Change the scale of the data plot

• Determine 3-point net measurements

• Calculate the area under a curve

• Label peaks and valleys

Note: The Survey Scan/Scanning program allows

you to measure only one unknown at a time. Auto 6, Auto 3 and Manual 6 are not available for scanned measurements.

Note: If you want to set a baseline expiration

time, press UTILITIES, then use the arrow keys to highlight Baseline Expiration. Press ENTER and set the desired time.

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight

Survey Scan or Scanning and press ENTER.

Recalling a test

1. With the Survey Scan/Scanning screen

displayed, press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

From this screen, you can:

• Set up test parameters

• Set up Cell Correction program

• Save a test

• View the list of stored tests

• Collect a baseline

• Scan unknowns

Setting up test parameters

1. With the Survey Scan/Scanning screen

displayed, use the arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure a blank or an unknown.

Collecting a baseline scan

Note: If your instrument is equipped with a

6-Position Cell Holder, be sure to place the blank in the B position. The instrument always uses the B position to collect the baseline.

1. With the Survey Scan/Scanning test parameters displayed, press Run Test.

2. Place the blank in the B position.

3. Press Measure Blank to collect the baseline.

When the instrument is finished measuring the blank, the message disappears.

Note: If you want to switch between tabular and

graphical displays, press Graph/Tabular.

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Thermo Electron Corporation 3-20

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.

2. If your instrument is equipped with a 6-Position Cell Holder, be sure to place the unknown in cell position #1.

3. Press Measure Sample to measure the unknown.

Note: If you want to switch between tabular and

graphical displays, press Graph/Tabular.

Note: You may need to use the up and down

arrow keys to view all the data for the scan.

Viewing & manipulating scan data

Within the Survey Scan/Scanning program, you can view and manipulate your results either in graphical form or in tabular form.

When you are working with graphical scan data, you need to press Edit Graph before you can perform other functions on the scan data.

When the edit graph screen appears, you can:

• Rescale the graph

• Perform mathematical operations on the graph

Rescaling graphical scan data

You can modify the scale of your scan data plot in two ways - automatically or manually. When you select Auto Scale, the instrument automatically scales the X- and Y-axes so all the data appears on the plot. When you select Manual Scale, you select specific minimum and maximum values for the X- and Y-axes. Whenever you modify the scale, the instrument also automatically recalculates and displays the new data plot.

Press Edit Scale to modify the scale. When the edit scale screen appears, you can:

• Use the cursor to identify specific points along the X-axis, change the scale and display the new graph

• Use the Manual Scale function to change the scale and display the new graph

• Use the Auto Scale function to change the scale and display the new graph

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3-21 BioMate 3 Operator’s Manuall

To use the cursor

1. With your scan data displayed on the edit scale screen, press Cursor. The cursor option appears

2. Press Cursor →→or Cursor ←←.to position the cursor line on the appropriate point on the graph. The instrument displays the data for the selected point.

3. When the cursor line is in the correct position, press Set Min X or Set Max X to accept the selected point. The instrument redraws the plot using the minimum and maximum value you have selected and displays the new graph.

To use the Manual Scale function

1. With your scan data displayed on the edit scale screen, press Manual. The manual scale options appear.

2. To set the minimum or maximum value for the X- or Y-axis, press Min Y, Max Y, Min X or Max X. A screen appears prompting you to enter the appropriate value.

3. Use the number keys to enter the correct value, then press the appropriate function key (Min Y, Max Y, Min X, Max X) to accept it. The instrument redraws the plot using the minimum and maximum values you have entered.

To use the Auto Scale function

1. With your scan data displayed on the edit scale screen, press Auto Scale. The instrument automatically adjusts the minimum and maximum values for the X- and Y-axes so all the data appears on the plot.

Performing calculations on the scan data

You can modify your graph by performing calculations on the data. From the Edit Graph screen press Math. When the Math screen appears, you can:

• Determine 3-point net values

• Calculate the area under a curve

• Label peaks and valleys

Determining 3-point net measurements

1. With your scan data displayed on the edit graph screen, press Math. The Math

Calculation screen appears.

2. Press 3-Pt Net to enter the 3-point Net Measurement screen. A screen showing the

cursor options and three cursor lines (designated for the left, center and right wavelengths) appears.

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Thermo Electron Corporation 3-22

3. Use Cursor →→and Cursor ←←to position the left cursor line to the desired wavelength value. The instrument calculates the 3-point net absorbance for the selected wavelengths.

4. Continue selecting the other wavelengths by pressing Next Cursor to activate the center and right cursor lines. Select the wavelengths by positioning the cursor with the Cursor

←←

and Cursor

→→

keys. Repeat until all three

wavelengths have been selected.

5. Press Enter Factor to access the set factor box. Enter the desired factor and press ENTER. The instrument calculates the value for the 3-point net absorbance for the selected wavelengths, multiplied by the selected factor.

Calculating the area under a curve

1. With your scan data displayed on the Edit Graph screen, press Math. The Math Calculation screen appears.

2. Press Area. The Area Under the Curve Measurement screen appears.

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. Select the wavelength by positioning the cursor with the Cursor

→→

and

Cursor

←←

keys.

5. Press Set Options to access the set options window.

6. Use the up and down arrows to highlight Factor. Enter the desired factor and press ENTER.

7. Use the up and down arrow to highlight Calculation baseline. Press ENTER to toggle between Zero and Tangent.

8. Press ESC to return to the area under a curve

screen. The instrument calculates the area under a curve for the selected wavelengths, factor and calculation method.

Labeling peaks and valleys

1. With your scan displayed on the edit graph screen, press Math. The Math Calculation screen appears.

2. Press Peaks & Valleys. The Label Peaks and Valleys window appears.

3. Use the arrow keys to select the type of labels

you want displayed and press ENTER. The instrument labels the selected items on your scan data plot.

Using “General Tests” Software

3-23 BioMate 3 Operator’s Manual

Viewing & rescaling tabular scan data

When you are working with tabular scan data, you need to press Edit Data before you can perform other functions on the scan data.

To use all the scan data

1. With your table of scan data displayed on the edit screen, press Use all data.

To select specific start and end wavelengths

1. With your table of scan data displayed on the edit screen, use the arrow keys on the keypad to move the highlight symbol (→→) to the appropriate data point in the table.

2. Press Start nm or End nm. The instrument highlights the selected data points.

You can press Graph to display the plot using the highlighted data points.

3-Point Net

When you use the 3-Point Net program, you can perform these tasks:

• Recall a test OR set up your test parameters

• Run the Cell Correction program

• Measure a blank

• Measure unknowns

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight

3-Point Net and press ENTER.

Recalling a test

1. With the 3-Point Net screen displayed, press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of

the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

From this screen, you can:

• Set up test parameters

• Run the Cell Correction program

• Save a test

• View the list of stored tests

• Measure a blank

• Measure unknowns

Setting up test parameters

1. With the 3-Point Net screen displayed, use the

arrow keys to highlight the name of the parameter you want to set.

2. When the parameters are set, you can press Save Test to save the test or Run Test to

measure a blank or unknowns.

Taking measurements

Taking measurements automatically (Auto 6 or Auto 3)

1. With the 3-Point Net screen displayed and the parameters set, press Run Test. The 3-Point Net measurement screen appears.

Using “General Tests” Software

Thermo Electron Corporation 3-24

2. Place the blank and the unknowns in the correct cell positions.

3. Press ENTER to start the measurements. The instrument automatically measures the blank first, then measures the unknowns and displays the sample measurements on the screen.

Taking measurements manually (using Manual 6 or Single Cell Platform)

1. With the 3-Point Net screen displayed and the parameters set, press Run Test. The 3-Point

Net measurement screen appears.

2. Place the blank and unknowns in the cell

holder. If your instrument is equipped with a 6Position Cell Holder, be sure to place the blank in the B position. You can place up to five samples in the cell holder.

3. Press Measure Blank to measure the blank. If your instrument is equipped with a 6-Position Cell Holder, it automatically moves to the B position to measure the blank. When it

completes the measurement, it returns to its previous cell position.

Multiple Wavelengths

When you use the Multiple Wavelengths program, you can perform these tasks:

• Recall a test OR set up your test parameters

• Run the Cell Correction program

• Add or delete wavelengths and factors

• Measure a blank

• Measure unknowns

To get started, press the TEST key on the keypad. When the Test Types screen appears, highlight

Multiple Wavelengths and press ENTER.

Recalling a test

1. With the Multiple Wavelengths screen

displayed, press Stored Tests. A list of stored tests appears.

2. Use the arrow keys to highlight the name of the test you want to recall and press ENTER. The parameters for the selected test appear on the screen.

From this screen, you can:

• Set up test parameters

• Run the Cell Correction program

3-25 BioMate 3 Operator’s Manual

Using “General Tests” Software

• Save a test

• View the list of stored tests

• Measure a blank

• Measure unknowns

Setting up test parameters

1. With the Multiple Wavelengths screen

displayed, use the arrow keys to highlight the name of the parameter you want to set.

*Refer to the procedures below for specific instructions on adding or deleting wavelengths and factors.

2. If you have previously selected the wavelengths you wish to measure, you can press Save Test to save the test or Run Test to measure a blank or unknowns.

3. If you have not selected the wavelengths, you can add wavelengths and factors as shown below.

Adding wavelengths & factors

Note: You can enter factors only when the

measurement mode is set to Concentration/Factor.

1. With the Multiple Wavelengths screen displayed, press Set nms. The wavelength screen appears, listing the wavelengths and factors specified for the measurements.

2. Use the arrow keys to highlight the position where you want to enter the first wavelength and factor pair.

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.

6. Continue until you have entered all the

wavelengths and factors.

Deleting wavelengths & factors

1. With the Multiple Wavelengths screen displayed, use the arrow keys to highlight Set nms. The wavelength screen appears, listing the wavelengths and factors specified for the measurements.

Note: If no wavelength values have been

entered, the wavelength and factor columns will be empty.

2. Use the arrow keys to highlight the first wavelength and factor pair you want to delete.

3. Press Delete nm.

Taking measurements

Taking measurements automatically (Auto 6 or Auto 3)

1. The Multiple Wavelength acquisition can be accessed from either the Set nms screen shown above or from the Multiple Wavelength set up screen. Press Run Test. The Multiple

Wavelength measurement screen appears.

2. Place the blank and the unknowns in the

correct cell positions.

3. Press ENTER to start the measurement. The instrument automatically measures the blank first, then measures the unknowns and displays the sample measurements on the screen.

Using “General Tests” Software

Thermo Electron Corporation 3-26

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.

4. With the list of wavelengths (and factors) displayed, press Measure Samples to measure the unknowns. The instrument measures the absorbance at each wavelength and displays it on the screen. If you have set the measurement mode to Concentration/Factor, the instrument also displays the calculated concentration at each wavelength.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.

Using “General Tests” Software

3-27 BioMate 3 Operator’s Manual

Using “General Tests” Software

Thermo Electron Corporation 3-28

Overview

The Performance Validation program allows you to run tests to check the performance of your instrument. Available tests include:

• Wavelength Accuracy - Internal

• Wavelength Accuracy - Standards

• Photometric Accuracy

• Noise Measurement

• Stray Light

• Internal Printer Test

• RS232C Test

Running the appropriate performance validation tests regularly and maintaining a log of your results helps document the reliability of the instrument and indicates potential performance issues.

Note: If you have a printer installed and turned

on, the instrument automatically prints out the test results for each performance validation test that you run. You can also press the PRINT key to print another copy of the results.

Accessing the Performance Validation tests

1. Press the TESTS key on the keypad. The Test Types screen appears.

2. Highlight Performance Validation and press ENTER. The Performance Validation screen

appears.

Troubleshooting checklist

If a Performance Validation test fails, follow the instructions below to help you diagnose common problems that may cause a test to fail. If a test continues to fail after you have tried all the recommendations in the list, follow the troubleshooting list for the test being run (included with the description of each test).

• Make sure you are following the instructions for the test properly.

• Make sure filters and standards are clean.

• Make sure the sample compartment door is closed while the test is running.

• Make sure the sample compartment is clear of any obstructions.

• Make sure the 6-Position Cell Holder is installed properly; run the test once with the sample compartment door open to verify that the 6-Position Cell Holder is moving smoothly.

• Turn the instrument power OFF, then ON; verify that no problems are indicated by the power-on diagnostics.

• Make sure the lamp is ON.

• Make sure the lamp compartment is clear of any obstructions.

Wavelength Accuracy - Internal

This test locates the peaks and displays the expected and measured wavelengths for the peaks at the following wavelengths:

• UV-Vis instruments - measures wavelength accuracy for the xenon lamp at 229, 529 and 883nm.

Using the Performance Validation Program

4-1 BioMate 3 Operator’s Manual

WARNING

Do not open the lamp compartment unless the instrument power is OFF.

Do not turn the instrument power ON unless the lamp compartment is closed!

When running the internal standard test, remember that:

• The wavelengths are preset and cannot be changed.

• The xenon lamp has a preset tolerance of ±2.0nm.

• The cell holder should be empty.

1. With the Performance Validation screen displayed, use the arrow keys to highlight

Wavelength Accuracy - Internal.

2. Press ENTER. The Wavelength Accuracy Internal screen appears.

3. Press Start Test to run the test. The results of

the test appear on the screen, indicating pass or fail for each wavelength.

If the test fails, follow these guidelines:

• Repeat the test several times to verify that the test is failing consistently.

• Contact technical support for more troubleshooting advice.

Wavelength Accuracy - Standards

This test measures the absorbance of a filter standard at up to five wavelengths and compares the results with specified tolerances. The wavelengths and tolerances are preset, but you should change them to the values on the certificate of calibration included with your standards.

Note: Only the middle wavelength of the

SPECTRONIC Standards wavelength standard is certified. The wavelength accuracy test passes or fails based on this wavelength alone. The other two wavelengths may be used for long-term repeatability testing. The

initial target values may be determined by running the wavelength accuracy test once, and taking note of the values reported in the Measured Wavelength column.

1. With the Performance Validation screen displayed, use the arrow keys to highlight

Wavelength Accuracy - Standards and press ENTER. The Wavelength Accuracy Standards screen appears.

Adding wavelengths

1. If you need to add a wavelength, press Add nm and enter the wavelength value in the Entry field.

2. When the value is correct, press Add nm

again to add the wavelength to the list. The screen changes to prompt you to enter the tolerance for the wavelength you just entered.

3. Enter the tolerance value in the Entry field.

4. When the value is correct, press Add Tolerance to add the tolerance.

Using the Performance Validation Program

Thermo Electron Corporation 4-2

Deleting wavelengths

1. If you want to delete a wavelength, use the

arrow keys to highlight the appropriate wavelength.

2. When the appropriate wavelength is highlighted, press Delete nm to confirm that you want to delete the wavelength.

Running the test

1. With the Wavelength Accuracy - Standards

screen displayed, make sure that the wavelengths and tolerances are set correctly.

2. Press Start Test to run the test. The results of the test appear on the screen, indicating pass or fail for each wavelength.

If the test fails, follow these guidelines:

• Repeat the test several times to verify that the test is failing consistently.

• Make sure the target value you entered for the calibrated wavelength is the same as the value printed on the SPECTRONIC Standards certificate.

• Make sure the tolerance value you entered for the calibrated wavelength is the same as the value given in the SPECTRONIC Standards User's Manual.

Photometric Accuracy

This test measures the absorbance (or %transmittance) of a set of standards and compares the results with specified tolerances. The absorbances and tolerances are preset, but you should change them to the values on the report of calibration included with your standards.

Note: You can display the tolerances for this test

in either absorbance or %transmittance.

1. With the Performance Validation screen displayed, use the arrow keys to highlight

Photometric Accuracy.

2. Press ENTER. The Photometric Accuracy

screen appears.

Selecting the mode

1. To switch between absorbance and %transmittance, press Change to %T (or Change to ABS) until the appropriate mode

appears.

Adding standards

You will need to set three values whenever you add a standard - the wavelength, the absorbance (or %transmittance) and the tolerance value.

1. If you need to add a standard, press Add Std and enter the wavelength value in the Entry field.

2. When the wavelength value is correct, press Add Std again to add the wavelength to the

list. The screen changes to prompt you to enter the absorbance (or %transmittance) for the wavelength you just entered.

3. Enter enter the tolerance value in the Entry field.

4. Press Start Test or Press ESC to save test.

Using the Performance Validation Program

4-3 BioMate 3 Operator’s Manual

Deleting standards

1. If you need to delete a standard, use the arrow

keys to highlight the appropriate standard.

2. When the appropriate standard is highlighted, press Delete Std to confirm that you want to delete the standard.

Running the test

1. With the Photometric Accuracy screen

displayed, make sure that the wavelengths, absorbance (or %transmittance) values and tolerances are set correctly.

2. Press Start Test to run the test. The results of the test appear on the screen, indicating pass or fail for each wavelength.

If the test fails, follow these guidelines:

• Repeat the test several times to verify that the test is failing consistently.

• Make sure you follow the guidelines provided with the standard reference materials.

• Contact technical support for more troubleshooting advice.

Noise Measurement

This test measures the amount of noise (peak-topeak) at specified wavelengths:

• UV-Vis instruments - measures noise at 230 and 340nm

All parameters are preset and cannot be changed. When running the noise test, remember that:

• The wavelengths are preset and cannot be changed.

• The Blank position should be empty.

• Position #1 should be used for the 2A filter in a 6-cell holder only (if measured).

1. With the Performance Validation screen displayed, use the arrow keys to highlight

Noise Measurement.

2. Press ENTER. The Noise Measurement

screen appears.

Using the Performance Validation Program

Thermo Electron Corporation 4-4

3. Make sure that the Blank position is empty and insert the 2A filter in position #1 if you are measuring at 2A.

4. Press Start Test to run the test. The results of the test appear on the screen, indicating pass or fail for each wavelength.

If the test fails, follow these guidelines:

• Repeat the test several times to verify that the test is failing consistently.

• Make sure the instrument is warmed up for at least 30 minutes, standby mode = OFF.

• Make sure the instrument is plugged into a stable power supply.

• Contact technical support for more troubleshooting advice.

Stray Light

This test measures the amount of stray light at selected wavelengths and compares them to specified tolerances. The wavelengths are preset and cannot be changed. You should change the tolerances for the desired wavelengths. Running the stray light test takes approximately thirty seconds.

When running the stray light test, remember that:

• You will need the SPECTRONIC Standards Stray Radiant Energy filters or equivalent.

• Position B should be empty.

• Position #1 should be used for SRE 220.

• Position #2 should be used for SRE 340.

• Position #3 should be used for SRE 400.

You may use other filters, but they must have <

–

0.1%T at the wavelength of interest.

1. With the Performance Validation screen displayed, use the arrow keys to highlight Stray Light.

2. Press ENTER. The Stray Light screen appears.

Running the test

1. With the Stray Light screen displayed, make

sure that the wavelengths and tolerances are set correctly.

2. Press Start Test to run the test. The results of the test appear on the screen, indicating pass or fail for each wavelength.

If the test fails, follow these guidelines:

• Repeat the test several times to verify that the test is failing consistently.

• Make sure all the filters being used are SPECTRONIC Standards Stray light filters, or exact equivalents.

• Contact technical support for more troubleshooting advice.

Internal Printer Test

The Internal Printer test allows you to verify that the internal printer is functional. To run the test, you will need to have the internal printer installed. Running the internal printer test takes no more than 20 seconds after you press Stop.

1. Verify that the internal printer is installed properly and is selected. If necessary, press the

UTILITY key, then select the internal printer.

2. With the Performance Validation screen

displayed, use the arrow keys to highlight Internal Printer Test.

Using the Performance Validation Program

4-5 BioMate 3 Operator’s Manual

3. Press ENTER. The Internal Printer Test screen appears.

4. Press Start Test to run the test. The test print routine appears on the printer.

While the test is running, you can press Stop Test to stop it.

If the test fails, follow these guidelines:

• Make sure that the internal printer is the selected printer device on the Utilities screen.

• Make sure that the internal printer is installed correctly. (Return to the main screen and press ENTER. If the paper does not move, the printer may not be installed correctly.)

• Make sure that the thermal paper is threaded with the thermal side toward the printer head (the outside surface of the roll is the thermal surface).

• Contact technical support for more troubleshooting advice.

RS232C Test

The RS232C test allows you to verify that the RS232C port is functional. To run the test, you will need to have the RS232 Test Plug (336035) attached to the RS232C port on the back panel of the instrument. Running the RS232C test takes approximately five minutes.

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.

3. Press ENTER. The RS232C Test screen

appears.

4. Press Start Test to run the test. When the test is complete, the message "RS232 OK" or RS232 Failed" appears on the screen.

While the test is running, you can press Stop Test to stop it.

If the test fails, follow these guidelines:

• Make sure that the test plug is installed correctly and is not loose or damaged.

• Contact technical support for more troubleshooting advice.

Using the Performance Validation Program

Thermo Electron Corporation 4-6

General information

The spectrophotometer supports a variety of sample-handling accessories. This section describes how to connect and use the following types of accessories:

• Cell holders and cell holder accessories

• Internal printer

• External computer

Cell holders & cell holder accessories

If the spectrophotometer includes a 6-Position Cell Holder, you can install a single-position cell platform. However, if your spectrophotometer is a Single-Position Cell Platform model, you cannot upgrade it to accommodate a 6-Position Cell Holder.

The following table lists the cell holders and cell holder accessories available for the spectrophotometer.

Connecting & Using Accessories

5-1 BioMate 3 Operator’s Manual

Catalog # Description

335916 Single Cell Holder Platform -with single cuvette holder installed. Included in 335900 and

335902 models.

336014 Test Tube Holder - Accommodates test tubes up to 25mm in diameter and up to 102mm

tall, C.O.D. reagent vials and Hach vials (24mm diameter and 60mm tall); fits on 335927 6-Position Cell Holder (holds three) or 335916 Single Cell Holder Platform (holds one).

335917 Adjustable Filter Holder - Accommodates glass or plastic filters up to 50mm long x

80mm tall x 10mm thick; minimum thickness of 1mm; fits on 335927 6-Position Cell Holder (holds three) or 335916 Single Cell Holder Platform (holds one).

335428 Filter Holder - Accommodates filters/lenses up to 50mm long x 80mm tall x 1-8mm thick;

fits on 335927 6-Position Cell Holder (holds three) or 335916 Single Cell Holder Platform (holds one).

335079 Thermal Block - Controls the temperature of one 10mm pathlength square cuvette within

the range of 20 to 100ºC; fits on 335927 6-Position Cell Holder (holds three) or 335916 Single Cell Holder Platform (holds one); requires external water bath and 335921 Accessory Door for routing circulating water.

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.

335911 Cylindrical Longpath Cell Holder - Accommodates a cylindrical cell with 10-50mm

pathlength, 22-25mm diameter; fits on 335927 6-Position Cell Holder (holds three) or 335916 Single Cell Holder Platform (holds one).

335912 Rectangular Longpath Cell Holder - Accommodates a rectangular cell with 10-50mm

pathlength, 12.5mm wide; fits on 335927 6-Position Cell Holder (holds three) or 335916 Single Cell Holder Platform (holds one).

336012 Cylindrical Longpath Cell Holder - Accommodates one cylindrical cell with 10-100mm

pathlength, 22-25mm diameter; requires 335916 Single Cell Holder Platform.

335112 Rectangular Longpath Cell Holder - Accommodates one rectangular cell with 10-100mm

pathlength, 12.5mm wide; requires 335916 Single Cell Holder Platform.

335989 Internal Printer Assembly - Includes 1 roll of paper.

335982* Peristaltic Pump - Includes set of Norprene pump tubing; used with 335171 Optical

Glass flowcell or 335172 Quartz flowcell and 335921 Accessory Door Kit. 115V, 50/60Hz.

335982-02 Same as 335982 except with Europlug 230 VAC

335982-04 Same as 335982 except with UK plug 230 VAC

Changing cell holders

If you want to use longpath cells (cylindrical or rectangular), use test tubes, measure solid filters or regulate cell temperature via an external water circulator, you must install the appropriate cell holders. You can easily remove the 6-Position Cell Holder installed in the instrument and install other accessory cell holders.

*Whenever you change from one type of cell holder to another, you must measure a blank. This ensures that the instrument can detect which type of cell holder is installed.

Removing the 6-Position Cell Holder

1. Open the sample compartment and let the sample compartment door rest on its hinge.

2. With one hand, loosen the captive thumbscrew.

3. With the other hand, pull straight up on the 6-

Position Cell Holder and lift it out of the sample compartment.

Installing the 6-Position Cell Holder

1. Open the sample compartment and let the sample compartment door rest on its hinge.

2. With one hand, carefully lower the 6-Position Cell Holder straight down into the sample compartment.

3. With the other hand, tighten the captive thumbscrew.

4. Close the sample compartment.

5. Take a blank measurement to ensure that the

instrument detects that you have installed the 6-Position Cell Holder.

Installing the Single-Position Cell Holder

1. With the sample compartment open, place the Single-Position Cell Platform as shown in Figure 5.

2. Tighten the screws securely.

Note: If the cell holder is not aligned correctly, you

will not be able to tighten the screws.

3. Take a blank Measurement to ensure that the instrument detects that you have installed the Single-Cell Platform.

Installing accessory cell holders

1. Make sure that you have the correct cell holder installed. If you want to use 100mm longpath cells, you must install the Single-Position Cell Holder.

2. Install the desired accessory cell holders by tightening the screw on each cell holder.

Note: You can install only three each of some

accessory cell holders. Make sure to place them in positions B, 2 and 4.

Connecting & Using Accessories

Thermo Electron Corporation 5-2

Catalog # Description

335921 Accessory Door Kit - Includes spout and four ports for circulating water around water-

jacketed cells, or for waste outlet for flowcell systems.

335977 Funnel Flowcell - 10mm pathlength, optical glass, for measurements between 335-

1100nm; fits on 335916 Single Cell Holder Platform (holds one).

335927 6-Position Cell Holder - platform with six (6) 336028 single cell holders installed.

333150 SPECTRONIC Standards

336029 Spacers - 5mm, set of 2, for use with 5mm short pathlength cuvettes in any square cell

holder.

336030 Spacers - 8mm, set of 2, for use with 2mm or 1mm short pathlength cuvettes in any

square cell holder.

335942 Serial interface cable to connect the spectrophotometer to an IBM-compatible PC.

331751 Ultra-microcell - 10 µl fill volume, 1mm pathlength, 40mm tall, quartz.

331752 Ultra-microcell - 70 µl fill volume, 10mm pathlength, 50mm tall, quartz. Requires 335916

Single Cell Holder Platform (holds one) for optimal performance

Note: If you want to use 100mm longpath cells, you must install the Single-Position Cell Platform.

Internal printer

Installing the internal printer

|| |

WARNING

| || |

Turn off the instrument and disconnect the

| |

power cord from the outlet before installing the

| |

internal printer.

1. Loosen the captive screw (#1, Figure 6) on the

lamp door by rotating it counterclockwise about ¼ turn.

2. Open the lamp door.

3. Use a pen or screwdriver to lift the tabs holding

the door to the hinge (#2 & #3, Figure 6).

4. Slide the door off the hinge.

5. Remove the printer (already installed on the

printer door) from its packing.

6. Unclip the connector wires on the door hinge.

7. Lower the hinge so it is out of the way.

8. Connect the wires (#4, Figure 6) and press into

place with a small screwdriver. There is only one way that the connectors will fit. Each connector has a slight D shape. Make sure the side of the connector with the shiny metal contacts (see Figure 6) and faces away from the printer and towards the plastic door.

9. Use the clip on the hinge to secure the wires.

10. Install the printer door by sliding it back onto

the hinge (#3, Figure 6).

11. Close the lamp door.

12. Tighten the captive screw (#1, Figure 6) on the

printer door to hold it securely in place.

13. Load the paper into the printer (see instructions

in Setting up the instrument).

Loading the paper in the internal printer

For instructions on loading the paper in the internal printer, see Setting up the instrument.

External computers

To connect an external computer, make sure that the pin-outs on the connectors are set according to the illustration below.

To connect an external computer, connect the computer cable to the 9-pin RS232C port on the back of the instrument (#2, Figure 2). Be sure to use a DB9 pin (female) to DB9 pin (female) interface cable (335942).

Contact technical support for more information about using an external computer with the spectrophotometer.

5-3 BioMate 3 Operator’s Manual

Connecting & Using Accessories

Protocol to use with external device:

Baud rate 19,200 Data bits: 8 Parity: Off Stop Bit: 1

Thermo Electron Corporation 5-4

Connecting & Using Accessories

The spectrophotometer is durable and reliable, so routine maintenance is minimal. This section includes complete instructions for:

• Routine care, cleaning and maintenance of the

instrument and cells

• Changing the fuse and voltage setting

This section also includes a list of replacement parts and accessories.

|| |

WARNING

| || |

Operating the instrument with the cover off

| |

exposes the operator to potentially dangerous

| |

voltages and ultraviolet (UV) radiation.

| |

Therefore, the distributor recommends that

| |

only authorized service representatives perform

| |

procedures requiring removal of the instrument

| |

cover and replacement of electrical components.

| |

To protect both yourself and the instrument, be

| |

sure to contact an authorized service

| |

representative to perform any service procedure

| |

you do not feel comfortable performing.

Routine care

Routine care for the spectrophotometer does not require a lot of time. To help minimize maintenance time and to increase the life and performance of your instrument, please follow these guidelines:

• To prevent dust from accumulating on and in

the instrument, always replace the dust cover when the instrument is not turned on. The dust cover, supplied with the instrument, is resistant to most aqueous solutions.

• Do not use or store the instrument in a

corrosive environment.

• Gently wipe the outside of the instrument with

a soft cloth to remove any dust or spills. Water, isopropyl alcohol and other common laboratory cleaning agents may be used if necessary.

• Always clean up spills to prevent or minimize damage to the instrument. If concentrated acids or bases, or any hydrocarbon materials, are spilled on the instrument, be sure to clean up the affected area immediately.

• Use water, alcohol or other common laboratory cleaning agents to clean the keyboard. It is recommended that you clean spills off the keyboard as soon as they occur.

Cleaning

Cleaning and maintenance of cells

Cleaning of cells both inside and out is important not only because any contaminating material may absorb light, but also because material within the cell may react chemically with subsequent reagents or standards introduced into the cell. Cleaning methods depend to some extent on the nature of the contaminating material. Sodium (or ammonium) hydroxide and dilute hydrochloric acid may be used to remove some acidic and basic contaminants, respectively. Clorox (undiluted or 1:1) is very effective in removing proteinaceous and bacterial contaminants. You may also use Cell Cleaning Solution (332260-169) to clean your cells.

Finally, soaking in chromic acid will remove most contaminants, but the acid should be handled, and disposed of, with care. Because of the exothermic reaction of the acid and water, any heat generated should be quickly dissipated to avoid altering the pathlength of the cell. Cells should not be placed in hot chromic acid.

Note: To prepare chromic acid cleaning solution,

slowly add (with stirring) 800mL of concentrated sulfuric acid to 458mL of distilled water containing 92 g of sodium dichromate (Na2Cr2O7•2H2O). This cleaning solution should be red-brown. Discard, using proper disposal methods, when green tinge appears.

Performing Maintenance Procedures

6-1 BioMate 3 Operator’s Manual

WARNING

Handle and dispose of chromic acid with care!

Cells with scratches in the optical path should be discarded because scratches will cause anomalous absorbance readings. Cells should be protected during cleaning and never thrown into a bath with glassware where they might get scratched, or placed in a wire rack that might scratch them. The outside of the cells may be wiped with a soft, lintfree tissue, and should be kept free of fingerprints.

Micro flowcells can be kept clean by:

• Flushing well with a solvent after use

• Aspirating dilute acid, base, non-filming detergent or Clorox through the cell in short bursts

• Storing with distilled water in the cell

Cleaning the windows of the sample compartment

Follow these guidelines to clean the windows of the sample compartment:

• Do not use acetone to clean the windows of the sample compartment. Instead, use a non-abrasive laboratory cleaning solution (Cell Cleaning Solution, 332260-169), distilled water or alcohol.

• Use the liquid and a soft, lint-free cloth to clean the windows. Do not apply too much pressure or the surface of the windows may be damaged. Be sure to remove all fingerprints.

Changing the fuse

The fuse is located in the power entry module located at the center of the back panel of the instrument (Figure 2).

• 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.

|| |

WARNING

| || |

If the fuse fails repeatedly, it may indicate a

| |

serious problem with the instrument. Contact

| |

your service representative as soon as possible.

1. Turn off and unplug the instrument.

2. Position the instrument so you can access the

power entry module on the back of the instrument.

3. Remove the power cord.

4. Insert a flat-blade screwdriver into the notch

(Figure 8) on the fuse cover and pry off the cover.

5. Use a flat-blade screwdriver to remove the fuse

holder (Figure 9).

6. Unsnap both fuses (Figure 10) to remove them.

7. Insert the new fuses, pushing them in so they

snap into place.

8. Replace the fuse cover.

9. Replace the power cord.

10. Plug the instrument back in the appropriate

outlet and turn on the power.

Note: If the fuse blows again, contact your

distributor or service at the number(s) listed on the back cover.

Performing Maintenance Procedures

Thermo Electron Corporation 6-2

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.

335989 Internal Printer Assembly.

333152 Sensitized Paper - (100 sheets) for SPECTRONIC Standards.

335965 Replacement Dust Cover.

335954 Printer Paper - Package of 5 rolls.

335904-10001 BioMate 3 Operator’s Manual.

335901-10020 Service Manual, includes printed service manual and CD ROM.

335901-10040 BioMate 3 Service Manual, includes CD ROM only.

335971 Replacement silicone tubing for 335982 Peristaltic pump, 5mm OD,

1.5mm ID, 25 foot roll.

Replacement parts

Performing Maintenance Procedures

6-3 BioMate 3 Operator’s Manual

Performing Maintenance Procedures

Thermo Electron Corporation 6-4

Appendix A - Specifications

A-1 BioMate 3 Operator’s Manual

Specifications

Table 1 Specifications for BioMate 3 spectrophotometers

BioMate 3

Spectral Bandwidth 5nm

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" x 2.8"

Photometric

Range 0.3 - 125%T; -0.1 - 3.0A; 0 - 9999C

Readout Absorbance, Transmittance, Concentration

Accuracy

0.5% or 0.005A, whichever is greater, up to 2A

Noise ≤ 1mA at 0A; ≤ 2mA at 2A, peak-to-peak at 340nm

Drift ≤ 1mA/hour

Stray Light

≤ 0.1%T at 220 and 340nm

Standard Interface Bi-directional RS232C

Standard Cell Holder 1-position and automatic 6-position cell holder

Keyboard Membrane keypad

Software DNA ratio/concentration with or without scanning

Direct protein at 280nm Protein standard curves Cell growth Oligo calculator - absorptivity, molecular weight, factor and theoretical T

Absorbance/Transmittance/Concentration Absorbance Ratio Absorbance Difference Standard Curve Kinetics Survey Scan Performance Validation Multiple Wavelength 3 Point Net

Test Storage Up to 40 sets of test parameters

Languages Software and Printout: English, French, German, Spanish, Italian

(user selectable)

Printer (optional) 40-column internal graphics

Power Requirements Selected automatically; 100 - 240 Volts

Appendix A - Specifications

Thermo Electron Corporation A-2

Table 2 Environmental and electrical

requirements (meets the IEC 1010-1 international safety standard)

Line voltages

100 - 240 VAC ±10%

50 - 60 Hz

80 VA max

Operating environment

The instrument meets the specifications on the previous page under the following conditions after a 30-minute warm-up period.

Ambient temperature: 5° to 35° C (41° F to 95° F)

Relative humidity - 20% - 80% RH

Storage environment

-20° C to 70° C (-4° F to 158° F) Relative humidity not to exceed 0.040 pounds moisture per pound of dry air. Allow instrument to adjust to room temperature for 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

BioMate 3

Dimensions 330W x 410D x 235H mm (13" x 16" x 9")

Weight 8.6 Kg (19lb)

Warranty 1 year

These specifications are valid only when the required environmental conditions (see below) are met.

When working in the range of 800 to 1100nm, allow the instrument to warm up for at least an hour.

Measured using NIST 930D filters

220nm and 340nm measurements with SPECTRONIC Standards (#333150)

Appendix B - Parameters

B-1 BioMate 3 Operator’s Manual

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

# Phot Accy Standards Used to determine photometric accuracy of unit

%Transmittance Sets of transmittance value

% of lamp life used Estimated percentage of lamp life used (based on typical lamp life of 5 years)

%Formamide Percentage of formamide contained in the sample

%GC Percentage of GC pairs contained in the sample

Absorbance Set absorbance value

Auto Print Turns automatic printout on or off

Base Sequence Sequence of bases contained in the sample

Beeper Turns audible signal on and off

Cell Correction Program that automatically corrects for variances in absorption between the

cuvetts used to hold and measure samples

Cell Pos # Position placed in light path; set by selection of sample positioner

Concentration Sets concentration value

Correction Mode Mode for cell correction collection

Cursor position on Indicates which option on the Test Types screen should be highlighted Test Types menus

Cursor position on Indicates which option on the Utility screen should be highlighted Utility menu

Curve Fit Type of Curve fit calculation

Date Standards Measured Date when standards were last measured with this instrument

Date/Time Setup Current date and time settings for the instrument

Delay Time Time from Test Initiation to first measurement; allows for sample equilibration

Diluent Volume Volume of diluent added prior to measurement

Dilution Multiplier Factor used to correct for sample dilution

Display Activity Indicates whether results should appear as units of enzyme activity

Display Protein Indicates whether results should include protein concentration

DNA ε(260) Extinction coefficient

DNA Mol. Wt. Molecular weight of DNA contained in sample

Factor Abs x Factor = Concentration

Abs/min x Factor = Result

Factor 1 Abs(WL1) x Factor = Result

Factor 2 Abs(WL2) x Factor = Result

B-2 BioMate 3 Operator’s ManualThermo Electron Corporation B-2

Appendix B - Parameters

Factor 3-31 Abs(WL3-31) x Factor = Result

Parameter Description

ID# Numeric Identifier - automatically increments during test until parameter is

reset or test is exited

Intercept Where line crosses the y-axis (abs where conc=0)

Interval Time Time between repeated readings

Language Language of any text on screen

Linearity Value To help determine the linearity of the reaction during the measurement, the

spectrophotometer offers a linearity parameter. This parameter is the difference between the changes in absorbance of two measurements as shown in the following example:

Time____ Abs___ ∆Α__ Line___ arity_____

1 .1 ---- ---2 .2 .1 ---3 .29 .09 P 4 .38 .09 P 5 .46 .08 P 6 .52 .06 F

Linearity is the ∆A between ∆A calculations. P = Pass F = Fail

Lock/Unlock Used to protect stored tests from accidental deletion or alteration

Low/High Limits Lowest & highest acceptable results, outside of which the result is flagged

as 'Low' or 'High'

Measurement Mode The type of photometric data reported for a measurement

Molarity of cation Molarity of Na+in incubation mixture

Number of Bases Number of bases in the oligonucleotide

Number of Matched Number of cuvettes that will be run in the Correction Program (maximum of

Cuvettes 5)

Number of Samples Number of samples to be measure in the whole test

Number of Standards Number of standards to be measured for standard curve

Phot Accy Tolerance ±Photometric accuracy acceptable

Pk-Pk Noise Tolerance ±Noise acceptable

Printer Selects output mode

Recorder Chart High/Low Range (high or low) setting for chart recorder

Ref. Wavelength 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

Appendix B - Parameters

B-3 BioMate 3 Operator’s Manual

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 nm/min for a scan

Setup Correction Initiates the procedure to collect the data necessary to correct for cuvette

variances

Slope ∆Abs/∆Concentration

SRE Tolerance ±Stray radiant energy acceptable

Standard Concentrations Concentration of standards used to generate standard curve for the test

Standby Time since last keystroke or instrument activity; powers down unit to

minimum energy required to keep lamp in warm-up status

Statistics Turns statistics function on or off; if ON, calculates average and

Std Dev of results;Statistics registers are cleared when Statistics = OFF&/or when instrument is OFF &/or when test parameters are changed &/or when test is saved (or resaved)

Stop Wavelength Ending wavelength for a scan

Test Name Defined by user to identify stored tests

Tm value Calculated melting temperature

Total Run Time Time from Run Initiation to end of test = Delay Time + Interval Times +

Measurement Times

Units Labels concentration results

Wavelength values Values for the analytical wavelengths

Appendix B - Parameters

Thermo Electron Corporation B-4

Appendix C - Calculations

C-1 BioMate 3 Operator’s Manual

Calculations

Table 1 Calculations for “Biotest” Software

Test Name Calculation(s) Default Displayed

Parameters Results

DNA/Protein Dilution Factor (Df) = diluent vol + sample volume A1= 260nm µg/mL (260, 280) sample volume A2= 280nm

ref

= 320nm

DNA concentration = [(A1– A

ref)f1

– (A2– A

ref)f2]Df

(optional)

f1= 62.9

Protein concentration = [(A2– A

ref)f3

– (A1– A

ref)f4

] Dff2= 36.0

f3= 1552

Ratio = A1- A

ref

f4= 757.3

A2- A

ref

dil.vol. = 0 smp.vol = 1

DNA (260, 230) Dilution Factor (Df) = diluent vol + sample volume A1= 260nm µg/mL

sample volume A2= 230nm

ref

= 320nm

DNA concentration = [(A1– A

ref)f1

– (A2– A

ref)f2

] D

(optional)

f1= 49.1

Protein concentration = [(A2– A

ref)f3

– (A1– A

ref)f4

] Dff2= 3.48

f3= 183

Ratio = A1- A

ref

f4= 75.8

A2- A

ref

dil vol. = 0 smp.vol = 1

DNA (260, 280) Dilution Factor (Df) = diluent vol + sample volume Start wavelength µg/mL with Scan sample volume = 225nm

Stop wavelength

DNA concentration = [(A1– A

ref)f1

– (A2– A

ref)f2

] D

= 325nm

A1= 260nm

Protein concentration = [(A2– A

ref)f3

– (A1– A

ref)f4

] DfA2= 280nm

ref

= 320nm

Ratio = A1- A

ref

(optional)

A2- A

ref

f1= 62.9 f2= 36.0 f

= 1552 f4= 757.3 dil.vol. = 0 smp.vo. = 0

DNA (260, 230) Dilution Factor (D

) = diluent vol + sample vol. A1= 260nm µg/mL

with Scan sample volume A2= 230nm

ref

= 320nm

DNA concentration = [(A1– A

ref)f1

– (A2– A

ref)f2

] ] D

(optional)

f1= 49.1

Protein concentration = [(A2– A

ref)f3

– (A1– A

ref)f4

] Dff2= 3.48

f3= 183

Ratio = A1- A

ref

f4= 75.8

A2- A

ref

dil.vol. = 0 smp.vol. = 1

Appendix C - Calculations

Thermo Electron Corporation C-2

Test Name Calculation(s) Default Displayed

Parameters Results

dsDNA Conc. = (F x A

260)Df

260nm µg/mL Factor

dsDNA

= 50

Conc. = (F x A

260)Df

260nm µg/mL

ssDNA, RNA Factor

ssDNA

RNA

= 40

Oligos Conc. = (F x A

260)Df

260nm µg/mL

(entered factor) Factor

oligos

= 33

Oligos (calc factor) Conc. = (F x A

260)Df

260nm µg/mL

F = factor calculated by Oligo Calculator

Bradford Second order 595nm µg/mL – standard Std. Conc.

of 0, 200, 400, 600, 800,1000

Bradford – micro Second order 595nm µg/mL

Std. Conc. of 0, 20, 40, 60, 80, 100

Lowry – standard Second order 550nm µg/mL

Std. Conc. of 0, 100, 200, 500, 1000, 2000

Lowry – micro Second order 750nm µg/mL

Std. Conc. of 0, 20, 50, 100, 200, 500

Second order 562nm mg/mL

(BCA) – standard Std. Conc.

of 0, 0.2, 0.4,

0.6, 0.8, 1.0

Second order 562nm µg/mL

(BCA) – micro Std. Conc. of 0,

0.5, 1, 2, 5, 10

Biuret First order through zero 540nm mg/mL

Std. Conc. of 0, 2, 4, 6, 8, 10

Direct UV (280) Conc. = (F x A

280)Df

280nm mg/mL Factor

280

= 1

Direct UV (205) Conc. = (F x A

205)Df

205nm mg/mL Factor

205

= 31

Warburg-Christian Dilution Factor (Df) = diluent vol. + sample vol. A1= 280nm mg/mL

sample volume A2= 260nm

f1= 1.55

Protein Concentration = [(A1)f1– (A2)f2] D

f2= 0.76

Cell growth None 600nm Abs

Appendix C - Calculations

C-3 BioMate 3 Operator’s Manual

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 %GC = # of (G + C) bases x 100 Percentage

entered above total # of AT(or U)GC

Molecular weight # units A, # units T, If entry does not include U: Molecular weight

# units G, # units C, MW = (312.2 x A) + (303.2 x T) = x daltons/M # units U + (329.2 x G) + (289.2 x C) + 18.02

If entry does include U: MW = (329.2 x A) + (306.2 x U) + (345.2 x G) + (305.2 x C) + 18.02

Absorptivity # units A, # units T, If entry does not include U: Extinction ε (260) # units G, # units C, ε

260

= (15,200 x A) + (8,400 x T) coefficient =

# units U + (12,010 x G) + (7,050 x C) M-1cm

-1

If entry does include U:

260

= (15,200 x A) + (9,900 x U)

+ (12,010 x G) + (7,050 x C)

Conversion Factor N/A Molecular Weight x 10

µg/mL

Extinction Coefficient

Calculation of Tm: # units A, # units T, Tm= 2(A + T) + 4(G + C) °C Oligos up to # units G, # units C 20 bases in length

Calculation of Tm: • # units A, # units T, Tm= 81.5C + 16.6log ((Na+)/ °C DNA-DNA hybrids # units G, # units C (1+0.7(Na+)) + 0.41(%GC) –

• M = molarity of cation 500/L – P – 0.63(%formamide)

• Fraction GC = fraction of G and C

• %form = %formamide in the sample

• L = # of base pairs

• P = % mismatching

Calculation of Tm: • # units A, # units T, Tm= 67°C + 16.6log ((Na+)/ °C DNA-RNA hybrids # units G, # units C (1+0.7(Na+)) + 0.8(%GC) –

• M = molarity of cation 500/L – P – 0.5(%formamide)

• Fraction GC = fraction of G and C

• %form = %formamide in the sample

• L = # of base pairs

• P = % mismatching

Calculations

Table 2 Calculations for BioMate Oligo Calculator

Appendix C - Calculations

Thermo Electron Corporation C-4

Calculation Entry Parameters Formula Displayed Units

Calculation of Tm: • # units A, # units T, Tm= 78°C + 16.6log ((Na+)/ °C RNA-RNA hybrids # units G, # units C (1+0.7(Na+)) + 0.7(%GC) –

• M = molarity of cation 500/L – P – 0.35(%formamide)

• Fraction GC = fraction of G and C

• %form = %formamide in the sample

• L = # of base pairs

• P = % mismatching

Conversion from • µg/mL and molecular pmol/µL= µg/mL x 1000 pmol/µL

weight from Oligo (calc DNA Mol. Wt. factor) test

Appendix C - Calculations

C-5 BioMate 3 Operator’s Manual

Calculations

Table 3 Calculations for Software

Calculation Calculation(s) Graphs

Standard Curves

Partial sums

Linear regression

(general case)

Linear regression

through zero

Segmented model

SX = Σx

SY = Σy

SXX = Σx

SYY = Σy

SXY = Σxiy

SQX = Σ(xi- x_)2= N*SXX - SX

SQY = Σ(yi- y_)2= N*SYY - SY

SSXY = Σ(xi- x_)(yi- y_) = N*SXY - SX*SY

where: xi= concentration of ithstandard

yi= absorbance of ithstandard N=number of standards

A = A(c)

where: A = absorbance

c = concentration

A(c) is defined by an equation of the form

A(c) = a4c4+ a3c3+ a2c2+ a1c + a

where: a

= Y-axis intercept

a1…a4= coefficients

The coefficients are computed using the least squares method.

A= a1* (c)

where: A = absorbance

c = concentration a1= slope

The slope is calculated as

a1= SXY

SXX

This model requires:

• Slope is not equal to zero

• At least one standard data point with concentration not equal to zero

The segmented model requires:

• Data for at least two standard data points with different concentrations and absorbances

• Slopes of all segments must be ascending (positive) OR descending (negative)

Appendix C - Calculations

Thermo Electron Corporation C-6

Calculation Calculation(s) Graphs

Validity of standard curves

Statistics

(Linear regression general case)

Linear regression

through zero model

Absorbance Ratio

Absorbance Difference

A(c1) > A(c2)

for all c1> c

A(c1) < A(c2)

for all c1> c

where: A = absorbance

c1, c2= concentration

If this is not the case, then there will be more than one solution within the specified domain, and the message “Curve cannot be used to determine unknown concentrations - it may produce ambiguous results” will appear when the curve is viewed.

where: n = degree of polynomial

Note: The calculation for the correlation

coefficient only applies to first-order linear regression curves (first-degree polynomials).

Absλ

Absλ1 − Abs

ref

Absλ

Absλ2 − Abs

ref

Result = Absλ

factor 1 - Absλ2∗

factor 2

(Absλ1- Absλ

ref

)*factor 1 - (Absλ2- Absλ

ref

)*factor 2

Valid non-linear standard curve

Invalid non-linear standard curve

Appendix C - Calculations

Valid non-linear standard curve

Invalid non-linear standard curve

C-7 BioMate 3 Operator’s Manual

Calculation Calculation(s) Graphs

3-Point Net

3-Point Net Absorbance

sample curve

Baseline corrected absorbance =

A2(A3+ ([A1

A3]



)

λ3

Appendix C - Calculations

Thermo Electron Corporation C-8

3-Point Net . . . . . . . . . . . . . . .3-24, 3-25, C-7

measurements . . . . . . . . . . . . . .3-20, 3-23

A/%T/C program . . . . . . . . . . . . . . . .3-8, 3-10

Absorbance & %Transmittance measurements 3-8

Absorbance Difference . .1-1, 3-16, 3-17, C-6

Absorbance Ratio . . . . . . . . . . .1-1, 3-15, C-6

Accessories . . . . . . . . . . . . . . . . . . . . . . . .5-1

Accessories, connecting & using . . . .1-3, 5-1

Area under a curve, calculating . . .3-20, 3-23

Auto 3/Auto 6 . . . . . .3-3, 3-5, 3-9, 3-10, 3-12,

3-13, 3-15, 3-16, 3-20, 3-25, 3-27

AutoPrint . . . . . . . . . . . . . . . . . . . . . . . . .3-12

Back panel . . . . . . . . . . . . . . .3, 1-1, 4-6, 6-2

Base sequence . . . . . . . . . . . . .2-6, 2-12, B-1

Baseline expiration . . . . . . . . . . . . . . . . . .1-2

Baseline scan, collecting . . . . . . . .3-20, 3-21

BCA (bicinchoninic acid) . . . . . . .2-7, 2-8, C-1

Biuret . . . . . . . . . . . . . . . . .2-7, 2-8, C-1, C-2

Bradford . . . . . . . . . . . . . . .2-7, 2-8, C-1, C-2

Calculations . . . . . . . . . . .2-11, 3-23, B-2, C-1

Calibration . . . . . . . . . . . . . . . . . . . . . . . . .1-1

Cell Correction program . . . . . . .1-4, 3-3, 3-4,

3-5, 3-8, 3-9, 3-12, 3-15, 3-16, 3-17,

3-18, 3-20, 3-24, 3-25, 3-26

Cell Growth . . . . . . . . . . . .2-11, A-1, C-1, C-2

Cell holders & cell holder accessories . . . . . .

3-4, 5-1, 5-2, 6-3

Cleaning . . . . . . . . . . . . . . . . . . . . . . .6-1, 6-2

Concentration measurements . . . . .3-6, 3-10

Concentration units . . . . . . .3-1, 3-2, 3-6, 3-7

Custom units . . . . . . . . . . . . . . . . . . . .3-1, 3-2

Date and time, setting . . . . . . . . . . . . . . . .1-2

Direct UV . . . . . . . . . .2-3, 2-9, 2-10, C-1, C-2

DNA . .2-2, 2-3, 2-12, A-1, B-1, C-1, C-3, C-4

DNA with scan . . . . . . . . . . . . . . .2-2, 2-4, 2-5

dsDNA . . . . . . . . . . . . .2-2, 2-5, 2-6, C-1, C-2

External computers . . . . . . . . . . . . . . . . . .5-3

Factor, entering . . . .3-7, 3-8, 3-10, 3-11, 3-26

Fuses, changing . . . . . . . . . . . . . . . . . . . .6-2

Glassware . . . . . . . . . . . . . . . .ii, 1-3, 3-3, 6-2

Graphical scan data, rescaling . . . . . . . .3-22

High Limit . . . . . . . . . . . . . . . . . . . . . . . . .3-12

Instrument, setting up . . . . . . . . . . . . . . . .1-1

Intercept . . . . . . . . . . . . . . . . .3-12, 3-13, C-5

Interface cable . . . . . . . . . . . . . . . . . .5-2, 5-3

Internal printer . . . . . . . . . . . . . . . . . . . . . .1-3

installing . . . . . . . . . . . . . . . . . . . . .5-1, 5-3

setting up . . . . . . . . . . . . . . . . . . . . . . .1-3

test . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-1

Interval Time . . . . . . . . . . . . . . . . . . . . . .3-17

Index

I-1 BioMate 3 Operator’s Manual

Keypad . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4

Kinetics . . . . . . . . . . . . . . . . . .1-1, 3-17, 3-18

rescaling & recalculating results 3-18, 3-20

Language, selecting . . . . . . . . . . . . . .1-1, 1-2

Lock test . . . . . . . . . . . . . . . . . . . . . . . . . . . .iii

Lowry . . . . . . . . . . . . . . . . . . . . .2-7, C-1, C-2

Maintenance procedures . . . . . . . . . . . . . .6-1

Manual 6 . . . . . . . . . . . . . . . . . . . . . .3-3, 3-5,

3-9, 3-11, 3-12, 3-13, 3-16, 3-17, 3-20,

3-25, 3-27

Multiple Wavelengths . . . . . . . . . . . . . . . .3-26

Noise measurement . . . . . . . . . . . . . .4-1, 4-4

Nucleic acid measurements . . . . . . . .2-1, 2-2

Number of Samples . . . . . . . . . . . . . . . . .3-12

Oligo calculator .2-2, 2-12, A-1, C-1, C-2, C-3

Oligos .2-2, 2-5, 2-6, 2-7, 2-12, C-1, C-2, C-3

Oligonucleotide . . .2-1, 2-2, 2-3, 2-12, B-2

Paper roll holders, installing . . . . . .4, 1-1, 1-3

Paper, loading . . . . . . . . . . . . . . . . . . . . . .1-3

Parameters . . . . . . . . . . . . . . . . . . . . . . . .B-1

Password . . . . . . . . . . . . . . . . . . . . . . . . . . .iii

Peaks and valleys, labeling . . . . . . . . . . .3-24

Photometric accuracy . . . . . . . . .4-1, 4-3, 4-4

Printer, installing . . . . . . . . . . . . . . . . . .5, 5-3

Protein Measurements . . . . . . . . . . . .2-1, 2-7

Replacement parts . . . . . . . . . . . . . . .6-3, C-2

RNA . . . . . . . . . . . . . .2-2, 2-3, 2-5, 2-12, C-1

Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .i

Sample compartment windows, cleaning .6-2

Scanning . . . . . . . . .1-1, 3-4, 3-12, 3-20, 3-21

Screen contrast, setting . . . . . . . . . . . . . . .1-2

Single Cell Platform . . . . . . . . . . . . . . . . . .3-5

Single-Position Cell Holder, installing . . . . . .5

Slope . . . . . . . . . . . . . . . . . . . .3-12, 3-13, C-5

SmartStart . . . . . . . . . . . . . . . . . . . . . . . . .3-2

Software password . . . . . . . . . . . . . . . . . . . .iii

Specifications . . . . . . . . . . . . . . . . . . . . . .A-1

SPECTRONIC Standards . . . . .4-2, 4-3, 4-5,

5-2, 6-3

ssDNA . . . . . . . . . . . . .2-2, 2-3, 2-5, C-1, C-2

Standard Curve . . . . . . . . . . . . . . . . . . . .3-11

editing . . . . . . . . . . . . . . . . . . . . . . . . .3-14

measuring the standards for . . . . . . . .3-12

Standard, measuring . . . . . . . . . . . . . . . . .3-7

Standby settings, selecting . . . . . . . . . . . .1-2

Stray Light . . . . . . . . . . . . . . . . . . . . .4-1, 4-5

Survey Scan . . . . . . . . . . . . . . . . . .3-20, 3-21

Test . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-5

Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-5

Internal Printer . . . . . . . . . . . . . . . . . . . .4-5

recalling .3-9, 3-10, 3-15, 3-16, 3-17, 3-20,

3-25, 3-26

RS232C . . . . . . . . . . . . . . . . . . . . . . . . .4-6

Index

Thermo Electron Corporation I-2

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 . . . . . . . . . . . . . . . . . .3-17, B-3

Unlock test . . . . . . . . . . . . . . . . . . . . . . . . .3-1

Utility parameters, setting . . . . . . . . . .1-1, 1-3

Warburg-Christian . . . . . .2-10, 2-11, C-1, C-2

Warranty . . . . . . . . . . . . . . . . . . . . . . . . . . . .ii

Wavelength accuracy . . . . . . . . . . . . . . . . .4-1

internal . . . . . . . . . . . . . . . . . . . . . . . . .4-1

standards . . . . . . . . . . . . . . . . . . . . . . .4-2

Z-dimensions . . . . . . . . . . . . . . . . . . .1-1, 1-2

I-3 BioMate 3 Operator’s Manual

Index

Thermo Electron Corporation I-4

Item No.: 335904-10001, Rev G 06/03 Component No.: 335904-10063, Rev G 06/03

Thermo BioMate 3 series, 335904, 335904P, 335905, 335905P Operator's Manual

Specifications and Main Features

Frequently Asked Questions

User Manual