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

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: [phone] or [phone]
Fax: [phone]
E-Mail: [e-mail]

THERMO ELECTRON CORPORATION

(Europe)
Mercers Row, Cambridge CB5 8HY, UK
Telephone: Int [phone]
Fax: Int [phone]
E-Mail: [e-mail]

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

s

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.

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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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2-3 BioMate 3 Operator’s Manual

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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Thermo Electron Corporation 2-4

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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2-5 BioMate 3 Operator’s Manual

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.

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.

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.

Using “Biotests” Software

Thermo Electron Corporation 2-6

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

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.

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.

Using “Biotests” Software

2-7 BioMate 3 Operator’s Manual

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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Thermo Electron Corporation 2-8

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.

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 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.

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.

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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2-9 BioMate 3 Operator’s Manual