Ultrospec™ 7000/8000/9000

UV-Visible Spectrophotometers
User Manual

Biochrom US Telephone: 1-508-893-8999

84 October Hill Rd Toll Free: 1-800-272-2775
Holliston, MA Fax: 1-508-429-5732
01746-1388 [email protected]
USA www.biochromspectros.com
CONTENTS:
CONTENTS:
CONTENTS:
1. HEALTH & SAFETY 4 11.2.1. BCA, Bradford, Lowry & Biuret Protein
1. 1.1.
HEALTHGeneral Safety
& SAFETY 4
4 11.2.1. Assays
BCA, Bradford, Lowry & Biuret Protein 47
1. 1.1.
HEALTH1.1.1. General
SafetyHazards
& SAFETY
General 4
4 11.2.2. Determination
BCA, Bradford, of
11.2.1. Assays Protein
Lowry Concentration
& Biuret Protein 47
1.2. Unpacking
1.1. Safety
1.1. General & Installation
Safety
1.1.1. General Hazards 5
4 using
11.2.2. Assays the BCA protein assay
Determination of Protein Concentration 47
47
46
1.2.1.
1.2. 1.1.1. Instrument
General
Unpacking Connections
Hazards
& Installation 6
4
5 11.2.3. Determination
11.2.2. using
Determination of
of Protein
Protein
the BCA protein Concentration
Concentration
assay 47
1.3. Equipment
1.2. Unpacking Operation
& Installation
1.2.1. Instrument Connections 7
5
6 using
11.2.3. using direct UV methods
the BCA protein
Determination assay
of Protein Concentration 50
46
47
1.3. 1.3.1.
1.2.1.
EquipmentControls
Instrument and Indicators
Connections
Operation 7
6
7 11.2.4. Protein
11.2.3. using UV UVof
Determination
direct Protein Concentration
methods 51
50
1.3.2.
1.3. Equipment Intended Use
Operation
1.3.1. Controls and Indicators 7
7 11.2.5. Protein
11.2.4. using A280UV methods
Proteindirect
UV 52
50
49
51
1.3.3.
1.3.2. Instrument
1.3.1. Controls
Intendedand
UsePreparation
Indicators 7
7 12. SAVING11.2.4.
AND Protein
11.2.5. PRINTING UV
A280 51
50
53
52
1.3.4.
1.3.2. Post
1.3.3. IntendedRun
InstrumentProcedures
UsePreparation 8
7 12.1. 11.2.5.
Saving Protein
Sample A280
Data 51
52
53
1.3.5. 12. SAVING AND PRINTING 53
1.3.4. Performance
1.3.3. Instrument Validation
Preparation
Post Run Procedures 8
7
8 12. SAVING
12.1. 12.1.1. Internal
ANDSample
Saving PRINTING Data 53
52
53
1.4. User
1.3.4. Maintenance
1.3.5. Post Run Procedures 8
8
Performance Validation 12.1. 12.1.2. USB
Saving Sample
12.1.1. InternalData 53
52
53
1.4. 1.4.1.
1.3.5. Troubleshooting
Performance Validation
User Maintenance 9
8 12.1.3.
12.1.1. USB
12.1.2. USB csv
Internal 53
52
53
1.5.
1.4. Customer
User Support Contacts
1.4.1.Maintenance
Troubleshooting 10
8
9 12.2. Automatic Saving 54
12.1.2. USB csv
12.1.3. 52
53
1.6. Service,
1.5. 1.4.1. Repair or Return
Troubleshooting 10
9 12.3.
1.7.
Customer
Disposal
Support Contacts 10
10 12.2. Manual
Automatic Saving
12.1.3. USB csv
Saving 54
53
52
54
1.5.
1.6. Customer Support
Service, Repair Contacts
or Return 10 12.4. Exporting
12.2. Manual
12.3. Automatic Data
Saving
Saving 54
53
54
2. 1.6. Service,
DisposalRepair
INTRODUCTION
1.7. or Return
TO THE ULTROSPEC 7000/8000/ 10 13. 12.3. Exporting
SAMPLE
12.4. Manual Saving
MANAGER Data 53
55
54
1.7.
9000 Disposal
SPECTROPHOTOMETER
2. INTRODUCTION TO THE ULTROSPEC 7000/8000/ 10
11 12.4.
13.1. Exporting
Deleting Datafrom the internal memory
data 54
53
55
13. SAMPLE MANAGER 55
2. USE
3. INTRODUCTION
9000 WITH DatrysTOPCTHE
SPECTROPHOTOMETER ULTROSPEC 7000/8000/
SOFTWARE 12
11 13. 13.2.
SAMPLE
13.1. Accessing
MANAGER
Deleting Sample
data fromManager from
the internal the main
memory 55
54
3. 9000
4. USE SPECTROPHOTOMETER
FREQUENTLY
WITH DatrysUSEDPCICONS
SOFTWARE 11
13
12 13.2. screen
13.1. Accessing
Deleting data fromManager
Sample the internal memory
from the main 56
55
54
3. USE WITH Datrys PCICONS
SOFTWARE 12 13.3.
13.2. Accessing
Accessing Sample
screen Sample Manager
Manager from
from within
the mainan 56
5.
4. PERFORMING
FREQUENTLY A MEASUREMENT
USED 14
13 application 56
4. FREQUENTLY
5.1. UltrospecUSED ICONS 13 screen
13.3. Accessing Sample Manager from within an 56
55
5. PERFORMING A7000/8000/9000
MEASUREMENT 14
14 13.4.
13.3. Recalled
Accessingfiles
application Sample Manager from within an 57
56
5.
6. PERFORMING
LAMP MODE A7000/8000/9000
5.1. Ultrospec MEASUREMENT 14
15 application 56
14. SAVING
13.4. METHODS
Recalled files 58
55
57
6. 5.1.
7. LAMP Ultrospec
TYPES MODE
OF BOXES 7000/8000/9000 14
16
15 13.4. Methods
Recalled files 57
14. 14.1.
SAVING METHODS saved to the internal memory 58
56
58
6.
8.
7. LAMP
TYPES MODE
SETTINGSOF BOXES 15
17
16 14. 14.2.
SAVINGMethods
METHODS folder 58
58
57
14.1. Methods saved to the internal memory
7. TYPES
8.1. OF BOXES
Date and time 16
17 14.3. Renaming
14.1. Methods folder
14.2. methods
saved folder
to the internal memory 59
57
58
8. SETTINGS 17
8.2. Regional 17 14.4. Locking
14.2. Renaming
14.3. saved
Methods folder methods
methods folder 59
58
57
59
8. SETTINGS
8.1. Date and time 17
8.3. 14.5.
14.3. Deleting saved methods 59
8.2. Data
8.1. Date Output
and
Regional time 18
17 14.4. Renaming
Locking methods
saved folder
methods 58
59
8.4. User Interface 18 14.6. Backing
14.4. Deleting
14.5. up
Locking saved method
savedmethods folders to USB
methods 60
58
59
8.2.
8.3. Regional
Data Output 17
18
8.5. 14.7.
14.5. Favourites folder 60
8.4. Accessories
8.3. Data Output
User Interface 18
18 14.6. Deleting up
Backing saved methods
method folders to USB 59
58
60
8.6. 14.8. Saving methods to USB 60
8.5. Instrument
8.4. User Interface
Accessories Settings 18
18 14.6. Favourites
14.7. Backing upfolder
method folders to USB 59
60
8.7.
8.5. Instrument
Instrument Status
8.6. Accessories Settings 18
18 15. 14.7. Saving
Favourites
PRINTING
14.8. folderto USB
methods 59
61
60
8.8.
8.7. Instrument
8.6. Instrument Information
Settings
Status 19
18 14.8. Internal
15.1. Saving methods
printer to USB 60
59
61
15. PRINTING 61
8.9.
8.8. Instrument
8.7. Instrument Settings
Status
Information 19
18
19 15. 15.2. Print
PRINTING via computer (PVC) 61
61
60
15.1. Internal printer
8.10.
8.8. Lamp Settings
8.9. Instrument Information
Settings 19
19 15.3.
15.1. Bluetooth
Internal printer 61
61
60
15.2. Print via computer (PVC)
9. 8.9.
USERInstrument
8.10. ACCESS
Lamp SettingsSettings 19
20 15.4.
15.2. Automatic
15.3. printing (PVC)
Print via computer
Bluetooth 61
61
60
8.10.
9.1. Lamp
Adding Settings
a user 19
20 15.5.
15.3. Manual
Bluetooth printing
15.4. Automatic printing 61
61
60
9. USER ACCESS 20
9. 9.2.
USEREditing
9.1. ACCESSaa user
Adding user 20
20 15.4. Manual
Automatic
ACCESSORIES
15.5. printing
printing 61
62
60
9.3.
9.1. Deleting
Editing a auser
9.2. Adding user 20
20 15.5. Manual
Fitting printing 61
62
60
ACCESSORIES 62
9.4.
9.2. Editing
9.3. Editing user
Deletinga auser access
user 21
20 16. ACCESSORIES
CELL Fitting
CHARGER 62
61
63
10. 9.3.
9.4. Deleting
APPLICATIONS
Editing user a user
access 22
20
21 16.1. Fitting
Operation 62
61
63
CELL CHARGER 63
10. APPLICATIONS access
9.4.
10.1. Editing
Single user
Wavelength 21
22
21
22 16.2. Saving
CELL Operation
CHARGER Method & Results 64
62
63
10. 10.2. Concentration
APPLICATIONS
10.1. Single Wavelength via factor 23
22
21 Incorrect
16.3. Saving
Operation Fitting& Results
Method 64
62
63
64
10.3. Wavescan
10.1. Concentration
10.2. Single Wavelength via factor 24
22
23 Using the
16.4. Incorrect
Saving MethodCell Charger to Create a
& Results 64
Fitting
10.4.
10.3. Kinetics
10.2. Concentration via factor 25
23 Standard
Incorrect Curve 64
62
Wavescan 24 Using the Fitting
Cell Charger to Create a 64
10.4. 10.4.1.
10.3. Kinetics Serial kinetics measurements
Wavescan 26
24
25 17. SipperUsing the Curve
Standard Cell Charger to Create a 63
65
64
10.4. 10.4.2.
Kinetics Parallel
10.4.1. kinetics
Serial kinetics measurements
measurements 28
25
26 17.1. Standard
Setting Curve
Sipper defaults 64
63
65
10.5. 10.4.1.
Trace Manager – Overlaying & manipulating Sipper 65
10.4.2. Serial
Parallelkinetics measurements
kinetics measurements 26
27
28 17.2.
SipperCalibration
Setting Sipper defaults
64
66
65
wavescan
10.5. 10.4.2.
Trace Manager and kinetics
Parallel –kinetics files
measurements
Overlaying & manipulating 30
28 Wash Mode 64
66
17.3. Calibration
Setting Sipper defaults 65
66
10.6. Trace
10.5. Standard
wavescan Curve
Manager and –kinetics
Overlaying
files & manipulating 32
30
29 Cleaning/Maintenance/Troubleshooting 65
67
17.4. Wash
Calibration
Mode 66
10.7.
10.6. Equation
wavescan
Standard Editor
and kinetics files
Curve 34
30
32
31 18. Wash Mode
TECHNICAL SPECIFICATIONS
Cleaning/Maintenance/Troubleshooting 66
68
67
11. 10.6.
10.7. Standard
LIFE SCIENCE Curve
EquationAPPLICATIONS
Editor 32
40
34
33 Cleaning/Maintenance/Troubleshooting 67
19. CHANGING TUNGSTEN
TECHNICAL SPECIFICATIONSAND DEUTERIUM LAMPS 69
67
68
11. 10.7.
11.1. Equation
Nucleic Acid
LIFE SCIENCE Editor
Applications
APPLICATIONS 34
41
40
39 TECHNICAL SPECIFICATIONS 68
11. 11.1. 11.1.1.
LIFE SCIENCE
Nucleic AcidDNA, RNA & Oligo
APPLICATIONS
Applications 41
41
40 TABLE OF ICONS
20. CHANGING TUNGSTEN AND DEUTERIUM LAMPS 71
69
11.1.2.
11.1. 11.1.1.
Nucleic AcidCyDye™ RNADNA
DNA,Applications
& Oligo 43
41 CHANGING
GLOSSARY
21. TABLE TUNGSTEN
OF BOXES AND DEUTERIUM LAMPS
OF ICONS 69
75
73
71
40
11.1.3.
11.1.1. T
11.1.2. DNA, Calculation
RNADNA
& Oligo 44
41 TABLE
11.2. Protein
CyDye™
m 43
42 LEGAL OF ICONS
GLOSSARY OF BOXES 71
79
75
11.1.2. Applications
11.1.3. TCyDye™
m
DNA
Calculation 47
43
44
43 GLOSSARY OF BOXES 75
11.1.3. Applications
11.2. Protein Tm Calculation 44
47 LEGAL 79
46
11.2. Protein Applications 47 LEGAL 79
29004782UM AA 10/2011 3

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5061-046 Rev1 2
Page finder
Page
1.
finder Appendix
Accessories 3 3.3.1.4. Inconsistent readings 16
3 3.3.1.5. Wrong volume being sipped 16
1. INSTALLATION 33 3.3.1.4. Inconsistent readings 16
14
4. INSTALLING THE INTERNAL PRINTER 17
3 3.3.1.5. Wrong volume being sipped 16
14
2. PASSIVE ACCESSORIES 46
3 5. INSTALLING THE INTERNAL PRINTER 19
2.1. Single Cell Holder 57 4. 17
15
2. PASSIVE ACCESSORIES
2.2. Variable Pathlength Cell Holder 567
2.1. 5. 19
2.3. Single
Water Cell Holder
Thermostatted Cell Holder 57
2.2.
2.4. Variable
Film HolderPathlength Cell Holder 57
2.3.
2.5. Water
Test TubeThermostatted
Holder Cell Holder 57
2.4. Film Holder
2.6. Peltier Controlled Fluid Circulator 678
2.5. Test
2.6.1.Tube Holder
General Information 678
2.6. Peltier Controlled
2.6.1.1. GeneralFluid Circulator
Warnings 68
2.6.1. General
2.6.1.2. Information
Quality, Reliability and Safety 68
2.6.1.1.
2.6.1.3. General Warnings
Safety Markings 68
2.6.1.2.
2.6.2. Quality,Description
Instrument Reliability and Safety 68
2.6.1.3.
2.6.2.1. Safety
ControllerMarkings
front and rear panel 789
2.6.2. Instrument
2.6.2.2. Description
Specifications 789
2.6.2.1. Controller
2.6.2.2.1. front and rear
Keypad/Display Unit panel 79
2.6.2.2. Specifications
2.6.2.2.2. Programmable Parameters 79
2.6.2.2.1.
2.6.2.2.3. Keypad/Display
Displayed ValuesUnit 79
2.6.2.2.2.
2.6.2.2.4. Programmable Parameters
Operating Specifications 79
2.6.2.2.3. Displayed Values
2.6.2.2.5. External Control Possibilities 79
2.6.2.2.4.
2.6.2.2.6. Operating
DimensionsSpecifications 79
2.6.2.2.5.
2.6.2.2.7. External
ElectricalControl
data Possibilities 79
2.6.2.2.6.
2.6.2.2.8. Dimensions
Description of Symbols 79
2.6.2.2.7.
2.6.2.2.9. Electrical
Environmental data conditions 79
2.6.2.2.8.
2.6.2.3. UserDescription
interface of Symbols 8
109
2.6.3.2.6.2.2.9. Environmental conditions
Installation 8
109
2.6.2.3.
2.6.3.1. User interface
Checking the serial number 10
8
2.6.3. Installation
4.6.3.2. Checking mains supply and fuses 10
8
2.6.3.1. Checking
2.6.3.2.1. Changingthe serial number
the Mains Voltage 10
4.6.3.2. Checking
Setting mains supply and fuses
and Fuses 10
8
2.6.3.2.1.
2.6.3.3. Changing
Instrument the Mains Voltage
set-up 8
10
Setting
2.6.3.3.1. Start up and Fuses 10
8
2.6.3.3. Instrument
2.6.3.3.2. Externalset-up
Connections 10
9
11
2.6.4.2.6.3.3.1.
Operating Start up
Instructions 10
9
11
2.6.3.3.2.
2.6.4.1. External
Manual Connections
operation 11
9
2.6.4. Operating
2.6.5. Maintenance Instructions 11
10
12
2.6.4.1.
2.6.5.1. Manual
Cleaningoperation
the instrument 11
10
12
2.6.5. Maintenance
2.6.5.2. Water level alarm 12
10
2.6.5.1.
2.6.6. Cleaning the instrument
Troubleshooting 12
10
2.6.5.2.
2.6.6.1. Water
Audiblelevel
alarm alarm 12
10
2.6.6.2.6.6.1.1.
Troubleshooting
Water level Alarm 12
10
2.6.6.1. Audible
2.6.6.1.2. Other alarm
system Alarms 12
10
2.6.6.1.1. Water level Alarm 12
3. ACTIVE ACCESSORIES 13
11
2.6.6.1.2. Other system Alarms 12
3.1. 8-Position Cell Changer 13
11
3. ACTIVE ACCESSORIES
3.2. 5-Position Thermostatted Cell Changer 13
14
12
3.1.
3.3. 8-Position Cell Changer
Sipper & Flowcell 13
14
12
3.2. 5-Position
3.3.1. SipperThermostatted
Troubleshooting Cell Changer 14
15
13
3.3. Sipper & Flowcell
3.3.1.1. Sample not being sipped 14
3.3.1. Sipper Troubleshooting
through Flowcell 15
13
3.3.1.1.
3.3.1.2. Sample not being being sipped
pumped right
through Flowcell 15
16
14
3.3.1.2.
3.3.1.3. Sample
Bubblesbeing pumped right
in Flowcell 16
14
through Flowcell 16
3.3.1.3. Bubbles in Flowcell 16
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5061-046 Rev1 2 3


1. HEALTH & SAFETY

1.1 Safety
1.1.1. General Hazards
There a number of warning labels and symbols on your instrument. These are there
to inform you where a potential danger exists or particular caution is required. Before
commencing installation, please take time to familiarize yourself with these symbols
and their meaning.
This instrument is intended for use by individuals trained in and familiar with the use
of spectrophotometers and their associated hazards. In the event of a malfunction
or hazard occurring, the user responsible shall disconnect the unit from power and
isolate for decontamination and /or repair.
This instrument is subject to the following hazards:

High voltages exist inside the unit. Repair and maintenance should only be carried out by individuals trained
specifically to work on these instruments.

The UV source contained within the unit generates a light beam that traverses the sample chamber and is
accessible in the lamp chamber. Under normal use the lamp beam is confined within the instrument. The unit
should not be operated with the sample chamber lid open or the lamp housing lid removed. Prolonged exposure to
the beam may cause permanent eye damage.

29004782UM AA 10/2011 4
1.1.1. General Hazards
There a number of warning labels and symbols on your instrument. These are there
to inform you where a potential danger exists or particular caution is required. Before
commencing installation, please take time to familiarize yourself with these symbols
and their meaning.
This instrument is intended for use by individuals trained in and familiar with the use
of spectrophotometers and their associated hazards. In the event of a malfunction
or hazard occurring, the user responsible shall disconnect the unit from power and
isolate for decontamination and /or repair.
This instrument is subject to the following hazards:

High voltages exist inside the unit. Repair and maintenance should only be carried out by individuals trained
specifically to work on these instruments.

The UV source contained within the unit generates a light beam that traverses the sample chamber and is
accessible in the lamp chamber. Under normal use the lamp beam is confined within the instrument. The unit
should not be operated with the sample chamber lid open or the lamp housing lid removed. Prolonged exposure to
the beam may cause permanent eye damage.

5061-046 Rev1 4
29004782UM AA 10/2011 4
 There are no bio-hazardous materials within the unit; however this unit could be used with bio-hazardous samples.
Before using the instrument the customer should have in place decontamination procedures designed to protect
laboratory workers from occupationally acquired infections. The sample chamber cell holders are removable and
may be decontaminated using the appropriate disinfectant for the bio-hazard in question, rinsed with distilled
water and then allowed to dry. The sample chamber and exterior may be wiped with a suitable disinfectant
cleaning wipe.
• Decontamination. Equipment returned for repair should include an appropriate decontamination certificate.
• It is the responsibility of the customer to ensure that the user of the equipment is provided with a safe working
environment.
• Any chemicals used in Analyses should be used, stored and disposed of in accordance with manufacturer’s
guidelines and local safety regulations.
• Toxic Fumes. Efficient laboratory ventilation must be provided when working with volatile solvents or toxic
substances.
• Waste disposal. Disposal of some solvents and chemicals may be classed as hazardous waste and must be
dealt with in accordance with local regulatory practice.
• Personal protective equipment. This is not required to operate the unit but the samples measured may require
PPE. A local risk assessment should be carried out.

This equipment may be connected and controlled from a PC. To preserve the integrity of the measuring equipment
it is essential that the attached PC itself conforms to basic safety and EMC standards and is set up in accordance
with the manufacturers’ instructions. If in doubt consult the information that came with your PC. In common with
all computer operation the following safety precautions are advised.
• To reduce the chance of eye strain, set up the PC display with the correct viewing position, free from glare and
with appropriate brightness and contrast settings.
• To reduce the chance of cross contamination from biological samples, use appropriate personnel protection
measures and disinfectant wipes on keyboard and mouse.

Care must be taken when handling all heated accessories.

1.2. Unpacking & Installation

• T
 hese instruments weigh approximately 18.5 kg. Follow your local regulations for
safe handling and lifting of this equipment.
• Inspect the instrument for any signs of damage caused during transit. If any
damage is discovered. Do not use the instrument and report the problem to your
supplier.
• T
 he instrument must be placed on a stable, level bench or table capable of taking
its weight with sufficient space around the instrument for ventilation to circulate
freely.
• Ensure your proposed installation site conforms to the environmental conditions for
safe operation.
• Indoor use.
• 5 to 40°C.
• Maximum relative humidity 90% up to 31°C decreasing linearly to 50% at 40°C.
• Extremes of temperature may require re-calibration of the unit for optimum
performance.
• If the instrument has been stored in a cold environment then it should be allowed
to come to thermal equilibrium for 2 to 3 hours before operation so that start up
calibration is not compromised by condensation.
 he equipment must be connected to the local supply outlet using the provided
• T
power cables. It can be operated from 90 to 264 V~ 50 or 60 Hz.
• Replace power inlet fuses only with the same type and rating as follows:

5061-046 Rev1 5
 • F
 or Deuterium/Tungsten units T 1.6 A H 250 V AC (Anti-Surge, High breaking
capacity).
• For Xenon units T 1.6 A H 250 V AC (Anti-Surge, High breaking capacity).
• Power rating is:
• 100 VA for Xenon units.
• 150 VA for Deuterium/Tungsten units.
• T
 he instrument should be positioned so that the power cable may be readily
removed in the event of a hazard or malfunction occurring.
• Site the instrument in an atmosphere free from dust and corrosive fumes.
• Use the on/off switch on the left hand side of the instrument. The instrument
will automatically perform some start up self diagnostic checks on switch on.
Please wait for these to finish before attempting to use the equipment.
1.2.1. Instrument Connections

USB B receptacle
for connection to PC
On / Off switch

Fuse holder

Mains inlet

Connector for external

powered accessories

USB A plug for USB memory sticks

(Ultrospec 7000, 8000 and 9000 stand alone units only)

Internal accessory connector

5061-046 Rev1 6
1.3. Equipment Operation
1.3.1. Controls and Indicators

USB LED Ultrospec

This indicates that
the instrument is
writing to the USB
memory stick. The
memory stick must
not be removed
whilst this LED is on.

POWER/STATUS INDICATOR LED

The LED indicates the status of the instrument.
Orange - during start up and calibration
Green - instrument is on and passed start up
calibration tests
Red - instrument is on and has failed start up
calibration tests

1.3.2. Intended Use

The instrument is intended to be used by scientists and technicians who possess
basic laboratory and technical skills and have the knowledge and understanding
of the hazards involved, with the unit and the samples used, to operate it in a safe
manner.
e.g. DNA/RNA/Oligo concentration and purity measurements as well as
e.g. DNA/RNA/Oligo
protein concentration and purity measurements as well as protein
determinations
determinations.

1.3.3. Instrument Preparation

• Switch on the unit and allow it to finish its start up calibration.
• B
est performance is obtained if the instrument is allowed to warm up and stabilize
for at least 30 minutes.
• I f applicable connect the unit to a PC using a USB cable and refer to the online
help and user manual.
• Select the appropriate application or method.
• Where relevant, set up the application parameters for the sample.
• F or Deuterium/ Tungsten units a precision mode is available. To use this mode
enter the desired application and switch to precision mode.
• S
elect cuvette cells to use. It is important to use cells of the correct type. Most
samples are measured using a standard 10 mm path length cell. Special cells and
accessories are available for larger or smaller path lengths and sample volumes.
It is important to use cells of the correct type. Some cells absorb UV and are not
suitable for UV sample measurement. Cells used for samples should be free from
dust, residue or scratches.

5061-046 Rev1 7
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 • B
efore preparing samples and sample reference blanks, you must be familiar with
hazards arising from handling the sample materials and where necessary observe
local regulatory practice, personnel protection equipment and measures designed
to ensure your safety.
• P
repare the sample blanks (references). A reference is typically the solution that
the sample is dissolved in. For Dual beam units the reference may be placed in the
reference path or a separate sample reference may be made by first placing the
reference in the sample path and performing a reference measurement.
• P
repare the sample solutions. The sample solution would normally comprise the
sample under test dissolved in the reference solution.
• W
hen placing the cells in the equipment ensure the cell is orientated so that the
light energy will pass through the cell.
• F or further information on running applications and methods refer to Chapter “10.
APPLICATIONS”.

1.3.4. Post Run procedures

• Empty cuvette cells of sample and rinse with deionized water.
• C
lean cuvettes periodically with commercially available cleaning solution or dilute
detergent solution followed by a thorough rinse in deionized water.
• N
ote that some samples and solvents may be classified as hazardous or bio
hazardous waste. The disposal of such substances must be carried out in
accordance with local regulatory practice.

1.3.5. Performance Validation

Good laboratory practice recommends that the unit is periodically checked for
optical performance.
• S
witch on validation checks. When the unit is powered up it performs wavelength
accuracy and lamp energy checks. Once complete the unit will beep and show a
green on light.
• P
eriodically wavelength, stray light and absorbance should be checked to ensure
the unit is performing to specification. Deterioration in performance may indicate
that the instrument needs servicing or that a poor baseline has been saved.
Performance validation can be carried using traceable reference materials.

1.4. User Maintenance

• O
ther than the Tungsten and Deuterium lamps in certain instruments there are no
user serviceable parts in this equipment.
• To prevent contamination:
• Cell holders and accessories should be removed and cleaned with commercially
available cleaning solution or dilute detergent followed by a thorough rinse in
deionized water. Allow to dry thoroughly before use.
• Casework and the sample compartment may be wiped down with commercially
available disinfectant wipes.
• The lamps used in the unit age over time and less energy will be available to pass
through the sample. Where energy has fallen to around 50% of the installation
energy you are advised to have the lamps changed. Deuterium and Tungsten
lamps may be replaced by the user, see section 20 for details. Xenon lamp
replacement can only be carried out by a qualified service engineer.

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 If the equipment is operated in a manner not specified, then the protection provided by the equipment may be
impaired and the instrument warranty withdrawn.

1.4.1. Troubleshooting
PROBLEM POSSIBLE CAUSE
Start up calibration fails Check sample (and reference) beam is clear before switch on. Possible optical
failure, contact service support.
Negative absorbance reading Check that sample and reference cells have not been swapped
Check sufficient height of sample solution (beam height is nominally 15 mm
above the cell base for normal measurements and it is recommended that it be
filled to 20 mm above the base).
Unexpected results Check for bubbles in solution.
Start up calibration fails Check sample (and reference) beam is clear before switch on. Possible optical
failure, contact service support.
Negative absorbance reading Check that sample and reference cells have not been swapped.
Check sufficient height of sample solution (beam height is nominally 15 mm
above the cell base for normal measurements and it is recommended that it be
filled to 20 mm above the base).
Absorbance values higher than expected Check for use of incorrect cell type.
Check cells are free from finger prints.
Check cells for contamination.
Check cell orientation.
Check reference used.
Possible optical alignment problem, contact service support.
Absorbance value lower than expected Check sufficient height of sample solution.
Check sample and reference are not the same.
Check sample compartment lid is properly closed.
Possible stray light issue, contact service support.
Instrument will not reference Check orientation of cuvette.
Check for use of incorrect cell type.
Poor reproducibility with nucleic acid Check for particles, try using background correction.
analysis Try increase in concentration.

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Note: If you experience any problems with your instrument, please refer to section
“1.4.1. Troubleshooting”.
If you require further assistance, please contact customer support :
1.5. Customer Support Contacts
Note: If you experience any problems with your instrument, please refer to section
“1.4.1. Troubleshooting”.
If you require further assistance, please contact customer support :

1.6.
visit: Service,
or email:
Repair or Return
www.biochromspectros.com
[email protected]
Good laboratory practice recommends that the unit be periodically serviced to
or telephone: (US) 1-800-272-2775 (UK) +44 1223 423723
ensure the unit is suitable for purpose. It is recommended that the instrument be
1-508-893-8999 +44 1223 427888
serviced annually. You can arrange this through your distributor. Prior to Inspection,
Servicing, Repair or Return of Medical and Laboratory Equipment the unit must be
1.6. Service, Repair or Return
decontaminated.
Good laboratory practice recommends that the unit be periodically serviced to
A returns policy operates on this equipment. Before returning the equipment to the
ensure the unit is suitable for purpose. It is recommended that the instrument be
distributor or manufacturer:
serviced annually. You can arrange this through your distributor. Prior to Inspection,
Servicing, Repair or Return of Medical and Laboratory Equipment the unit must be
decontaminated.
A returns policy operates on this equipment. Before returning the equipment to the
distributor or manufacturer:

Please contact [email protected] for the correct paperwork and instructions.

1.7. Disposal
Decontamination
In use this product may have been in contact with bio-hazardous materials. Before disposal all accessories should
be removed and thoroughly cleaned in disinfectant and then rinsed with distilled water. All outside surfaces and
1.7. Disposal
sample chamber walls must be wiped down with disinfectant wipes suitable for purpose.
Decontamination
WEEE
In use this product may have been in contact with bio-hazardous materials. Before disposal all accessories should
Abelabel
removed
with aand thoroughly
crossed-out cleaned
wheeled insymbol
bin disinfectant and then
indicates rinsed
that the with distilled
product is coveredwater. All outside
by the surfaces and
Waste Electrical
sample chamber walls must be wiped down with disinfectant wipes suitable for purpose.
Electronic Equipment (WEEE) Directive and is not to be disposed of as unsorted municipal waste. Any products
marked with this symbol must be collected separately and in accordance with local regulatory practice.
WEEE

A label with a crossed-out wheeled bin symbol indicates that the product is covered by the Waste Electrical and
Electronic Equipment (WEEE) Directive and is not to be disposed of as unsorted municipal waste. Any products
marked with this symbol must be collected separately and in accordance with local regulatory practice.

29004782UM AA 10/2011 10

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 2. INTRODUCTION
TO THE Ultrospec
7000/8000/9000
SPECTROPHOTOMETER
The Biochrom Ultrospec 7000/8000/9000 are a range of standalone, easy to use,
dual beam UV-visible spectrophotometers with high resolution color touch screens.
All spectrophotometers offer a comprehensive range of spectrophotometric and life
science applications.
A spectrophotometer is an optical arrangement that is designed to pass light
energy through a sample. The reduction of transmittance of the light energy and
corresponding absorbance peaks, caused by the sample under test, can be used
in a qualitative way to determine sample composition or in a quantitative way, by
comparing with known concentration standards, to determine the concentration of a
sample. In other types of studies the tracking of absorbance over time can be useful
to study chemical reactions and biological processes.
The Ultrospec 7000/8000/9000 range of spectrophotometers are designed to
produce light energy from the far ultraviolet through visible light in the range
190 to 1100 nm. Many materials, and in particular solutions of materials will
absorb light energy within this region. This makes the Ultrospec 7000/8000/9000
spectrophotometers applicable to a wide range of market sector needs including
applications in Life sciences, clinical, pharmaceutical, cosmetics, food & drink,
agricultural, industrial, environmental, toxicology, water treatment and teaching.
There are a large number of published methods and assays available for these.
The icons described throughout this manual use the names quoted in Chapter “20.
TABLE OF ICONS”, if you are unsure of any of their functions please refer to this
section.
For detailed descriptions of the functions of parameter boxes please refer to Chapter
“21. GLOSSARY OF BOXES”.
Note: Throughout this manual all screen shots are shown on a white background,
this is purely for illustrative purposes.

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3. USE WITH Datrys PC
SOFTWARE
When connected to a PC the Ultrospec 7000/8000/9000 spectrophotometers can
be controlled using the Datrys PC software package. Operation using Datrys PC
software is described in the Datrys user manual or Datrys help file.

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 4. FREQUENTLY USED
ICONS
Button Name Function
Forward
Advances to the next screen in a sequence
arrow

Back arrow Returns to the previous screen in a sequence

Tick Confirms selection/entry. Saves and exits

Cross/exit Exit without saving

Buttons On The Sample Measurement Screen

Take
Performs a reference measurement
reference

Take
Performs a sample measurement
measurement

Opens the options menu on the sample measurement

Options arrow
screen

Buttons On The Options Menu

Method Takes the user from the sample measurement screen to

parameters the first method parameter screen

Allows the user to manually save sample data to a

Save data
specified location.

Allows the user to save the current method parameters to

Save method
the internal memory or a USB stick

Print Prints the sample data from the specified printer

Auto print Toggles auto print on and off

Sample
Accesses Sample Manager
Manager

Trace
Accesses Trace Manager (wavescan and kinetics only).
Manager

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 5. PERFORMING A
MEASUREMENT
5.1. Ultrospec 7000/8000/9000
The Ultrospec 7000/8000/9000 are dual beam UV-Visible
UV/visible spectrophotometers
that contain cell holders for both samples (situated at the front of the cell
chamber) and references (situated at the back of the cell chamber). As dual beam
spectrophotometers continually reference against the reference cell holder it is
possible to perform measurements in one of three ways.
To reference against air:
1. Insert a cuvette containing the sample solution in the sample cell holder, ensure
the reference cell holder is empty and close the sample chamber lid.
2. Press take measurement.
3. Repeat until all sample data has been collected. See the section Saving and
Printing for post measurement options.
To reference against a solvent:
1. Insert a cuvette containing the sample solution in the sample cell holder, insert a
cuvette containing the solvent in the reference cell holder and close the sample
chamber lid.
2. Press take measurement.
3. Repeat until all sample data has been collected. See the section Saving and
Printing for post measurement options.
Note: This methodology is used throughout the user manual.
To correct for both solvent and cell effects (simulate matched cuvettes):
1. Insert cuvettes containing the solvent in both the sample and reference cell
holders and close the sample chamber lid.
2. Press take reference.
3. Remove the cuvette containing solvent from the sample cell holder, empty out the
solvent and replace with the sample solution.
4. Insert the cuvette containing the sample solution in the sample cell holder and
close the sample chamber lid.
5. Press take measurement.
6. Repeat steps 4 and 5 until all sample data has been collected. See the section
Saving and Printing for post measurement options.
Note: This methodology ensures the most accurate measurements.

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6. LAMP MODE
When creating a method using an Ultrospec 7000/8000 or 9000 spectrophotometer
the user will have the option of setting the Lamp Mode to Precision or Pulse. These
modes are described below.
Precision
Precision Mode is used for applications requiring the most accurate measurements.
Both the Tungsten and Deuterium lamps will remain permanently switched on.
Pulse
Pulse mode is used to help preserve lamp life and reduce running costs as the
Tungsten and Deuterium lamps will be switched off after 15 minutes of inactivity.
Note: As the Ultrospec 7000 uses a Xenon lamp, measurements can only be made in
pulse mode.

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7. TYPES OF BOXES
Biochrom Ultrospec instruments use different kinds of boxes for parameter selection and
entry. These include:

Alphanumeric Text Entry

The alphanumeric text entry box allows the user to enter letters, numbers and
symbols by pressing the abc, 123 and λμ! buttons, respectively. It is possible to
toggle between upper and lower case letters and through a list of symbols by
pressing the abc and λμ! buttons twice.
Note: The layout of the screen is dependent on the text entry mode set under User
Interface in Settings.

Numeric Entry
The numeric entry box allows the user to include numbers in the method
parameters. Depending on the numeric box selected it may be possible to add both
positive and negative numbers.

Combo Box
Where there are greater than two options, the user will be presented with a combo
box listing all of these. If there are greater than 8 options the user can scroll
through these using either the page up and page down arrows or the scroll bar.
Note: If a box only contains two options i.e. On or Off, pressing this box will toggle
between the options and not produce a combo box.

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8. SETTINGS
Settings are accessed via the Settings button on the main screen (see below).

Note: When User Access Is turned on the Settings option will only appear on the
main screen for users with Administrator or Supervisor privileges.

8.1. Date & Time

The Ultrospec 7000/8000/9000 will arrive with the US EST and date set. This can be
changed by pressing the Date and Time button.
After the desired date and time have been entered, select the tick to save and exit
or the cross to exit without saving.

8.2. Regional
The Ultrospec 7000/8000/9000 will arrive with the language set to English. This can
be changed by pressing the Language button; the options are English, French,
German, Spanish, Chinese and Japanese.
To save any alterations press the tick, to exit without saving press the cross.

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8.3. Data Output
This is the default saving and printing settings that will be used in all application
method parameters.

8.4. User Interface

Allows the user to set the desired brightness level of the screen, the alphanumeric
text entry mode and the duration after which the screensaver will be displayed (if
required).

8.5. Accessories
Displays accessories that are fitted to the instrument and allows the user to set the
desired accessory parameters. For specific details see the Accessories section.

8.6. Instrument Settings

The following options are included under instrument settings:

8.7. Instrument Status

This displays the current status of the instrument.

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 8.8. Instrument Information
Displays the serial number, user-interface (UI) version, build and release dates and
instrument control (IC) version.

8.9. Instrument Settings

Instrument Settings allows the user to:

1. Collect a new, temporary baseline. This will be stored until the instrument is
switched off.
2. Save the temporary baseline. This will become the permanent baseline and be
stored until overwritten.
3. Restore the original baseline. If measurements show the temporary baseline to
be poor quality the permanent baseline can be restored.
Note: Using the Ultrospec 9000 the bandwidth at which the baseline is measured is
selected by pressing the Bandwidth box

8.10. Lamp Settings

Displays the current lamp status and allows the user to reset lamp life (Tungsten
and Deuterium lamps only).
To exit at any time press the exit button located in the bottom right hand corner.

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9. USER ACCESS
The Ultrospec 7000/8000/9000 have the option to assign users different access
rights. These are set via the user access button.
Note: User access is only available to users who have administrator privileges.

9.1. Adding a user

To add a new user to the instrument, press the ‘Add user’ button. The Ultrospec
7000/8000/9000 can store up to 16 individual users. Each user is given a user
name (using alphanumeric entry), a 4-digit password and assigned to one of three
user groups depending on the access level they require. The table below outlines
the features each user group can access.

User Run Applications Save Sample Delete Sample Data Access Settings Access
Group & Saved Methods Data from the instrument’s Save Methods Menu User
memory Settings
Limited
3 3 7 7 7 7
Supervisor
3 3 3 3 7 7
Admin
3 3 3 3 3 3

9.2. Editing a user

To edit a user’s details, highlight the desired user and press the ‘Edit user’ icon. This
allows the username, password and user group to be edited/updated as above.

9.3. Deleting a user

To delete a user from the instrument, highlight the desired user and press the ‘Add
user’ icon. Any methods or data created by this user will not be deleted. Note: It is not
possible to delete the default administrator account.

9.4. Editing User Access

To disable user logins and user access, highlight the default administrator account
and press the ‘Edit User’ icon to display the screen right.
Note: With Show Login set to No the instrument will not display the ‘Switch User’
button on the main screen and the instrument will always be in Administrator mode.

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10. APPLICATIONS

Single Wavelength Absorbance, % transmission or concentration measurements

at a single, specified wavelength.
Wavescan Wavelength scan between two, user defined wavelengths in
the range 190 to 1100 nm. The Ultrospec 7000/8000/9000
allows data overlay, post-scan data manipulation and user
configurable peak and valley functions.
Kinetics Serial and parallel measurements of absorbance versus time
to determine rate or end points. The Ultrospec 7000/8000/9000
allows data overlay, post-scan data manipulation and user
defined sectors.
Standard Curve Concentration measurement at a single wavelength
determined by the generation of a calibration curve of known
standards.
Equation Editor Allows users to create their own unique methods that include
calculations and thresholds.

10.1. Single Wavelength

The Single Wavelength application performs simple absorbance (A) and %
transmission (%T) measurements on samples, measuring the amount of light that has
passed through a sample relative to a reference (this can be air).

Measurement Parameters
Set Mode to Absorbance or %T. Wavelength, Bandwidth (Ultrospec 9000 only),
Integration Time and Lamp Mode can be set as required. The Sample Seed entered
under Sample will be the filename used for any data file saved automatically. You
may advance to the next screen at any time by pressing the forward arrow and
return to the previous screen by pressing the back arrow.

Set the outputs required in your method. For more information see the section
Saving and Printing.

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21
Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

10.2. Concentration via factor

This mode within the Single Wavelength application makes simple concentration
measurements on samples. Concentration is obtained by multiplying the measured
absorbance at a specific wavelength by a factor. The factor may be known in
advance or may be calculated by the instrument by measuring a standard of known
concentration. Examples of concentration measurements include cholesterol, glucose
and urea.
Measurement Parameters
From the main screen of the Ultrospec 7000/8000/9000 select Applications followed
by Single Wavelength to display the screen below.
Set Mode to Concentration. Wavelength, Bandwidth (Ultrospec 9000 only),
Integration Time and Lamp Mode can be set as required.
You may advance to the next screen at any time by pressing the forward arrow
and return to the previous screen by pressing the back arrow.

Set Factor Method as required, enter Factor using numeric entry and Units using
alphanumeric entry.

Set the outputs required in your method. For more information see the section
Saving and Printing.

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Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
Note: For assays where there is no established concentration factor, calibration
should be carried out using prepared standards (see Standard Curve for details of
how to perform this).

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

10.3. Wavescan
A measurement of the absorbance or %transmission of a sample over a specified
wavelength range is one of the most useful physical characteristics of a compound,
both as means of identification (qualitative analysis) and of estimation (quantitative
analysis). The observed features arise due to the various electronic transitions that
are possible within a molecule. The Ultrospec 7000/8000/9000 offer a range of post-
scan data manipulation options including: 1st order derivative, enabling identification
of multiple, unresolved peaks; 2nd order derivative, enabling identification of peak
shoulders (inflections); 4th order derivative, which identifies both multiple peaks
and inflections at the same time; Smoothing, utilizes the Savitzky-Golay algorithm
to smooth data and increase the signal to noise ratio; Enhanced, which enhances
features, sharpening peaks and valleys.
Measurement Parameters.
Use Max Wavelength and Min Wavelength to set the required wavelength range
(the Ultrospec 7000/8000/9000 scan from high to low wavelengths). Set Step, Mode
and Scan Speed as required. If Scan Speed is set to Integration the user will also be
required to set the Integration Time.
You may advance to the next screen at any time by pressing the forward arrow
and return to the previous screen by pressing the back arrow.

Set Lamp Mode, Bandwidth (Ultrospec 9000 only) and Sample Overlays as required.
The Sample Seed entered under Sample will be the filename of any automatically
saved file.
Note: With Sample Overlays set to ≥2 the data all wavelength scans will be
automatically saved to the instrument’s internal memory and will be displayed in
Trace Manager.

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 This measurement parameters screen allows the user to set the following
parameters:
Feature Detection: Determines the number of peaks or valleys that will be
automatically detected. Options are Coarse, Sensitive or Custom.
Feature Type: The feature types that will be detected by the software. Options are
Peaks or Valleys.
Feature Sort: Determines the how the features will be displayed in the data table.
Options are Wavelength or Magnitude.
Draw Peaks: Switches the display of peak cursors on and off. The cursors show
vertical dashed lines displaying the measured peak height and horizontal dashed
lines showing the peak width.
Custom Peak Height: Only displayed if Feature Detection is set to Custom. This
is the minimum height the peak has to be above the higher of the two adjacent
minima for the peak to be detected.
Custom Peak Width: Only displayed if Feature Detection is set to Custom. This is
the minimum width of the peak as determined by the difference in wavelength
between the higher of the two adjacent minima and the opposing intersection of
that higher minimum level and the peak profile.

Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
With Feature Detection set to Coarse, Sensitive or Custom the sample measurement
screen will display a table below the scan. This table will display the Feature Type
selected in the method parameters. To manually add a peak or valley to the table,
position the cursor over the desired feature by either touching the feature or using
the left and right cursors and press an empty cell in the table.
Note: Details of how to perform overlays, data manipulation and selecting saved
files can be found in the Trace Manager section.

10.4. Kinetics
Kinetics measurements made using a UV/visible spectrophotometer measure the
change in absorbance at a single, fixed wavelength over a specified period. This
can be used to provide useful information when an appropriate factor, defined in a
reagent kit protocol, is applied. Reagent test kits are routinely used for the enzymatic
determination of compounds in food, beverage and clinical laboratories.
UV/visible spectrophotometric kinetic assays are considered one of the most
convenient measurements for enzymatic assays since they allow the rate of the
reaction to be measured continuously.

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10.4.1. Serial Kinetics Measurements
Serial kinetics is the measurement of the absorbance of a single sample over a
specified duration at a specified interval. As these instruments are capable of taking
up to 1 reading per second serial kinetics measurements can be used for rapid rate
reactions.
Note: Without a cell changer connected, the instrument is only capable of performing
serial kinetics measurements.
Measurement Parameters
Wavelength, Bandwidth (Ultrospec 9000 only), Integration Time and Lamp Mode can
be set as you require. The Sample Seed entered under Sample will be the filename
of any automatically saved file. No. of Samples is described below.
Note: Measurement Mode only appears if a cell changer is connected. If this option
is not displayed the instrument will perform a serial kinetics measurement.
Note: When performing a serial kinetics measurement with >1 sample the
measurement proceeds as follows: Sample 1 will be measured for the full duration
at the specified interval, after this is complete sample 2 will be measured for
the full duration at the specified interval. The measurement will continue in this
manner until all samples have been recorded. When measuring >1 sample, all data
will be overlaid at the end of the measurement and automatically saved to the
instrument’s internal memory.
Set the Delay (time before first measurement), Duration (total measurement time,
up to 180 minutes), Interval (duration between readings, from 1 second to duration)
and Integration Time that you require.
Note: The integration time is determined by the interval (i.e. the maximum
integration time is half the interval time).

Mode has options for Delta A, Final A and Slope and is the value that will be
multiplied by the Factor to give the Result on the sample measurement screen.
Units are entered using alphanumeric text entry and will appear on any printed or
exported data. Y min and Y max are what is displayed during the measurement,
the y axis auto-scales upon completion.

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 Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking a Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
Note: Measurements will commence after the specified Delay period (if applicable).

A measurement can be stopped at any time by pressing the Stop button at the
bottom of the screen. All data collected to this point will be displayed on screen and
can be saved.

The data displayed in the table below the scan refers to the full measurement
range. To obtain data for a specific section it is necessary to add sections, this is
done as follows: Set the cursor to the desired start position by either pressing on
the scan or using the cursors, select t0 from the options menu, set the cursor to the
desired end position and select t1 from the options menu. This can be repeated to
add up to 4 discrete sections.
Note: Sections must be added in numerical order i.e. t1 must be added after t0, t2
after t1 etc.

With sections defined, the data displayed in the table below the scan is determined
by the position of the cursor. Only when the cursor is positioned in the section of
interest will this data be displayed.
A line of best fit can be added to any section by positioning the cursor in the
desired section and selecting the add line of best fit button from the options menu.
Note: Details of how to perform overlays, data manipulation and selecting saved
files can be found in the Trace Manager section.

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Saving & Printing
For details of manual saving and printing see the Saving and Printing section.

10.4.2. Parallel Kinetics Measurements

Parallel kinetics is the measurement of the absorbance of >1 sample (up to 8) at a set
interval over a specified duration. E.g. for 4 samples a measurement would proceed
as follows: The instrument will measure samples 1 to 4, pause for the appropriate
interval, measure samples 1 to 4, pause and continue in this manner until the full
duration has been reached.
Note: As parallel kinetics requires a cell changer the option of performing a parallel
kinetics measurement is only available when a cell changer is connected.
Measurement Parameters
Wavelength, Bandwidth (Ultrospec 9000 only), Integration Time and Lamp Mode can
be set as you require. The Sample Seed entered under Sample will be the filename
of any saved file. No. of Samples is described above. Measurement Mode should be
set to Parallel
Note: For parallel kinetics measurements the minimum number of samples is 2.

Delay and Duration (up to 180 minutes) can be set as required. The options
available under Interval are determined by the number of samples set on the
previous page.

Mode has options for Delta A, Final A and Slope and is the value that will be
multiplied by the Factor to give the Result on the sample measurement screen.
Units are entered using alphanumeric text entry and will appear on any printed or
exported data. Y min and Y max are what is displayed during the measurement,
the y axis auto-scales upon completion.

Set the outputs required in your method. For more information see the section
Saving and Printing.

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 As parallel kinetics requires a cell changer, you will be given the option of viewing
the prompt for sample position before collecting data. All other cell changer
parameters are determined by the method parameters. This prompt is shown
below.

Taking a Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000),
insert a cuvette containing the reference solution in the reference cell holder
and a cuvettes containing samples in positions 1 through 8 and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.

A measurement can be stopped at any time by pressing the Stop button at the
bottom of the screen. All data collected to this point will be displayed on screen and
can be saved.

The data displayed in the table below the scan refers to the full measurement
range of the selected trace (see below for selecting a trace). To obtain data for a
specific section it is necessary to add sections, this done as follows: Set the cursor
to the desired start position by either pressing on the scan or using the left and
right cursors, select t0 from the options menu, set the cursor to the desired end
position and select t1 from the options menu. It is possible to add up to 4 discrete
sections.
Note: Sections must be added in numerical order i.e. t1 must be added after t0, t2
after t1 etc.

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 With sections defined, the data displayed in the table below the scan is determined
by the position of the cursor. Only when the cursor is positioned in the section
of interest will this data be displayed. This refers to the selected scan only and is
indicated by the color of the column headers in the table.
A line of best fit can be added to any section by positioning the cursor in the
desired section and selecting the add line of best fit button from the options menu.

To allow post scan data manipulation all samples measured are automatically
included in Trace Manager (see below for full details of Trace Manager).
Note: The data displayed in the table below the scan refers to the Selected sample
only.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

10.5. Trace Manager – Overlaying &

Manipulating Wavescan & Kinetics Files
Trace Manager is the application used by the Ultrospec 7000/8000/9000 to overlay
and manipulate wavescan and kinetics files. Samples are loaded into Trace Manager
as described below:
Using Sample Manager
Wavescan and kinetics files can be loaded directly into Trace Manager by selecting
the required files from Sample Manager on the main screen. This procedure is
outlined below:
Highlight the required files by pressing on the appropriate row and load these into
Trace Manager by pressing the Sample Manager icon (bottom right corner). If
the files you require are not displayed on the screen you can scroll through the
pages using the up and down arrows. Pressing on the Sample ID and Date column
headers will sort the files alphabetically and chronologically, respectively.
Note: If a USB memory stick is inserted, it is possible to toggle between files stored
on the internal and USB memories using the icon in the left hand corner. The icon in
the top right corner of the screen will display the memory that is currently in use.

All recalled files will be displayed on the Trace Manager screen (up to 8). The color
of the Slot number will be the color of the trace when it is displayed on screen.
To toggle which files are displayed on the measurement screen press in the
appropriate Display box (up to 8 files can be displayed). To select which files data
will be displayed on the measurement screen press in the appropriate Selected box
(only one file may be selected). Press the forward arrow to view the overlaid data.

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From Within An Application
To overlay saved files with a live trace displayed, Trace Manager can be accessed
from within the application. This procedure is required for Limited users as they do
not have the ability to access Sample Manager on the main screen.
Trace Manager can be accessed from the Wavescan and Kinetics measurement
screens using the Trace Manager icon on the options menu.

When accessed with no overlays displayed, Trace Manager will be empty. Files are
added to this screen by selecting the Sample Manager icon in the left hand corner
of the screen and loading saved files as described below.

Highlight the required files by pressing on the appropriate row and load these into
Trace Manager by pressing the Sample Manager icon. If the files you require are
not displayed on the screen you can scroll through the pages using the up and
down arrows. Pressing on the Sample ID and Date column headers will sort the files
alphabetically and chronologically, respectively.
Note: If a USB memory stick is inserted, it is possible to toggle between files stored
on the internal and USB memories using the icon in the left hand corner. The icon in
the top right corner will display the memory that is currently in use.

All recalled files will be displayed on the Trace Manager screen (up to 8). The color
of the Slot number will be the color of the trace when it is displayed on screen.
To toggle which files are displayed on the measurement screen press in the
appropriate Display box (up to 8 files can be displayed). To select which files data
will be displayed on the measurement screen press in the appropriate Selected box
(only one file may be selected). Press the forward arrow to view the overlaid data.

Post Scan Manipulation

Trace Manager allows the user to manipulate recalled wavescan and kinetics data
using the procedure outlined below.

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 With the required files loaded into Trace Manager press the appropriate Trace
Output box to display the manipulation options.

Wavescan post scan manipulations are:

Sample Data Displays the raw wavescan data (this is the default option).
1st – 4th Derivative Displays the derivative data to the desired order.
Smoothed Uses the Savitzky-Golay algorithm to reduce noise and
smooth the data.
Enhanced Enhances features, sharpening peaks and valleys.
Kinetics post scan manipulations are:
Sample Data Displays the raw kinetics data (this is the default option).
Low Applies a low level of smoothing to the data.
Medium Applies a medium level of smoothing to the data.
High Applies a high level of smoothing to the data.
After the manipulations and display options have been set as required press
the forward arrow in the right corner to display the recalled data on the sample
measurement screen.
Note: For wavescan and serial kinetic measurements with overlays set to >1
and parallel kinetic measurements, data will be automatically saved into the
instrument’s internal memory and displayed in Trace Manager. To ensure the
optimum performance of the instrument it is recommended that unwanted files
are deleted from the internal memory at regular intervals (see Sample Manager –
deleting files from the internal memory).

10.6. Standard Curve

The construction of a multi-point calibration curve from standards of known
concentration to quantify unknown samples is a fundamental use of a
spectrophotometer. The Ultrospec 7000/8000/9000 range of instruments has the
advantage of being able to store calibration curves with a method. Each calibration
curve can be created using up to 9 standards, with each standard measurement
being made of up to 3 replicates.
Creating a Standard Curve
Set Wavelength, Bandwidth (Ultrospec 9000 only), Integration Time and Lamp Mode
as required. The Sample Seed entered under Sample will be the filename of any file
saved automatically.

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 Calibration can be set to Standards (the user is required to prepare and measure
standards) or Manual (the user inputs both the standard concentrations and
standard absorbances). Set Standards, Replicates, Curve Fit and Units as required in
your application.

Set the concentration values for each of the standards using the numeric entry box.

Set the outputs required in your method. For more information see the section
Saving and Printing.

To create the standard curve when using replicates press the replicates button in
the bottom right corner to take you to the screen shown overleaf. With Replicates
off standards can be measured directly as described overleaf.
Note: Pressing the save method icon before any standards have been measured
will save the method parameters only. Recalling a method containing method
parameters only requires the user to construct a standard curve before measuring
samples.

To create a standard curve using dual beam instruments (Ultrospec

7000/8000/9000) insert the cuvette containing the reference solution in the
reference cell holder and the cuvette containing the first standard/replicate in
the sample cell holder and press the take measurement button. The reference
measurement will be automatically subtracted from the standard measurement.
Continue recording all standards/replicates until the standard curve has been
completed. To repeat any standard measurements simply press the desired result,
insert the correct standard and press take measurement.
Note: After all replicates have been taken for a particular standard pressing
the replicates icon takes the user to the next standard that was specified in the
method.

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 To ignore any outlying standard measurements, press the tick in the appropriate
row to toggle it to a cross. Any ignored measurement will be automatically
removed from the standard curve. These can be reinstated by pressing the cross.

Taking A Measurement
After the standard curve has been collected press the forward arrow to proceed to
the sample measurement screen.
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert the cuvette containing the reference solution in the reference cell holder and
the cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
To view the standard curve whilst on the sample measurement screen, simply
press the ‘View Curve’ icon that appears under the options menu.
Note: Saving the method using the Save Method icon that appears on the options
menu will save both the method parameters and the standard curve. Recalling
a method containing method parameters and standard curve allows the user to
measure samples directly.
Saving & Printing
For details of manual saving and printing see the Saving and Printing section.

10.7. Equation Editor

The Equation Editor application allows users to create their own unique methods that
include calculations and thresholds. Examples of methods that can be created using
Equation Editor include percentage strength calculations and olive oil and chlorophyll
analyses.
Getting Started
The use of Equation Editor is outlined below.
Measurement Parameters
The first screen of Equation Editor allows the user to set the measurement
parameters that will be used for all subsequent measurements. Bandwidth
(Ultrospec 9000 only), Integration Time, Lamp Mode and Mode are used as in all
other applications. The use of Prompt between λ and Scan are described below.

Prompt between λ off The instrument will measure wavelength 1, measure

wavelength 2, measure wavelength 3 etc and then perform
any calculations.
Prompt between λ on The instrument will measure wavelength 1, prompt, measure
wavelength 2, prompt, measure wavelength 3 etc and then
perform any calculations. This is used for equations that
require wavelength measurements of different samples e.g.
chlorophyll analysis.
Scan off The instrument will only measure the wavelengths specified
in the sample specification table (see below). Having scan off

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 speeds up analyses as only the required wavelengths are
measured.
Scan on The instrument will perform a full wavelength scan over a
range set under the sample measurement parameters screen.
With scan on the user can set both the scan speed and the
step size.
You can advance to the next screen at any time by pressing the forward arrow and
return to the previous screen by pressing the back arrow.
Using the Sample Measurement table the user inputs all of the measurements
that are required in the method i.e. the screen left shows a fixed wavelength
measurement at 430.0 nm that is named 430. Data is inputted as described on next
page. Before any data is inputted Name will read ‘Not set’ and will not appear in
the Sample Data list on the Equation Builder.

Name Pressing this allows the user to input an alphanumeric name for the
measurement. The name inputted here will be used as the Sample Data
in the Equation Builder (inputted data only appears in the Equation
Builder if the user has defined a name).
Wavelength Pressing this produces the number entry box that allows the user to
input the (λ) wavelength for measurement.
Function Pressing this displays a combo box with the following options.
Abs / %T at λ – measurement will be at the wavelength inputted by
the user only.
Peak closest to λ – the instrument automatically finds the peak
closest to the inputted wavelength.
Valley closest to λ – the instrument automatically finds the valley
closest to the inputted wavelength.
+/- Used with Peak closest to λ and Valley closest to λ only. This is the
range over which the instrument will scan for a peak or valley from the
inputted wavelength.
Del Pressing this deletes the row. If the data is used in an equation this will
also be deleted.
Equation Editor has four options for sample naming conventions.
These are shown below:

Default The sample name consists of Sample and an incrementing number.

Auto Increment The sample name is a combination of sample seed and an
incrementing sample number. The user will be prompted to enter the
sample seed for each new batch of samples.
Prompt for ID The user is prompted to enter the sample name before running each
sample.
Fixed List The user will be prompted to enter the number of samples required.
Sample names for each sample are then entered on the subsequent
screens. The inputted sample names are saved for each method.

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 The Standard Specification screen is used to declare a list of all of the standard
solutions which will be referenced when creating an equation.
E.g. the equation for percentage strength at 500 nm compares the absorbance of a
sample to the absorbance of a control standard. This is where the control standard
would be defined.

Standard names are entered by pressing on the desired row and entering the
standard name using alphanumeric text entry. Standard measurements can be
made for any measurements specified in the Samples table.

The Constant Factor Specification screen is used to declare any constants used in the
equation. Data is inputted as described below. Before any data is inputted Constant
Name will read ‘Not set’ and will not appear in the Constants list on the Equation
Builder.
Constant Name Pressing this allows the user to input an alphanumeric name for
the constant.
Value Pressing this produces the number entry box that allows the user
to input the value of the constant.
Units Pressing this allows the user to enter units for the constant using
alphanumeric text entry. If this column is left blank, no units will be
displayed on exported or printed data.
Del Pressing this deletes the row. If the constant is used in an equation
this will also be deleted.
The Variable Factor Specification screen is used to declare any variables used in
the equation. Data is inputted as described below. Before any data is inputted,
Variable Name will read ‘Not set’ and will not appear in the Variables list on the
Equation Builder.

Variable Name Pressing this allows the user to input an alphanumeric name for the
variable factor.
Default Pressing this produces the number entry box that allows the user to
input the default variable factor. Default values can be edited during
a measurement.
Units Pressing this allows the user to enter units for the variable factor
using alphanumeric text entry. If this column is left blank, no units
will be displayed on exported or printed data.
Change Each Pressing this toggles between sample and batch. When set to
sample the method will prompt for a variable to be entered before
each sample measurement. When set to batch, the method will
prompt for a variable to be entered at the start of each sample
batch.

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 The Equation Viewer screen provides an overview of any equations created, as well
as allowing the user to create new or edit existing equations. Data is inputted as
described below. Before any data is inputted Name will read ‘Not set’ and will not
appear on the results screen.

Name Pressing this allows the user to input a unique, alphanumeric name
for the equation. The names entered here will be displayed in the
‘Equations’ combo box on the Equation Builder screen as well the results
screens. Therefore any equation can be easily identified when using it in
other equations.
Equation Pressing this takes the user to the ‘Equation Builder’ (see below). Any
equation constructed in the Equation Builder will be displayed in this
box.
Units Pressing this allows the user to enter units for the result of the equation
using alphanumeric text entry. If this column is left blank no units will be
displayed alongside the result.
Del Pressing this deletes the row and removes the equation.
The Equation Builder allows the user to create any equations required in the
method. Data is inputted as described below. To allow data to be inserted or
deleted the cursor can be moved left and right using the left and right arrows. Data
can be deleted using the delete icon and thresholds added using the thresholds
icon (see below).

Variables Pressing on this displays a list that contains any variables added to
the ‘Variables’ table by the user. Selecting the desired variable enters it
into the equation.
Constants Pressing on this displays a list that contains any constants added to
the ‘Constants’ table by the user. Selecting the desired constant enters
it into the equation.
Equations Pressing on this displays a list that contains any equations that have
been created in this method. Selecting the desired equation enters it
into the equation.
Sample Data Pressing on this displays a list that contains all of the readings
specified by the user in the Sample Measurement table. Selecting the
desired sample data enters it into the equation.
Symbols Pressing on this displays a list containing mathematical symbols and
the logic gates AND and OR. Selecting the desired symbol enters it into
the equation.
Numbers Pressing this produces the number entry box that allows the user to
directly input numbers into the equation.
Note: All of the data above appears in the lists as it was inputted in the appropriate
table.
After the equation has been inputted the user has two options. If the result is to be
viewed as a number, press the back arrow to return to the Equation Viewer screen.
If the result is to be viewed with a user specified pass/fail limit press the ‘Thresholds’
button to set appropriate thresholds for the measurement.

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 The first thresholds screen allows the user to input how many thresholds are
required for a result.

With Thresholds set to 3 the screen will display the table layout shown left. Setting
Thresholds to 2 and 1 will reduce the number of values you can input to 2 and 1,
respectively.

Value Pressing this produces the number entry box that allows the user to
directly input numbers for threshold values.
Name Pressing this allows the user to enter the text that will be displayed for each
result using alphanumeric entry.
Using the example above: A result of ≥100 will return the answer Position 1, a result
of <100 and ≥50 will return the answer Position 2, a result of <50 and ≥10 will return
the answer Position 3 and a result of <10 will return the answer Position 4.
Note: When using AND or OR logic in an equation the result will be returned as a
binary (1 = true and 0 = false). These can be incorporated into the thresholds by
setting the Thresholds to 1, Value to 1 and setting the appropriate names (as the
name above value corresponds to ≥1 this is the response that will be displayed for
true results).
After all of the thresholds have been set, pressing the forward arrow will return the
user to the Equation Builder screen. The Equation Viewer screen can be accessed
using the back arrow.
Continue as described above until all equations have been created. Once complete
pressing the forward arrow will take the user to the output options screen below.
Set the outputs required in your method. For more information see the section
Saving and Printing.
Note: Automatically saving sample data with sample naming set to ‘Prompt for
ID’ or ‘Fixed list’ will save the data using the first inputted sample name as the
filename.

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Performing A Measurement – No Standards
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
Note: Pressing on the equation name allows the user to view the equation and the
individual measurement results.

Using Standards
When performing a measurement using a method that includes standards, the first
press of the take measurement button will produce a message box that prompts
the user to insert a specific standard. After all standards have been measured,
subsequent presses of the take measurement button will perform sample
measurements.

Saving Methods And Exiting

As methods developed using Equation Editor may have taken time to input, the
software will prompt the user to save the method before exiting. Pressing the
cross will return to the user to the results screen, where they can save the method,
pressing the tick will exit without saving. Details of method saving can be found in
the Saving Methods section.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

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11. LIFE SCIENCE
APPLICATIONS
This contains two sub folders; Nucleic Acids and Protein. The contents of these sub
folders are detailed below:

Nucleic Acids
DNA Utilizes the absorbance measurements at 230, 260 & 280 nm with
optional background correction to perform a concentration and purity
check for DNA samples.
RNA Utilizes the absorbance measurements at 230, 260 & 280 nm with
optional background correction to perform a concentration and purity
check for RNA samples.
Oligo Utilizes the absorbance measurements at 230, 260 & 280 nm with
optional background correction to perform a concentration and purity
check for oligo samples.
CyDye DNA Measures the labelling efficiency of fluorescently labelled DNA
probes to ensure that there is sufficient amount of each probe to give
satisfactory signals. The DNA yield is measured at 260 nm whilst the
incorporation of the dyes is measured at the absorption maxima.
This method is also useful for measuring the yields and brightness of
fluorescently labelled in-situ hybridization probes.
Tm Calc The Tm Calculation application calculates the theoretical melting point
from the base sequence of a primer. It is done using nearest neighbour
thermodynamic data for each base in the nucleotide chain in relation
to its neighbour.
Protein
BCA™ Quantitative determination of protein concentration utilising the
absorbance measurement at 562 nm.
Bradford Quantitative determination of protein concentration utilising the
absorbance measurement at 595 nm.
Lowry Quantitative determination of protein concentration utilising the
absorbance measurement at 750 nm.
Biuret Quantitative determination of protein concentration utilising the
absorbance measurement at 546 nm.
Protein UV Direct UV determination of protein concentration at 280 nm using the
Christian Warburg calculation.
Protein A280 Direct UV determination of protein concentration using BSA, IgG,
Lysozyme, Molar Extinction. Mass Extinction or E1% calculations.

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11.1. Nucleic Acid Applications
11.1.1. DNA, RNA & Oligo
Nucleic acids can be quantified at 260 nm because it is well established that solutions
of DNA and RNA in 10 mm pathlength cells with an optical density (absorbance) of
1.0 have concentrations of 50 µg/ml and 40 µg/ml, respectively. Oligonucleotides
typically have a factor of 33 µg/ml, although this does vary with base composition
and can be calculated if the base sequence is known.
Concentration = A260 × Factor
Ultrospec 7000/8000/9000 use the default factors 50, 40 and 33 for DNA, RNA and
oligonucleotides, respectively. Compensation for dilution and pathlength can also be
entered.
Nucleic Acid Purity Checks
• Nucleic acids extracted from cells are accompanied by proteins and extensive
purification is required to separate these protein impurities. The ratio of
A260/A280 gives an indication of a sample’s purity, with pure DNA and RNA
preparations typically having ratios of ≥1.8 and ≥2.0, respectively. Deviations
from these values indicate the presence of impurities, but care must be taken
when interpreting results.
• Concentration also affects both the A260 and A280 readings. If a solution is
too dilute, the readings may be at the instrument’s detection limit and results
may vary as there is less distinction of the A260 peak and A280 slope from the
background absorbance. For accurate measurements A260 should always be
greater than 0.1.
• Elevated A230 values can also indicate the presence of impurities (230 nm is
near the absorbance maximum of peptide bonds and also indicates buffer
contamination since EDTA and other buffer salts absorb at this wavelength).
When measuring RNA samples, the A260/A230 ratio should be >2.0. Ratios lower
than 2.0 generally indicate contamination with guanidinium thiocyanate, a
reagent commonly used in RNA purification and which absorbs over the
230-260 nm range. A wavelength scan of the nucleic acid is particularly useful for
RNA samples.
Background Correction
• To compensate for the effects of background absorbance caused by turbidity,
high absorbance buffer solutions and the use of reduced aperture cells the
Ultrospec 7000/8000/9000 have the option of background correction at a
320 nm.
• When used, A320 is subtracted from A260 and A280 prior to use so that:
Concentration = (A260 - A320) × Factor
Abs ratio = (A260 - A320) / (A280 - A320)
Abs ratio = (A260 - A320) / (A230 - A320)
• The use of background correction can remove variability due to handling effects
of low volume disposable cells.
Spectral scan of nucleic acid
Note: An absorbance maximum near 260 nm and absorbance minimum near
230 nm, a flat peak near 260 nm and steep slope at 280 nm and very little
absorbance at 320 nm.

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Measurement Parameters
Set Pathlength and Dilution Factor to the required values. Check above to see if
Background correction is required. To perform a scan over the range
220–330 nm for each measurement set Scan to On. Set Units to encompass
the expected concentration of your samples, the default Factor will update
automatically depending on the units selected i.e. for units of µg/ml the default
factor will be 50.00. If the Factor required differs from the default value this can be
edited using numeric entry.
You may advance to the next screen at any time by pressing the forward arrow
and return to the previous screen by pressing the back arrow.

Bandwidth (Ultrospec 9000 only), Integration Time and Lamp Mode can be set as
you require. The Sample Seed entered under Sample will the filename of any saved
file.

Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
If Background is set to On the A320 result will be included in the left hand column
and automatically subtracted from the displayed A230, A260, A280, A260/A230,
A260/A280 results.

If Scan is set to On in method parameters a scan of the most recently run sample
can be viewed by pressing the View Scan icon in the options menu.
Note: When saving sample data, scan files will not be saved. The Wavescan
application should be used to save scans of nucleic acid samples.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

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11.1.2. CyDye DNA
The measurement of the labelling efficiency of fluorescently labelled DNA probes
before 2-color micro-array hybridization ensures that there is sufficient amount
of each probe to give satisfactory signals. The data also provides an opportunity
to balance the relative intensities of each fluorescent dye by adjusting the
concentration of each probe before hybridization. The DNA yield is measured at
260 nm whilst the incorporation of the dyes is measured at the absorption maxima.
This method is also useful for measuring the yields and brightness of fluorescently
labelled in-situ hybridization probes.
Measurement Parameters
Number of Dyes, this can be set to 1 or 2. Dye 1 Name allows the user to select
the dye used in the measurement, the Ultrospec 7000/8000/9000 have 19 dyes
pre-programmed and the option for user entry using the Custom Dye option. λ
Max, Extinction Coefficient and Correction Factor are only editable when using the
Custom Dye option.
You may advance to the next screen at any time by pressing the forward arrow
and return to the previous screen by pressing the back arrow.
With Number of Dyes set to 2, the next method parameter screen allows the user to
specify the second dye used in the measurement.

If the measurement requires the calculation of DNA Concentration and/or DNA

Quantity the relevant nucleic acid can be inputted. A custom factor can be entered
by selecting Custom in Nucleic Acids.

This parameters screen allows the user to set the pathlength of the cuvette being
used, whether background correction is required and at what wavelength, the
dilution factor and volume of the sample in µl. All of these will be used in the
calculations.

Bandwidth (Ultrospec 9000 only), Integration Time and Lamp Mode can be set as
you wish. The Sample Seed entered under Sample will the filename of any saved
file.

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 Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking a Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
If Background Correction is set to On the Background Wavelength set in the method
will be included in the left hand column and automatically subtracted from all
results.

To toggle between DNA & dye parameters press the toggle icon on the options
menu. CyDye DNA measurements are wavelength scanning measurements, to view
the scan for a particular measurement press the scan button in the options menu.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

11.1.3. Tm Calculation
The Tm Calculation application calculates the theoretical melting point from the
base sequence of a primer. It is done using nearest neighbour thermodynamic data
for each base in the nucleotide chain in relation to its neighbour (Breslauer et al,
Proc.Natl. Acad. Sci. USA, 1986, 83, 3746). The data obtained are useful in both the
characterization of oligonucleotides and in calculating Tm for primers used in PCR
experiments.
The ACGT/U sequence entered in the method parameters is used to calculate
the theoretical Tm, the theoretical absorbance (Absorbance units/mmol) and the
conversion factor (mg/ml). This is possible as the stability of a bent and twisted
sequence of bases such as an oligonucleotide is dependent on the actual base
sequence. These calculated thermodynamic interactions between adjacent base
pairs have been shown to correlate well with experimental observations.
The Tm Calculation application uses matrices of known, published thermodynamic
values and extinction coefficients to calculate Tm and the theoretical absorbance/
factor of an entered base sequence.
Tm is calculated using the equation:-

Tm = ΔH × 100 - 273.15 + log [salt]

ΔS + (1.987 × loge(c/4 +53.0822)

where ΔH and ΔS are the enthalpy and entropy values, respectively summed from
respective 2 × 4 × 4 nearest neighbour matrices

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 c is the Primer concentration of oligonucleotide (pmoles/ml) in the
calculated Tm or the measured concentration in measured Tm. In the latter
case, concentration is obtained from the equation:
c = Abs(260 nm) × Calculated factor × pathlength multiplier × 10 000
MW
Calculated factor and MW are defined below.
[salt] is the buffer molarity plus total molarity of salts in the hybridization solution
(moles/l).
Weights for ΔS are indexed by adjacent paired bases. A similar equation applies to
weights for ΔH, again indexed by adjacent bases.
Note: Bivalent salts may need normalising using a multiplying factor of 100 because
of their greater binding power.
Theoretical Absorbance
The Theoretical Absorbance is based on a calculation as follows:
For each adjacent pair of bases (nearest neighbours) an extinction coefficient weight
is accumulated using a 4 × 4 table (one for either DNA or RNA). This total weight is
doubled and then for each internal base a counterweight is subtracted using another
1 × 4 table. The end bases are excluded from the latter summation.
Total Extinction Coefficient E = Σ (2 × aTable[base_type][base(n)][base(n+1)])-
Σ(tTable[base_type][base(n]])
Conversion Factor
The Conversion Factor is given by = Molecular weight ABCDE
Σ EABCDE
where
EABCDE = [2 × (EAB +EBC +ECD +EDE) –EB –EC –ED]
• The molecular weight (MW) of a DNA oligonucleotide is calculated from:
MW (g/mole) = [(dA × 312.2) + (dC × 288.2) + (dG × 328.2) + (dT × 303.2.)] + [(MWcounter-ion) × (length of oligo in bases)]
(for RNA oligonucleotide, (dT × 303.2) is replaced by (dU × 298.2)
The MW calculated using this equation must be adjusted for the contribution of the
atoms at the 5’ and 3’ ends of the oligo.
For phosphorylated oligos: Add [17 + (2 × MW of the counter-ion)]
For non-phosphorylated oligos: Subtract [61 + (MW of the counter-ion)]
The MW (g/mole) of the most common oligo counter ions are:
Na (sodium) 23.0
K (potassium) 39.1
TEA (triethylammonium) 102.2
Other Defaults to 1.0 (variable 0.1–999.9)
Calculated molecular weight: a weight is added for each base looked up from a
table. The weight of the counter ion is added for every base from a small table for
the known ions. If phosphorylated, then the system adds 17.0 plus two counter ions
otherwise it subtracts 61.0 and one ion.
Theoretical Absorbance: for each adjacent pair of bases (nearest neighbours) a
weight is accumulated using a table. For each internal base a weight is subtracted
using another table. Separate tables are used for DNA and RNA.
Calculated factor: this is the calculated molecular weight divided by the theoretical
absorbance.

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Measurement Parameters
Set the required Base Type (DNA/RNA), whether the base is Phosphorylated, the
Primer Concentration (pmoles/ml), Buffer Molarity and Counter Ion. Counter Ion has
options for Na (sodium), K (potassium), TEA (triethylammonium) and Other, allowing
the user to set the required molecular weight (MW) of the counter ion.

Set the Pathlength and Integration Time you require. Base Sequence allows the user
to enter the known base sequence triplets using the buttons A, C, G and T/U. To
improve readability a comma is added after each triplet.

Bandwidth (Ultrospec 9000 only) and Lamp Mode can be set as you wish. The
Sample Seed entered under Sample will the filename of any automatically saved
file.

Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking a Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert a cuvette containing the reference solution in the reference cell holder and
a cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

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11.2. Protein Applications
The Ultrospec 7000/8000/9000 contains dedicated methods for both colorimetric
protein assays and direct UV measurements.

11.2.1. BCA, Bradford, Lowry & Biuret Protein Assays

The BCA, Bradford, Lowry and Biuret protein assays are well established
spectrophotometric methods for determining the amount of protein in a sample.
The exact choice of the assay depends upon the concentration of protein being
measured and the detergents/reducing agents used in purification. Detailed protocols
are supplied with all assay kits and should be followed closely to ensure accurate
results are obtained. An outline of the protein assays offered by the Ultrospec
7000/8000/9000 is provided below:
Bradford method: Quantifies the binding of the dye Coomassie Brilliant Blue to an
unknown protein and compares this binding to that of different,
known concentrations of a standard protein at 595 nm. The
standard protein is usually bovine serum albumin (BSA).
Biuret method: Depends on reaction between Cu2+ ions and amino acid residues
in an alkali solution. The resulting copper complex absorbs light at
546 nm.
BCA method: Depends on reaction between Cu2+ ions and amino acid
residues. In addition, this method combines this reaction with the
enhancement of Cu+ ion detection using bicinchoninic acid (BCA)
as a ligand, giving an absorbance maximum at 562 nm. The BCA
process is less sensitive to the presence of detergents used to
break down cell walls.
Lowry method: Depends on quantifying the color obtained from the reaction
of Folin-Ciocalteu phenol reagent with the Tyrosyl residues of
an unknown protein and comparing with those derived from a
standard curve of a standard protein at 750 nm (usually BSA).

11.2.2. Determination Of Protein Concentration Using The

Bicinchoninic Acid (BCA) Protein Assay
The principle of the bicinchoninic acid (BCA) protein assay relies on the formation of
a Cu2+-protein complex under alkaline conditions, followed by reduction of the Cu2+
to Cu+. The amount of reduction is proportional to the amount of protein present.
BCA forms a purple-blue complex with Cu+ in alkaline environments, thus providing
a basis to monitor the reduction of alkaline Cu2+ by proteins. The BCA assay can be
used to quantify proteins in the concentration range 0.2 to 1.0 mg/ml. It is compatible
with many detergents but not compatible with reducing agents such as dithiothreitol
above 1 mM.
Getting Started
It is always advisable to prepare the standard in the same buffer as the sample to
minimize any interference effects. BCA assays are routinely performed at 37°C. Color
development begins immediately and can be accelerated by incubation at higher
temperatures. Higher temperatures and/or longer incubation times can be used for
increased sensitivity.
Materials Required
Bicinchoninic Acid Kit for Protein Determination.
Suitable tubes with caps to hold and mix 2.1 ml samples and to heat at up to 60°C.
Plastic disposable cuvettes.
Standard protein solution of known concentration (1 mg/ml).
Incubator or block heater to heat sample tubes.
Preparation Of The BCA Working Reagent.
BCA reagents A and B are available commercially from a number of different sources.
Instructions given here are for the kit supplied by Sigma Aldrich, other methods will
be similar. Always refer to the manufacturer’s instructions.
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1. Mix 50 parts of Reagent A (a solution containing bicinchoninic acid, sodium
carbonate, sodium tartrate and sodium bicarbonate in 0.1 N NaOH, pH 11.25) with
1 part of Reagent B (4% (w/v) CuSO4.5H2O), preparing sufficient reagent for all the
standards and samples. 2 ml of working reagent is required for each sample.
2. Mix until the solution is a uniform light green color. The solution is stable for 1 day.
Standard Preparation
1. Prepare a series of protein standards ranging in concentration from 0.2 to
1.0 mg/ml such that the final volume for the assay is 0.1 ml. The Ultrospec
7000/8000/9000 can measure up to 9 standards and up to 3 replicates.
2. Add 2.0 ml of the BCA working reagent to each standard, vortex gently and
incubate using one of the following parameters: 60°C for 15 minutes, 37°C for
30 minutes or room temperature from 2 hours to overnight.
3. If required, allow the tubes to cool to room temperature.
Sample Preparation
1. Prepare the unknown samples as described above ensuring that the final volume
is 0.1 ml.
2. Add 2.0 ml of the BCA working reagent to each sample, vortex gently and
incubate using one of the following parameters: 60°C for 15 minutes, 37°C for
30 minutes or room temperature from 2 hours to overnight.
3. If required, allow the tubes to cool to room temperature.
Creating A Standard Curve
For BCA measurements Wavelength is set to 562.0 nm. Bandwidth (Ultrospec 9000
only), Integration Time and Lamp Mode and Sample can be set as you wish.
You may advance to the next screen at any time by pressing the forward arrow
and return to the previous screen by pressing the back arrow.

Set Calibration to Standards, Curve Fit to Zero Regression and enter Units of
mg/ml. The number of standards and replicates can be set as you wish (for
optimum accuracy it is recommended that the number of standards is ≥4 and
replicates is >1).
Note: With Calibration set to Standards the user is required to prepare and measure
standards with Calibration set to Manual the user inputs both the standard
concentrations and absorbances.

Enter the concentration of prepared standards using the numeric keypad.

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 Set the outputs required in your method. For more information see the section
Saving and Printing.

To create the standard curve when using replicates press the replicates button in
the bottom right corner to take you to the screen shown below. With Replicates off
standards can be measured directly as described below.
Note: After all replicates have been taken for a standard pressing the replicates
icon takes the user to the next standard that was specified in the method.

To create a standard curve using dual beam instruments (Ultrospec

7000/8000/9000) insert the cuvette containing the reference solution in the
reference cell holder and the cuvette containing the first standard/replicate in
the sample cell holder and press the take measurement button. The reference
measurement will be automatically subtracted from the standard measurement.

Continue recording all standards/replicates until the standard curve has been
completed. After the standard curve has been collected press the forward arrow to
proceed to the sample measurement screen.

To ignore any outlying standard measurements press the tick next in the
appropriate row to toggle it to a cross. Any ignored measurement will be
automatically removed from the standard curve. These can be reinstated by
pressing the cross.
Note: Pressing the save method icon before any standards have been measured
will save the method parameters only. Recalling a method containing method
parameters only will require the user to construct a standard curve before
measuring samples.

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Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert the cuvette containing the reference solution in the reference cell holder and
the cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
To view the standard curve whilst on the sample measurement screen, simply
press the ‘View Curve’ icon that appears under the options menu.
Note: Saving the method using the Save Method icon that appears on the options
menu will save both the method parameters and the standard curve. Recalling
a method containing method parameters and standard curve allows the user to
measure samples directly.
Saving & Printing
For details of manual saving and printing see the Saving and Printing section.

11.2.3. Determination Of Protein Concentration Using Direct UV

Methods
The direct UV method of protein determination has a number of advantages over
traditional colorimetric assays in that it does not rely on an external protein standard
and the sample is not consumed in the assay. However the presence of nucleic
acid in the protein solution can have a significant effect due to strong nucleotide
absorbance at 280 nm. This can be compensated by measuring A260 and applying
the equation of Warburg and Christian for the protein crystalline yeast enolase
(Equation 1).
Protein concentration (mg/ml) = (1.55 × Abs280) – (0.76 × Abs260) 1
Protein concentration = (Factor 1 × Abs280) - (Factor 2 × Abs260) 2
Ultrospec 7000/8000/9000 use default A260 and A280 factors of 0.76 and 1.55,
respectively. These factors can be edited so that the equation can be applied to other
proteins (Equation 2). Compensation for background, dilution and pathlength can also
be entered.
To customize Equation 2 for a particular protein, the A260 and A280 values should
be determined at known protein concentrations to generate simple simultaneous
equations, which, when solved provides the two coefficients. In cases where Factor 2
is found to be negative, it should be set to zero since it means there is no contribution
to the protein concentration due to absorbance at 260 nm.
The A260/A280 ratio also gives an indication of protein purity; a ratio of 0.57 can be
expected for pure protein samples.
Background Correction
• To compensate for the effects of background absorbance caused by turbidity,
high absorbance buffer solutions and the use of reduced aperture cells the
Ultrospec 7000/8000/9000 can use background correction at 320 nm.
• When used A320 is subtracted from A260 and A280 prior to use so that:
Protein concentration = [Factor 1 ×(Abs 280 - Abs 320)] - [Factor 2 ×(Abs 260 - Abs 320)]
Ratio = (Abs 260 - Abs 320) / (Abs 280 - Abs 320)
• The use of background correction can remove variability due to handling effects
of low volume disposable cells.

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11.2.4. Protein UV
Measurement Parameters
Set Pathlength and Dilution Factor to the required values. Check above to see
if background correction is required. The default values for A260 Factor and
A280 Factor are 0.76 and 1.55, respectively; these can be edited by pressing the
appropriate box. Set Units to encompass the expected concentration of your
samples.

You may advance to the next screen at any time by pressing the forward arrow and
return to the previous screen by pressing the back arrow.
Bandwidth (Ultrospec 9000 only), Integration Time and Lamp Mode can be set as
you wish. The Sample Seed entered under Sample will the filename of any saved
file.

Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert the cuvette containing the reference solution in the reference cell holder and
the cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
If Background is set to On the A320 result will be included in the left hand column
and automatically subtracted from the displayed A260, A280 and A260/A280
results.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

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11.2.5. Protein A280
Measurement Parameters
Select the Mode you require, Ultrospec 7000/8000/9000 have options for Christian
Warburg, BSA, IgG, Lysozyme, Molar Extinction, Mass Extinction and E1% (for Molar
Extinction the user will also be required to enter the molar extinction coefficient,
and molecular weight and atomic units for Mass Extinction).
Set Pathlength and Dilution Factor to the required values. Check above to see if
background correction is required.

Set Units to encompass the expected concentration of your samples. Bandwidth

(Ultrospec 9000 only), Integration Time and Lamp Mode can be set as you wish. The
Sample Seed entered under Sample will the filename of any saved file.

Set the outputs required in your method. For more information see the section
Saving and Printing.

Taking A Measurement
To take a measurement using dual beam instruments (Ultrospec 7000/8000/9000)
insert the cuvette containing the reference solution in the reference cell holder and
the cuvette containing the sample in the sample cell holder and press the take
measurement button. The reference measurement will be automatically subtracted
from the sample measurement.
If Background is set to On the A320 result will be included in the left hand column
and automatically subtracted from the displayed A260, A280 and A260/A280
results.

Saving & Printing

For details of manual saving and printing see the Saving and Printing section.

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12. SAVING & PRINTING
Ultrospec 7000/8000/9000 UV-Visible
UV/visible spectrophotometers allow users to save and
print sample data. This can either be included automatically as a method parameter
or performed manually from the sample measurement screen. This section
details the saving and printing options offered by all Ultrospec 7000/8000/9000
spectrophotometers.

12.1. Saving Sample Data

The Ultrospec 7000/8000/9000 allows users to save sample data in three different
formats:

12.1.1. Internal
The sample data is saved to the instrument’s internal memory format. See the
Sample Manager section for details on saving and recalling data from the internal
memory.
Note: To ensure the optimum performance of the Ultrospec 7000/8000/9000 it is
recommended that unwanted data be deleted from the instrument’s internal memory
at regular intervals.

12.1.2. USB
The sample data is saved to a USB memory stick in format that can be read by
Ultrospec 7000/8000/9000 spectrophotometers only. Files in this format cannot be
opened by Microsoft Excel™ or other spreadsheet programs.
Note: Sample data will be saved to the Ultrospec 7000/8000/9000 Samples directory
on the USB memory stick; if this directory is not present it will be created.

12.1.3. USB CSV

The data is saved to a USB memory stick in comma separated variable (CSV)
format allowing it to be opened directly using Microsoft Excel or other spreadsheet
programs. Files in this format cannot be opened using the instrument.
Note: To view the data displayed in the File Created, Date and Time cells in a
recognized format this will need formatting as described below:
File Created: Right click in the appropriate cell and select Format Cells from the
list, select Custom dd/mm/yyyy h:mm from the list on the right hand
side (see below) and select ok.

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 Date / Time: Right click in the appropriate cell and select Format Cells from the
list, under Category select Date or Time and the desired format from
the list on the right hand side (see below) and select OK.

12.2. Automatic Saving

The option to save sample data automatically is set under method parameters.
With Auto Save set to on, the save location can be set to Internal, USB or USB CSV
(the USB options are only available if a USB memory stick is inserted).
The filename given to an automatically saved file will be either the Sample Seed
entered in the method parameters or, if the user chooses not to enter a Sample
Seed, Default. The Ultrospec 7000/8000/9000 will only save one ‘Default’ file per
application; subsequent saves of files without a sample seed will overwrite the
previous default file.
As sample data is saved when the user exits the application, removing a USB
memory stick before exiting will result in loss of data.
Note: All files are appended with a unique time and date stamp it is therefore
possible to create two or more files sharing the same name.
Note: With Overlays ≥2 in Wavescan and Number of Samples ≥2 in Kinetics the
overlaid data will always be saved automatically to the instrument’s internal
memory.

12.3. Manual Saving

If a method does not require sample data to be saved each time a measurement
is taken it is possible to manually save sample data in one of the formats outlined
above. This procedure is described below:
After collecting all required sample measurements select save sample data from
the options menu on the sample measurement screen to display the dialogue box
shown left. The save location and filename are set by pressing the Save to and
Sample Name boxes, respectively. If no Sample Name is entered the file will be
titled Default.
Note: Any sample data saved manually will override the auto save function

12.4. Exporting Data

The Ultrospec 7000/8000/9000 allow users to recall saved sample data from the
internal memory or a USB memory stick and save this in another format. This is done
as follows:
Recall saved data using Sample Manager and press the save sample button on the
options menu to display the save sample dialogue box. Set the desired save location
and filename using the Save to and Sample Name boxes, respectively and press the
tick to confirm the data export.

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13. SAMPLE MANAGER
Sample Manager is the application used by the Ultrospec 7000/8000/9000 for saving
and recalling data from both the instrument’s internal memory and the instrument’s
USB format. Sample Manager can be accessed from either the main screen using the
Sample Manager button (below left) or from within an application using the Sample
Manager icon on the options menu (below right).

To recall a saved file, highlight the desired file and press the Sample Manager
icon in the right hand corner of the screen. Data will be displayed on the Sample
Measurement screen (see Recalled Files below).
With a USB memory stick inserted it is possible to toggle between the internal and
USB memories using the icon in the left hand corner of the screen. The location of
the displayed data will be indicated by the icon in the top right hand corner.

Sample Manager has been designed to make finding saved files as simple as
possible. Therefore it is possible to arrange files alphabetically, by application or by
date/time saved by pressing the column headers Sample ID, Application and Date,
respectively.
If there are too many saved data files to fit on a single screen this is signified at the
top of the screen, e.g. Page 1 of 2. Scrolling through the screens is achieved using the
up and down arrows at the bottom of the screen.
Note: Sample Manager can only display the first 100 sample data files; if the internal
memory or USB stick contains >100 files these can be viewed be deleting or moving
(USB only) unwanted data.

13.1. Deleting Data From The Internal Memory

To ensure that the internal memory of the instrument does not contain too many
unwanted data files, Sample Manager allows you to delete files. This can be done in
one of three ways:
Deleting a single file: Highlight the file for deletion and press the delete button.
Deleting multiple files: Highlight multiple files and press the delete button.
Deleting all files: Press the ‘Delete all’ icon at the bottom of the screen.
Note: It is only possible to delete data using Sample Manager accessed from the
main screen. Sample Manager does not allow a user to delete sample data files from
a USB memory stick; this must be done using a PC.
Sample Manager allows the user to lock files saved to the internal memory to prevent
the accidental deletion of files containing precious data. To lock files, highlight the
required data and press the lock icon at the bottom of the screen. Locked files are
signified by the lock icon in the right hand column. Once a file is locked selecting
‘Delete’ or ‘Delete All’ does not clear this data from the instruments’ internal memory.

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 To unlock a file, highlight the appropriate locked data and press the lock icon at the
bottom of the screen.
Note: As sample data files saved to a USB memory stick must be deleted using a PC
it is not possible to lock USB sample data using Sample Manager.
To exit from Sample Manager press the ‘Exit’ icon.

13.2. Accessing Sample Manager From The

Main Screen

When accessed from the main screen Sample Manager will display all files held on
the internal memory or USB memory stick and allows the user to lock and delete
files saved to the internal memory. As Sample Manager accessed from the main
screen allows users to delete files from the instrument’s internal memory this option
is disabled for Limited users.
To allow post scan manipulation of saved wavescan and kinetics data, files loaded
from Sample Manager are loaded directly into Trace Manager (see Trace Manager
section for details).
Note: With large numbers of files held on the internal memory there may be a short
delay before Sample Manager opens.

13.3. Accessing Sample Manager From Within

An Application

When accessed from within an application Sample Manager will only display files
belonging to that specific application and only allows users to recall saved data and
lock files.

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13.4. Recalled Files
When recalled, sample data files will display the first sample recorded in a
measurement. To access all sample data within a recalled file press the Sample box
to display a list of all samples contained within the file. Pressing on the desired file
will populate the boxes on the sample measurement screen with the saved data.
Choosing to measure another sample with an old sample’s data displayed simply
updates the sample measurement screen and the appropriate boxes.
Note: Wavescan and kinetics sample data is recalled using Trace Manager. For
details see the Trace Manager section for details.

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14. SAVING METHODS
The Ultrospec 7000/8000/9000 allow users to store methods to both instruments
internal memory and to USB memory sticks. The procedure for saving methods is
described below:
After selecting the desired application and setting the required method parameters
select the Save Method icon from the options menu on the sample measurement
screen. Set the desired file name and save location using the dialogue box shown
below.

Pressing the Folder box produces a list of available save locations. USB will only
appear on the list if a USB memory stick is inserted.
Pressing the Method Name box allows the user to set the desired method name
using alpha numeric text entry.
Press the tick to save and exit or the cross to exit without saving.

14.1. Methods Saved To The Internal Memory

Methods saved to the instrument’s internal memory are stored in either the
Methods or Favorites folders, both of which are accessed via the main screen.
The Biochrom Ultrospec are capable of storing up to 90 methods on the
instrument’s internal memory.

14.2. Methods Folder

The Methods folder is made up of 9 folders each capable of storing up to 9
methods. The method folder icons have been designed to give the user an
indication of the number of methods that are stored in that folder.

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14.3. Renaming Method Folders
Using the Rename Folder icon on the options menu (the left hand icon) it is possible
to rename any of the 9 method folders using alphanumeric text entry.

14.4. Locking Saved Methods

Using the lock folder icon on the options menu (the center icon) it is possible to
add pass code protection to any of the method folders. Locked folders cannot be
renamed and are indicated by a padlock.

Within a methods folder it is possible to add pass codes to individual methods and
to lock them from deletion using the lock icon on the options menu (the center
icon). Locked methods can be unlocked by using the unlock icon on the options
menu (the right hand icon), selecting the desired method and entering the correct
pass code.

14.5. Deleting Saved Methods.

Within a methods folder it is possible to delete saved methods using the delete icon
on the options menu (the left hand icon) and selecting the desired file.
Note: Locked methods must be unlocked to allow deletion.

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14.6. Backing Up Method Folders To USB
With a USB stick inserted it is possible to use the USB icon on the options menu (the
right hand icon) to:

Backup Folder: Copies all methods from a specified folder to a USB memory
stick.
Restore Folder: Copies a backed up method folder from the USB memory
stick to the internal memory.
Backup All Folders: Copies all method folders from the internal memory to a USB
memory stick.
Restore All Folders: Copies all backed up method folders from the USB memory
stick to the internal memory.

14.7. Favourites Folder

The Favourites folder is capable of storing up to 9 user defined methods. Methods
stored in the Favourites folder can be locked and deleted as described above.

14.8. Saving Methods To USB

To save files to a USB memory stick follow the procedure described above and
select USB in the Folder box. The USB option will only appear in the list if a USB
memory stick is inserted.
Methods saved to a USB memory stick will appear in the Ultrospec 7000/8000/9000
Methods folder in the root directory.
Note: Although it is possible to save an unlimited number of method files to a USB
memory stick only 9 can be displayed on the instrument at any one time. As these
will only be read from the Ultrospec 7000/8000/9000 Methods folder, additional
files can be stored in other locations

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15. PRINTING
Printing Sample Data
The Ultrospec 7000/8000/9000 allows users to print sample data in one of three
ways:
Note: Only available printers will be shown in the Print to… options box.

15.1. Internal Printer

Fitting of the internal printer is described in the Ultrospec 7000/8000/9000
Accessories Manual at the end of this manual.

15.2. Print Via Computer (PVC)

Print via Computer (PVC) is an application running under Windows™ to enable the
Ultrospec 7000/8000/9000 to transfer data into a PC environment. From there the
data can be printed or saved in a variety of formats, including graphics and text
formats or as an Excel file. PVC can store data either to a common directory or be
configured to save to independent directories by both file format and connection.
PVC is capable of supporting several instruments simultaneously, limited only by
hardware and the speed of the host system and is able to operate via USB and
Bluetooth simultaneously.
Installation and operating instructions for PVC can be found on the PVC CDROM.

15.3. Bluetooth®
The Bluetooth accessory is a factory fitted option.

15.4. Automatic Printing

The option to print sample data automatically is set under method parameters.
With Auto Print set to on, the print location can be set to one of the available
options.

15.5. Manual Printing

If a method does not require sample data to be printed each time a measurement
is taken it is possible to manually print sample data. This procedure is described
below:
Set the desired print location in Print to… After collecting all required sample
measurements select the Print icon from the options menu on the sample
measurement screen.

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16. Cell Changer
16.1. Operation
With a cell changer connected, the Accessories folder under Settings will contain
the Cell Changer icon. This provides the user with the means to set the default
configuration for the cell changer accessory.
Prompt User
Yes: The Cell Changer parameter screen is displayed as part of the
application parameters, allowing the user to set cell changer
parameters each time an application is run. The default configuration
set here pre-selected.
No: The Cell Changer parameter screen is not displayed as part of
the application parameters. The default settings configured in the
Accessories folder are used.
The Prompt feature is designed to save the user time and effort configuring each
application for the cell changer and will also allow accessory parameter screens to
be skipped on loading applications.
Use As Single Cell
Yes: Stops the cell changer accessory moving, meaning that the cell
position 1 will remain in the sample beam for each measurement.
When enabled, the options related to cell changer are removed from
the screen. As this option allows the user to use the cell changer as a
standard single cell holder this removes the need to keep swapping
accessories.
No: The cell changer accessory will be used.
Operation
Automatic: By pressing the Start Measurement button the unit will collect the
number of samples specified automatically.
Manual: By pressing the Start Measurement button the unit will measure
the first sample, display a prompt to start next measurement,
measure the second sample, prompt display a prompt to start next
measurement etc.
Number Of Samples
Allows the user to set the number of samples to be measured using the numeric
entry box. In Fixed Wavelength applications, if the number of samples is >8 the user
will be prompted to load the cell changer after the first 8 samples. In Wavescan
and Kinetics the maximum number of samples is 8.
Note: Number of Samples refers to the number of samples only and does not
include standard or reference measurements.
Prompt For Cell Pos
On: After pressing the Start Measurement button the software will display
the positions each sample should be placed.
Off: The unit will perform the measurement without displaying this
message.
The Cell Changer parameter screen that is displayed in the application method
parameter screens is shown right (with use as single cell on or off). All options are
as described above.

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Taking A Measurement With A Cell Changer
When using the cell changer the software will not display the Take Reference
button.
Ultrospec 7000/8000/9000 As these instruments continually reference against the
reference cell holder there is no requirement to perform
a reference measurement before collecting sample
data.
The icon in the top right corner of the sample measurement screen indicates the
cell position that is in the sample measurement beam.

16.2. Saving Methods & Results

Any method saved with the cell changer connected will save the inputted accessory
parameters. If a user attempts to use a cell changer method without this accessory
connected the software will display the warning, 'The following accessories are
missing: Cell Changer The cell changer must be fitted before this method can be
loaded.'.

16.3. Incorrect Fitting

If the cell changer is fitted incorrectly it will not be recognized during the instruments’
start up calibration tests. If this occurs the instrument should be switched off,
disconnected from the mains and the accessory refitted, paying close attention to
the internal accessory connector.

16.4. Using The Cell Changer To Create

A Standard Curve
Pressing the take measurement button when on the Replicates screen will
re-measure the highlighted replicate only. This measurement will always be made
from cell position 1 of the cell changer.

Pressing the take measurement button on the construct standard curve screen will
re-measure all standards whether measuring replicates or not.

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17. Sipper
The Sipper and Flowcell accessories for the Ultrospec range of instruments are
designed as an aid to speed up sample handling. The system comprises a peristaltic
pump head that is controlled by the software to sip a known, calibrated volume
of sample and move this into a Flowcell which is in the sample position of the
spectrophotometer.
The Sipper can be set up and used within all applications and Sipper parameter are
stored as part of an application method.

17.1. Setting Sipper defaults

It is simple to customize the default parameters of the Sipper for a particular
installation by setting all of the default values. Every application will then load
these defaults each time the Sipper page is opened however they can be changed
within the application. These default values are set within the instrument under the
Settings, Accessories, Sipper Icons and are stored even when the instrument is
switched off.

Sip Volume
• Amount of sample to be sipped up. Range of values = 0.3 ml to 50 ml.
Note: working with volumes less than 1 ml will require careful setting of the air gap to
minimize cross contamination between samples.
Air-gap
• Gap between successive samples which is set by pumping air after the tube has
been removed from the sample liquid – set in cm of tubing. Range of values = 0
to 200 cm.
The Sipper has the ability to program an air gap between samples to help minimize
cross contamination and to allow users flexibility to work with different volumes and
lengths of Sipper inlet tubing. When the start button is pressed the Sipper pumps up
the volume of sample that is set within the method and the user is then prompted to
remove the tubing from the sample. After a short delay the pump starts again and
the sample is moved along the tubing and air is sucked into the end of the tubing.
The default air gap set in the software is 40 cm which has been set to work with a
65 cm length of tubing on the Flowcell inlet. If a different length of tubing is used then
a different default air gap will need to be set. To calculate this default air gap:
• Measure the length of tubing connected to the Flowcell tubing inlet and take
20 cm from this value.
• From the home page go into a single wavelength method and enter through until
you get to the Sipper parameter page. Set the volume to 1 ml and the air gap to
the value measured above. Set the settle time to 1 second and Auto read to off.
• Sip a sample of water, remove the tube from the sample when prompted and
note the position of the end of the sample slug – you need this to be stopping
above the inlet position to the Flowcell. For a 1 ml sample volume you should
have this stopping 15-25 cm above the Flowcell inlet. To move the position of the
sample press the menu icon, parameters icon, step through the method until you
reach the Sipper parameters and adjust the air gap value. Increasing the value
will move the end of the sample closer to the Flowcell inlet, lowering the value
will move it further away.
• Once the value has been determined exit the Single wavelength application, go to
Settings, accessories, Sipper and enter this value in the default air gap box.
Settle time
• Amount of time before the system is ready to measure after the sample has
entered the Flowcell. Value entered in seconds. Range of values = 1 to 30 seconds
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Sip Mode
• Choice of Waste or Return. Waste mode turns the pump head in one direction
and the sample goes to waste after measurement. If return is set then pressing
the start button a second time will reverse the motor and the sample will be
pumped back out of the inlet tube into the sample vessel. Cross contamination
between samples will be worse if return mode is used.
Auto Read
• Auto read on will automatically start the measurement in the current application
after the settle time has passed. If Auto read is off the user will manually have to
press the reference or run icon for each measurement.
If you press the Settings, accessories, Sipper icons as well as the defaults that have
been set above there are other icons at the bottom of the screen for Calibration of
the Sipper volume and washing of the Sipper.

17.2. Calibration
The Sipper software contains a routine that allows users to calibrate the Sipper
to ensure that the volume of liquid set within the method matches the actual
volume being sipped. Before starting the calibration routine check that it is actually
necessary:
• Sample volume – set up a single wavelength method which includes the Sipper
and set the sip volume to 1 ml. Fill a 10 ml measuring cylinder, sip 5 times from
the measuring cylinder taking notice of the messages regarding removing the
tube for the air gap. After 5 sips divide the volume of sample sipped by 5 – the
value should be approximately 1 ml. If the value varies by more than 0.2 mls then
re-calibrate the Sipper as below:
• Fill a 10 ml graduated measuring cylinder with water up to the 10 ml line. Press the
calibrate icon, put the end of the sample tube into the measuring cylinder, press
the start button and the Sipper will start pumping. Once this has finished repeat
4 more times. Read off from the measuring cylinder the actual amount that has
been sipped and enter it into the box on the screen and then press the Tick icon
to exit.
If you need to rest the calibrations to the default value then sip once and enter the
value of 1 ml.

17.3. Wash mode

This enables you to wash the Sipper at the end of a batch of samples. Press the wash
icon, dip the sample tube into water and allow it to flush the system.
Using the Sipper within an application
All Sipper parameters can be set as part of a method, the following screen will appear
as part of the application method when the Sipper is connected. The screen will open
using the default Sipper values stored under the Settings, Accessories, Sipper Icons.
The process of using the Sipper is as follows:
1. Choose the application that you want to run by pressing the relevant icon.
2. Set up the instrument parameters, data handling parameters and then Sipper
parameters. The Sipper parameters shown will be the ones that are set on the
Sipper default page. These Sipper parameters can be changed as part of this
application method and the new values saved as part of the method.
3. Put the sample tubing into the reference solution and press the silver button on
the front of the Sipper. System will sip the set volume and then prompt you to
remove the sample tubing.
4. System will then pump the set air gap and then wait the set settle time. If auto
read is on the system will automatically reference, if it is off then press the
clear cuvette icon to reference.

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 5. Put the sample tube into the sample, press the silver button on the front of
the Sipper. System will sip the set volume and then prompt you to remove the
sample tubing.
6. System will then pump the set air gap and then wait the set settle time. If auto
read is on, the system will automatically run the sample, if it is off then press
the orange cuvette icon to run the sample. Repeat for subsequent samples.

17.4. Cleaning/Maintenance/Troubleshooting
To ensure good performance from your Sipper system it is essential that routine
maintenance is carried out.
After batch of samples
• Run the Sipper Wash mode pumping deionized water, for 1 minute then remove
sample tubing and pump air until all liquid is pumped into the waste vessel.
At end of day
• Open up pump head to relax pressure on pump head tubing.
Weekly
• Check pump head tubing for signs of wear – replace if necessary.
• Check all connections for leaks.
• Depending upon types of sample being run it may be advantageous to clean the
Flowcell properly (e.g. if “sticky” protein solutions are being run). Unscrew the 2
connectors, take the Flowcell out of the instrument, fill with a detergent solution
and leave to soak overnight. Empty and then flush with deionized water for 1
minute using the wash mode.
Problems with Sipper systems are generally caused by wrongly set parameters or
poor maintenance. Typical faults and their cures include:
Sample not being sipped
• Check pump head closed.
• Check pump head tubing for damage.
• Check Flowcell is connected and connectors are tightened.
• Check PTFE tubing is pushed firmly into pump head tubing.
• Check PTFE tubing is not crushed or damaged.
• Check Flowcell for blockages.
• Check waste pipe for blockages.
Sample being pumped right through Flowcell
• Check air gap and reset to correct value.
Bubbles in Flowcell
• Check Flowcell connectors are tightened.
• Clean Flowcell with detergent solution.
Inconsistent readings
• Check volume being sipped – try increasing the volume.
• Adjust air gap so the end of the sample is closer to the Flowcell inlet - more of the
sample flushes the previous sample out of the Flowcell.
Wrong volume being sipped
• Check Sipper calibration.

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18. TECHNICAL
SPECIFICATIONS
Parameter Ultrospec 7000 Specification Ultrospec 8000 Specification Ultrospec 9000 specification

Configuration Dual Beam Dual Beam Dual Beam

Lamp Xenon Tungsten/Deuterium Tungsten/Deuterium

Wavelength Range 190 nm to 1100 nm 190 nm to 1100 nm 190 nm to 1100 nm

Wavelength +/- 0.5 nm across wavelength +/- 0.3 nm across wavelength +/- 0.3 nm across wavelength
Accuracy range range range

Wavelength
+/- 0.1 nm +/- 0.1 nm +/- 0.1 nm
Reproducibility
Variable (0.5 nm, 1 nm, 2 nm,
Bandwidth 2 nm 1 nm
4 nm)
Toluene in Hexane
>2.0 >2.0 at 1 nm bandwidth
EP Resolution

<0.025% T at 220 nm using NaI <0.025% T at 220 nm using NaI

<0.050% T at 220 nm using NaI
Stray Light and 340 nm using NaNO3 and 340 nm using NaNO3
and 340 nm using NaNO3
<1% T at 198 nm using KCl <1% T at 198 nm using KCl

Photometric Range -4 A to 4 A -4 A to 4 A -4 A to 4 A

+/-0.002 A at 0.5 A +/-0.002 A at 0.5 A +/-0.002 A at 0.5 A

Photometric
+/-0.004 A at 1 A +/-0.004 A at 1 A +/-0.004 A at 1 A
Accuracy
+/-0.006 A at 2 A +/-0.006 A at 2 A +/-0.006 A at 2 A

Photometric
+/-0.002 A at 1A +/-0.002 A at 1A +/-0.002 A at 1A
Reproducibility

Scan Speed >2400 nm/min >2400 nm/min >2400 nm/min

+/-0.0003 A/hr in precision +/-0.0003 A/hr in precision

Zero Stability +/-0.001 A/hr
mode mode

< 0.00020 A RMS @ 0A at < 0.00005 A RMS @ 0A at < 0.00005 A RMS @ 0A at

Noise 700 nm and 500 nm over 20 700 nm and 500 nm over 20 700 nm and 500 nm over 20
measurements measurements measurements

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19. CHANGING
TUNGSTEN AND
DEUTERIUM LAMPS
Lamps should only be removed after they have cooled completely, attempting to remove lamps before they have
cooled may result in injury.

1. Switch off the Ultrospec 8000/9000 and ensure that the instrument is
disconnected from the mains.

2. From the back of instrument remove the screws securing the lamp chamber (this
is located above the fan grating).

3. Remove the lamp chamber lid to reveal both the Tungsten and Deuterium lamps
(see below).

Tungsten Lamp Deuterium Lamp

LAMP CHAMBER OF THE Ultrospec 8000 & 9000

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Removing & Replacing The Tungsten Lamp
To remove the tungsten lamp, pull the metal clip away from the tip of the lamp and
carefully pull the lamp to remove.
To insert the new lamp, pull the metal clip away from the housing to provide space
for the new lamp to be inserted and carefully insert the pins of the lamp into the
lamp housing. When inserted in the housing carefully place the metal clip on the tip
of the lamp.
Note: When replacing a tungsten lamp, the lamp envelope must not be touched. If
the envelope is touched during installation the lamp must be thoroughly cleaned with
a light cloth.
Removing & Replacing The Deuterium Lamp
The Deuterium lamp is removed by carefully pulling the lamp upwards. To insert the
new lamp, line up the lamp pins with the holes in the lamp housing and push into
place. The Deuterium lamp can only be inserted in the correct position.
Note: After installation the Deuterium lamp must be thoroughly cleaned with a light
cloth to remove any marks.
Replacing The Lamp Chamber Lid
After the new lamp has been installed the lamp chamber lid should be replaced and
screwed in place. The instrument will now be ready to use.
Note: A new baseline should always be measured after installing a lamp. This
procedure is described in “8.6. Instrument Settings” on page 18. The baseline
should only be collected after the lamp has warmed up sufficiently (at least 30
minutes).
Resetting Lamp Life
With new lamps installed it is necessary to reset the lamp life on the software, this
is done as follows:
From the main page, select Settings followed by Instrument Settings.

Select the lamp status icon at the bottom of the screen and press the appropriate
Reset Lamp Life icon to reset the lamp life information for the desired lamp. The
icons are detailed in the Table of Icons section.
Note: Only users with Administrator privileges are capable of resetting lamp life
information. For PC variants, lamp life can be reset using Datrys software. See
Datrys user manual or on-line help for more details.

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20. TABLE OF ICONS
Icon Title Function

Back arrow Returns the user to the previous screen.

Forward arrow Advances the next screen in a sequence.

Displays the relevant options menu, the exact content of the menu will depend upon
Open options menu
the location.

Page down Allows the user to navigate to the next page.

Page up Allows the user to navigate to the previous page.

Used in the wavescan and kinetics applications to move the cursor left. The position
Cursor left
of the cursor and the corresponding x and y values are displayed above the scan.

Used in the wavescan and kinetics applications to move cursor right. The position of
Cursor right
the cursor and the corresponding x and y values are displayed above the scan.

When used in the CyDye DNA application this toggles the data displayed between
Toggle data viewed/reset
DNA and dye data. Under Instrument Settings this will reset a value.

Delete all Deletes all saved data/methods. Delete all is a two stage process.

Delete Deletes the highlighted data/method. Delete is a two stage process.

Used in Equation Editor. This allows users to add thresholds (pass/fail) limits to their
Thresholds
results.

OK/accept Used to confirm/accept any changes.

Exits from an application or screen. If exit is selected without saving, any changes
Exit
will be lost.

Lock Locks sample data file/method folder against accidental deletion.

Unlock Unlocks a locked method folder.

Used in Sample Manager to access sample data files stored on the instrument’s
Instrument internal memory or to indicate that the data being displayed is from the internal
memory.

Add linear section Used in the kinetics applications to view a line of best fit on the scan.

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 Icon Title Function

Used in kinetics applications to view data in a specific section. It is possible to add t0

Section
through to t7.

Methods saved internally can be stored in one of nine method folders (each capable
Method folder
of storing up to nine individual methods).

Accessed via the options menu on the methods screen, this allows the method folder
Rename method folder
to be renamed.

Used in the nucleic acid applications DNA, RNA and Oligo this allows the user to view
Toggle view scan on or off
a survey scan of the last sample run (in the region 220–320 nm).

Accessed via the options button on the sample screen. Pressing this button toggles
Toggle auto print on or off
auto print on and off.

Accessed via the options button on the sample measurement screen. Pressing this
View method parameters
button takes the user back to the method parameters.

Accessed via the options button on the sample measurement screen. Pressing this
Print data
button prints the sample data.

Accessed via the options button on the sample measurement screen. This allows a
Save method parameters
method to be saved to a location specified by the user.

Accessed via the options button on the sample measurement screen. This allows
Save sample data
sample data to be saved to a location specified by the user.

Accessed via the options button on the sample measurement screen. Displays the
Sample Manager
sample data held in either the internal memory or on a USB memory stick.

Accessed via instrument settings. This displays instrument information such as

Instrument Information
product name, serial number etc.

Accessed via instrument settings. This allows the user to set the default bandwidth,
Instrument Settings
save new baselines and view the date of the last service.

Instrument Status Accessed via instrument settings. This displays the current status of the instrument.

Accessed via instrument settings. This displays the lamp status and allows the user
Lamp Settings
reset the lamp life (8000 & 9000 only).

Save instrument options Accessed via instrument settings. This saves the instrument options.

Displayed on the status bar. This indicates that the cell changer is connected and the
Cell changer number
cell position that is in the sample beam.

Displayed on the status bar. This indicates that the instrument will automatically
Auto print - Bluetooth
print all sample data to the Bluetooth device.

Auto print - internal Displayed on the status bar. This indicates that the instrument will automatically
printer print all sample data to the internal printer.

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 Icon Title Function

Displayed on the status bar. This indicates that the instrument will automatically
Auto print - USB
print all sample data to the USB printer.

Deuterium lamp off Displayed on the status bar. This indicates that the Deuterium lamp is off.

Deuterium lamp fail Displayed on the status bar. This indicates that the Deuterium lamp has failed.

Deuterium lamp on Displayed on the status bar. This indicates that the Deuterium lamp is on.

Deuterium lamp warming Displayed on the status bar. This indicates that the Deuterium lamp is warming up.

Tungsten lamp fail. Displayed on the status bar. This indicates that the Tungsten lamp has failed.

Tungsten lamp off Displayed on the status bar. This indicates that the Tungsten lamp is off.

Tungsten lamp on Displayed on the status bar. This indicates that the Tungsten lamp is on.

Tungsten lamp warming Displayed on the status bar. This indicates that the Tungsten lamp is warming up.

Xenon lamp failed Displayed on the status bar. This indicates that the Xenon lamp has failed.

Displayed on the status bar. This indicates that the instrument is performing a
Instrument busy
measurement.

Printing to Bluetooth Displayed on the status bar. This indicates that the instrument is printing to a
device Bluetooth device.

Displayed on the status bar. This indicates that the instrument is printing to the
Printing to internal printer
internal printer.

Displayed on the status bar. This indicates that the instrument is printing to a USB
Printing to USB
printer.

Toggle view standard When used in standard curve applications i.e. Lowry protein assay, this toggles the
curve sample measurement screen to display or hide the standard curve.

Replicates Used in standard curve applications to collect data from a group of replicates.

Take sample
Commences a sample measurement.
measurement

Take reference
Commences a reference measurement.
measurement

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 Icon Title Function

Used in text entry mode to move the cursor backwards (left) and delete any
Backspace/delete
unwanted characters.

Forward space Used in text entry mode to move the cursor forwards (right).

Lower case Selects lower case letters when in text entry mode.

Symbols Selects symbols when in text entry mode.

Upper case Selects upper case letters when in text entry mode.

Numeric Selects numeric entry when in text entry mode.

Used in the wavescan and kinetics applications. This allows the user to overlay up
Trace Manager to 8 samples data files and to choose what type of data is displayed i.e. raw data,
smoothed data, 1st derivative.
Used on the Sample Manager screen to access data stored on a USB memory stick.
USB Used in the options menu in the methods folder to allow the user to backup methods
to a USB memory stick.

Displayed under User Access, this allows anyone with Administrator privileges to add
Add user
another user to the instrument.

Displayed under User Access, this allows anyone with Administrator privileges to
Delete user
delete users from the instrument.

Displayed under User Access, this allows anyone with Administrator privileges to edit
Edit user
currently users’ parameters.

Used in the wavescan and kinetics applications. This allows the user to zoom into a
Zoom in
specific region of a scan.

Used in the wavescan and kinetics applications. This allows the user to zoom out and
Zoom out
return to the original scan.

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21. GLOSSARY OF
BOXES
Box Function

Toggles between on and off. Used in all applications to set whether sample data is printed
automatically or not.

Toggles between on and off. Used in all applications to set whether sample data is saved
automatically or not.

Can be toggled on and off. Used in nucleic acid and protein measurements to subtract
the absorbance value at 320 nm. This is done to allow for the effects of turbidity, high
absorbance buffer solutions and the use of reduced aperture cells.

Set by numeric entry. Used in CyDye DNA measurements only and enables the user to
specify the wavelength of background correction.

For variable bandwidth instruments (Ultrospec 9000) this gives the option to set the
bandwidth to 4, 2, 1 or 0.5 nm for a measurement. For fixed bandwidths instruments
(Ultrospec 7000 & 8000) this box will be greyed out.

Used in Tm calculation to set the sequence of bases. The bases A, C, G, T can be added in
DNA mode and the bases A, C, G, U can be added in RNA mode. Bases are grouped in threes
to improve readability.

Used in Tm calculation to toggle between DNA and RNA base types.

Used in User Interface in Settings to set the brightness of the screen.

Numeric entry, used in Tm calculation only.

Buffer molarity = buffer molarity + total molarity of salt (moles / L).

Used in all standard curve applications to set the method used to collect the standard
curve. Options are for Standards or Manual.

Set by numeric entry, used in the CyDye DNA application only. This is the correction factor
applied to the absorbance of the dye at a specified wavelength.

Used in Tm calculation only this allows the user to add the type of counter ion used. The
options are sodium (Na), potassium (K), triethylammonium (TEA) or other. If other is selected
the molecular weight of this counter ion must be added using Other MW.
Used in all standard curve applications this is the curve fit that will be applied to the
standards’ absorbance values. Options are Zero Regression, Regression, Interpolation and
Cubic Spline.

Alphanumeric entry for custom dye name, used in CyDye DNA only.

Numeric entry. This is the delay required before a kinetic measurement commences.

Numeric entry. This is used in nucleic acid and protein applications to compensate for the
absorbance of highly concentrated samples.

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 Box Function
Used in wavescan only, this switches display of peak cursors on and off. Peak cursors show
vertical dashed lines displaying the measured peak height and horizontal dashed lines
showing the peak width.

Numeric entry. This is the duration over which a kinetic measurement is performed.

Used in CyDye DNA application only. This is the first dye type used in the measurement.

Used in CyDye DNA application only. This is the second dye type used in the measurement
(where applicable).

Numeric entry for CyDye DNA application only. This is the extinction coefficient of the
specified dye. Note for dyes included in the Ultrospec software these values are not editable
and the box will be greyed out.
Numeric entry to 3 decimal places. In concentration and nucleic acid measurements
multiplying absorbance readings by this factor gives the concentration value. In kinetic
measurements the result is calculated by multiplying this factor by absorbance, delta
absorbance or the slope.
Used in wavescan measurements only. This determines the sensitivity of the peak or valley
detection i.e. sensitive will detect more peaks or valleys than course. Options are; Off,
Coarse, Sensitive or Custom (when custom is selected the minimum peak height and width
must be entered).

Toggles between wavelength and absorbance, used in wavescan measurements only. This
determines how features will be ordered in the peak/valley table below the scan.

Toggles between peaks and valleys, used in wavescan measurements only. This determines
what feature type will be detected.

Used in User Access to set the group a user will belong to and what access they will be
granted.

Used in all applications. This is the duration the instrument will take a reading at an
individual wavelength. The longer the integration time, the greater the signal to noise ratio
and the greater the accuracy.

Numeric entry. This is the interval at which serial kinetics readings will be taken.

Used by the Ultrospec 8000 & 9000 in all applications to toggle between Precision and Pulse
mode.

Numeric entry. This is the upper limit of a wavescan measurement. Note that when using
the Ultrospec 7000/8000/9000 the max wavelength must always be greater than the min
wavelength by at least the step value.

Toggles between the kinetics measurement modes, serial and parallel.

Numeric entry. This is the lower limit of a wavescan measurement. Note that when using
the Ultrospec 7000/8000/9000 the max wavelength must always be greater than the min
wavelength by at least the step value.

Used in the Single Wavelength, Kinetics and Protein A280 applications to set the required
measurement mode.

Used in CyDye DNA application only, this sets the nucleic acid used in the measurement.

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 Box Function

Toggles between 1 and 2. Used in CyDye DNA application only to set the number of dyes
used in the measurement.

Numeric entry. This option is only used if the counter ion type in the Tm calculation is set to
Other.

Used in User Access to set a password for new users.

Used in the nucleic acid applications, Protein A280 and Protein UV. This is the pathlength of
the cuvette used in the measurement. Options are for 10, 5, 2 and 1 mm.

Toggles between yes and no. Used in Tm calculation to set if the sample to be measured is
phosphorylated or not.

Numeric entry to 3 decimal places. Used in Tm calculation to sets the primer concentration
in pmole/mL.

Used in all applications to set the desired print location. Only available printers are
displayed.

Toggles between On and Off, used in Equation Editor only. With Prompt on the
measurement will proceed as follows: measure wavelength 1, prompt for sample, measure
wavelength 2, prompt for sample etc.
Used in all standard curve applications. This is the number of times a standard
measurement is repeated before the mean of these values is plotted on the standard curve.
Options are off (1 measurement), 2 or 3.

Used in wavescan measurements, this determines how many samples will be overlaid on
the graph. Options are off, 2 to 8.

Used in kinetic measurements, this sets the number of samples that will be measured
during the method. Options are 1, 2 or 3.

Used in all applications to set the desired save location. Only available locations are
displayed.

Toggles between on and off. Used in DNA/RNA/Oligo measurements this sets whether, as a
further analytical tool, the instrument will also perform a scan over the wavelength range
220-320 nm.
Used in wavescan measurements, this determines the speed at which the scan is
performed. Options are Slow, Medium, Fast or Integration. Note that when integration is
selected the user will be prompted to set the integration time (see box above).

Used in User Interface in Settings to set the time before the screen-saver will be
displayed.

Used by the Default Administrator in User Access to set if user login will be displayed or not.

Used in all standard curve applications. This is the number of standards that will be used to
create the standard curve; options are from 1 to 9.

Numeric entry to 2 decimal places. Used in all standard curve applications this is the
concentration of the standard.

Used in wavescan measurements, this determines the interval at which wavescan

measurements are made (in nm). Options are for 0.1, 0.2, 0.5 or 1 nm. Smaller intervals give
greater detail but lead to longer scan times.
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 Box Function

Used in User Interface in Settings to set the text entry mode used for alphanumeric text
entry.

Used in applications that give a concentration result. Units are entered via either
alphanumeric entry or from a list of options.

Used in User Access when creating a new user.

Numeric entry to 3 decimal places, this is used in the CyDye DNA application and is the
volume of the probe in µL.

Numeric entry to 1 decimal place and is used in all fixed wavelength applications to
determine the wavelength at which the measurement will be performed.

Numeric entry to 1 decimal place. Used in the CyDye DNA application, this is the
wavelength at which the absorbance of the dye will be measured. Note for dyes included in
the Ultrospec software these values are not editable and this box will be greyed out.

Numeric entry to 3 decimal places. This is the maximum value of the Y axis shown during
a kinetics measurement. Note the graph will automatically re-scale at the end of the
measurement to give the optimum Y max.

Numeric entry to 3 decimal places. This is the minimum value of the Y axis shown during
a kinetics measurement. Note the graph will automatically re-scale at the end of the
measurement to give the optimum Y min.

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Ultrospec™ 7000/8000/9000
Accessories

5061-046 Rev1
1. Installation
Before installing any accessory in the Ultrospec 7000/8000/9000 you must ensure
that the instrument is disconnected from the mains.

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2. PASSIVE
ACCESSORIES
Accessories that do not interact with the instrument’s software are named passive
accessories. Their installation is described below:
To allow easy access to the thumbscrew at the front of the accessory open the cell
chamber lid and lift out the front panel (below left).

With the front panel removed the accessory is removed and replaced as outlined
below:
1. Loosen the front thumb screw by turning anti-clockwise.

2. With the thumb screw fully unscrewed, lift the accessory and gently pull
forward.

3. To insert the desired accessory, lift the front end, slide into the brackets at
the back of the cell chamber (indicated by the two arrows) and tighten the
thumb screw by turning clockwise.

With the accessory inserted simply replace front panel, switch on the instrument and
it will be ready to use.

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2.1. Single Cell Holder (supplied with unit)
The single cell holder is designed to take measurements of 10 mm pathlength
cuvettes. All Ultrospec 7000/8000/9000 are supplied with a single cell holder as
standard.

2.2. Variable Pathlength Cell Holder 80-7100-05

The variable pathlength cell holder is designed to use 1, 2, 5, 10, 20, 50 & 100 mm
pathlength cells. To accommodate different pathlengths the clips should be moved to
secure the cell and spacers used as required.

2.3. Water Thermostatted Cell Holder 80-7100-03

The water Thermostatted cell holder is designed to work with water circulators to
achieve constant temperatures in the range 5 to 80°C. The accessory has to be
connected to an external fluid circulator so that the water flows into the bottom of
the cell holder (the right hand inlet) and flows out through the top of the cell holder
(the left hand outlet).

2.4. Film Holder 80-7100-12

The film holder is designed to measure the absorbance of solid materials including
thin flexible sheet materials such as plastic, acrylic, gelatine. Applications also include
the quality control of tinted optical lenses.

2.5. Test Tube Holder 80-7100-11

The test tube holder allows samples to be measured in a test tube of between 10 and
24 mm diameter and up to 160 mm tall.

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2.6. Peltier Controlled Fluid Circulatior 80-7100-50

2.6.1. General Information

2.6.1.1. General Warnings
• Check the voltage selector
• Always disconnect the mains plug before starting any work inside the instrument
• Set the temperature to the required values on power on
• If using substances dangerous for health and the environment, observe the laws
and the standards in force in the laboratory where this instrument is used
• If using flammable or explosive substances take the necessary precautions

2.6.1.2. Quality, Reliability and Safety

This equipment has been designed with emphasis on QUALITY, RELIABILITY and
SAFETY, and we will accept responsibility for these aspects only if the following
conditions are met:
• Electrical installation of the room or building in which the equipment is to be used
must comply with regulations specified in the country where the equipment is to
be used.
• The equipment must be used in accordance with the instructions for use provided
by Biochrom.
• All modifications and repairs to the equipment must be carried out by Biochrom
or its authorized agents.
• Modifications must not be carried out unless they conform to approved
Engineering Service Information issued according to the appropriate Biochrom
procedure.
• The equipment installation must be carried out in accordance with local
requirements for responsibility and warranty.

2.6.2. Instrument Description

The Controller is a Peltier effect thermostatting system using an internal sealed liquid
circuit allowing full compatibility and connection to all thermostattable accessories.
The Peltier effect is based on the reversed thermoelectric effect. This is a
phenomenon in which a temperature difference is caused by a flow of current
through a closed circuit consisting of two different metals.
The Controller provides temperatures ranging from 20°C to 60°C with ± 1°C stability
and ± 0.1°C repeatability. The features of the Controller include:
• Peltier effect for heating and cooling the liquid of circulation
• Internal flow pump to circulate the liquid
• The Controller can operate in either manual or remote control via a USB port
• T
 he Controller is supplied with one set of thermally insulated connection tubes to
connect the Controller to any thermostattable accessory
• The Controller is supplied with a water level sensor to ensure correct operation
• T
 he Controller is supplied with high temperature sensor to avoid damaging the
system and malfunctions

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2.6.2.1. Controller front and rear panel
The front and the rear panel have grids to dissipate the heat generated in the
unit. Two fans force the air movement. These grids must be free to guarantee the
instrument specifications.
The front panel features the display with keypad.
The rear panel features the mains power connection with mains voltage selector, the
USB connector for remote control, the mains switch and the “Water Fill” inlet and
outlet connections.
2.6.2.2. Specifications
2.6.2.2.1. Keypad/Display Unit
The keypad/display unit has a LCD screen. All programmable parameters can be
displayed in specific menus.
Three buttons are used to access the various functions and change the set
parameters.
2.6.2.2.2. Programmable Parameters
• Temperature
2.6.2.2.3. Displayed Values
• The current thermostat temperature
• The set temperature
• The heating/cooling power
2.6.2.2.4. Operating Specifications
• Temperature range from 20°C to 60°C
• Temperature accuracy better than ± 0.15°C from 20°C to 60°C
• Temperature repeatability typically ± 1°C
• Temperature stability typically ± 0.1°C
• Specifications valid for ambient temperatures from 15°C to 35°C
2.6.2.2.5. External Control Possibilities
• USB as standard.
2.6.2.2.6. Dimensions
Width: 170 mm Height: 280 mm Depth: 430 mm Weight: 6 kg
2.6.2.2.7. Electrical data
• Mains supply: 115/120 V or 220/240 V AC 10% (factory setting 220/240 V)
• Frequency: 50/60 Hz
• Power: 120 VA

2.6.2.2.8. Description of Symbols
CAUTION (Refer to accompanying documents).
Symbol identifying the use of substances dangerous for health and environment. For these substances reference
must be made to the laws and standards in force in the laboratory where this instrument is used. If using flammable
or explosive substances take the necessary precautions.
Note: Connection to the protective ground is ensured through the power supply cable
which has to be in accordance with CEE 7 (IEC 23-5).
2.6.2.2.9. Environmental conditions
Performance and safety of the Controller are guaranteed at all times if it is operated
under the following environmental conditions:
• Installation category II with smaller transient over voltages (standard IEC 664)
• Pollution degree 2 (standard IEC EN 61010-1)
• The instrument is designed for internal use and altitudes below 2000 m
• Mains voltage fluctuations must not exceed 10% of the nominal voltage
• In locations where the relative humidity is lower than 80%
• In locations free from dust or vapours of solvents and acids

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• Room temperature between 10°C and 35°C
2.6.2.3. User interface
The menu-driven interface of the Controller allows the user to set the temperature
and to view the configuration.
Three buttons are used to access the various functions and change the set
parameters.
The multi-functional Controller with its display is described below under manual
operation.

2.6.3. Installation
2.6.3.1. Checking the serial number
The plate containing the serial number is located on the rear panel at the base of the
unit. Check that this number is identical to the serial number on the delivery note. If
not, please inform Biochrom immediately.

2.6.3.2. Checking mains supply and fuses

The Controller is factory set to operate at 220 VAC.
For operation at a voltage of 120 VAC, the voltage selector at the rear of the
Controller unit must be reset as described below.
Power supply Type of fuse - 250 V
240 V T 1 A, slow-blow
120 V T 2 A, slow-blow
Adjustment for frequency change between 50 and 60 Hz is not necessary.

Voltage selector
with fuse

Main switch

Fig. 3-1: Selecting the voltage

2.6.3.2.1. Changing the Mains Voltage Setting and Fuses
The voltage set is shown in the window of the voltage selector below the mains input
connection. To change this setting switch off the unit at the mains switch, remove the
mains cable and proceed as follows:
Slide out the fuse holder by inserting a small screwdriver alternatively into the two
slots at the left and right and pulling it out of the housing.
Remove the original fuses and replace with those of correct rating (see above) and
push the holder back in position.
Move the slider of the voltage selector with a screwdriver to the desired value. The
new selected voltage will be now visible.

2.6.3.3. Instrument set-up

2.6.3.3.1. Start up
The Controller is supplied completely assembled. It is only necessary to make the
appropriate connections.
Before starting the Controller you should familiarize yourself with the key functions.
• Position the Controller at a suitable position in your system.
• Leave at least 5 cm in front and the back of the Controller for free air circulation.

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• Unscrew the tap on the “Vent” connector.
• Mount the “Vent” connector supplied with the instrument.
• Connect the supplied tubes to “Water in” and “Water out” fast connections.
• Connect the tubes to the accessory to be thermostatted.
• Switch on the Controller.
• The instrument initializes and after one minute it is ready to go.
• Check the system for water level (“Water level alarm sensor).
2.6.3.3.2. External Connections
The Controller has no special electrical external connections which would allow relay
control etc.
Operations are performed either manually or via remote control using the USB
connection.
Contact Biochrom for further information about the remote control functions.

2.6.4. Operating Instructions

2.6.4.1. Manual operation
Main page and functions of the buttons
Page Display L button Middle button R button
Stand by Stand by On
Current temperature Modify the
Normal status Set temperature Menu Off temperature
Heating / cooling power (R) setpoint
Main
Temperature setpoint Flashing selected parameter Down Up Change
Reset alarm /
Alarm status Alarm description Menu Beep on / off
Change (1)
Menu Menu selection Scroll Select Exit
(1) Only if the manual alarm reset option has been configured
Menu page and functions of the buttons
Menu Description L button Middle button R button
Parameter User parameters Scroll Select Exit
Configure Configuration parameters Scroll Select Exit
Diagnostic Diagnostic values Scroll Select Exit
Parameters setting
User parameters and functions of the buttons
Number Description Default value L button Middle button R button
P-01 Temperature unit of measure °C Scroll Select Change
P-02 Auto start (after switching on) NO Scroll Select Change
P-03 Contrast 5 Scroll Select Change
P-04 Beep on/off YES Scroll Select Change
P-05 Manual alarm reset NO Scroll Select Change

Configure parameters
A password is required to enter this menu.

CAUTION: all these parameters are correctly set in the factory: no changes should be made by the user.

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Diagnostic parameters
Description Unit of measure
Cell temperature °C
Radiator temperature °C
Water resistance Kohm
Power %
Cell voltage Volt

2.6.5. Maintenance
The Controller requires very little routine maintenance by the user.

Any operation that requires the units to be opened must only be performed by Biochrom technicians or
authorized personnel.

Always unplug from the mains when opening the units.

2.6.5.1. Cleaning the instrument
For normal cleaning operations on the instrument only use a cloth dipped in water or
neutral detergent, do not use organic or abrasive solvents.
2.6.5.2. Water level alarm
Check for signs of water level. It is recommended that this is done prior to starting
analysis. If a “Water level” alarm is signalled immediately check for spillage in the
accessory compartment and remove it with appropriate measures. Using the refilling
bottle supplied to fill the system with liquid via the inlet or outlet connectors until the
light turns off.

2.6.6. Troubleshooting
The Controller is able to indicate malfunctions and incorrect use. The messages
available are directly visible on the display, indicated audibly or transmitted via USB
for remote communication.

2.6.6.1. Audible alarm

The Controller will send an audible alarm if either a leakage was detected or another
failure occurs.
2.6.6.1.1. Water level Alarm
The Controller is equipped with a “Water level” sensor. This means even small leakage
will be detected.
After the leakage is signalled on the Controller press the RESET ALARM button and
remove the leakage immediately by checking all connections and fill up the system
with distilled water.
2.6.6.1.2. Other system Alarms
The following alarms are available:
• Cell temperature too high
• Radiator temperature too high
• Cell temperature sensor failure
• EEPROM memory failure
If one of these alarms is activated, the Controller will signal the failure by an audible
signal and display relative messages on the display.
Action: Switch off the instrument immediately!
If the failure does not disappear after the instrument is switched on again, contact
service.

IMPORTANT!
THE CONTROLLER IS SHIPPED ALREADY FILLED WITH DISTILLED WATER. DURING INSTALLATION, WHEN CONNECTING THE
TUBING THE WATER LEVEL IN THE TANK WILL DROP AND WILL NEED TO BE TOPPED UP. ONLY USE THE DISTILLED WATER
SUPPLIED IN THE SEPARATE 200 CC CONTAINER INSIDE THE PACKAGING TO TOP UP THE WATER IN THE UNIT.

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3. ACTIVE ACCESSORIES
Accessories that interact with the instrument’s software are named active
accessories.
The installation of active accessories that use the internal accessory connector is
outlined below.
Note: The Ultrospec 7000/8000/9000 will be supplied with a single cell holder as
standard; this is removed as described above.

1. T
 o insert the accessory, lift the front end, slide into the brackets at the back of
the cell chamber (indicated by the two arrows) and tighten the thumb screw
by turning clockwise.

2. With the accessory inserted and secured using the thumb screw, plug the
15-pin plug into the internal accessory connector.

3. With the accessory inserted and plugged into the internal accessory
connector, replace front panel and switch on the instrument. The accessory
will be calibrated during instrument start-up.

3.1. 8-Position Cell Changer 80-7100-08

The 8-position cell changer is designed to speed up analysis by allowing users to
automatically measure samples. With a cell changer connected the software will
allow the user to perform parallel kinetics measurements.

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3.2. 5-Position Thermostatted Cell Changer 80-7100-09
The 5-position thermostatted cell changer is designed to speed up analysis
by allowing users to automatically measure samples that are at a controlled
temperature. With a cell changer connected the software will allow the user to
perform parallel kinetics measurements.
The 5-position changer is fitted as shown and the water tubing connected to an
external water circulator. The inlet from the circulator should be connected to the
right hand connector.

3.3. Sipper & Flowcell 80-7100-36 (sipper only)

The Sipper is designed to speed up analysis by allowing users to automatically
measure samples by pumping them through a Flowcell using a peristaltic pump
head. To install the Sipper carry out the following steps

Pump head Start/Stop button

Sample beak – to
Flowcell inlet

From Flowcell
outlet

Sipper cable

• Remove the front accessory panel by pulling it upwards

• Plug the Sipper cable into the accessory connector port and slide the Sipper
panel into the slot
Biochrom supplies the Sipper with a choice of Tubing kits and Flowcell
depending upon customers applications
80-7100-37 Tubing kit for TES Sipper. Includes 6 × Marprene™ pump head tubes and 1 m PTFE waste tubing
80-7100-38 Acid Tubing kit for TES Sipper. Includes 6 × Viton™ pump head tubes and 1 m PTFE waste tubing
80-7100-40 10 mm pathlength Quartz Flowcell 80 µl volume
Spare tubing is available under the following part numbers
80-2080-74 Pump head tubing for Sipper. Includes 6 x Marprene pump head tubes
80-7100-39 Acid pump head tubing for Sipper. Includes 6 x Viton pump head tubes
80-2026-34 PTFE waste tubing
80-2055-13 PTFE tubing with Flowcell connectors
The tubing supplied with the Flowcell from Biochrom is 150 cm in length to
allow customers flexibility in how they sip from their sample vessels. Unless you
require tubing this long for your application take the tubing with the short Flowcell
connector attached and cut the tubing to 65 cm in length.
• Screw the short Flowcell connector into the inlet port on the Flowcell which
is marked with an arrow and then feed the tubing through the metal “sample
beak” on the Sipper from the inside out.

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 Sipper outlet – to
Sipper inlet – from
pump head tubing
sample beak

• Take the tall Flowcell connector and connect it to the outlet port of the Flowcell.
Slide the whole Sipper unit up and feed the end of the tube through the hole in
the front panel underneath the pump head, once again from the inside out and
then slide the Sipper unit back down in it’s slot.
• Push the end of this tubing firmly into the end of the supplied pump head
tubing. Open the pump head by lifting the front lip and feed in the pump head
tubing with the tubing that you have just connected on the left hand side. Close
the pump head.

Front lip

• Take the spare piece of clear tubing with no connectors and push it firmly into
the other end of the pump head tube. Put the other end of this into a suitable
waste container.
Before using the Sipper to run samples the following checks can be carried out to
check it is performing properly – see the relevant software manual for how to do
this on your instrument.
• Check for leaks - Set the Sipper running in rinse mode, sip water and check that
there are no leaks.
• Default air gap – the Sipper works by pumping up the selected volume of
sample, telling the user to remove the end of the tubing from the sample and
the system then pumps again to introduce an air gap between samples. The
length of this airgap is set within the software but is dependant upon the length
of tubing being used – the software default should be OK if you have cut your
tubing to 65 cm long, if you are using a different length you may need to
change your default air gap.
• Sample volume – set up a fixed wavelength method which includes the Sipper
and set the sip volume to 1 ml. Fill a 10 ml measuring cylinder, sip several
samples and check the volume being sipped is approximately 1 ml, if not
recalibrate the Sipper as explained in the relevant software manual.

3.3.1. Sipper Troubleshooting

Problems with Sipper systems are generally caused by wrongly set parameters or
poor maintenance. Typical faults and their cures include:
3.3.1.1. Sample not being sipped
• Check pump head closed
• Check pump head tubing for damage
• Check Flowcell is connected and connectors are tightened

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• Check PTFE tubing is pushed firmly into pump head tubing
• Check PTFE tubing is not crushed or damaged
• Check Flowcell for blockages
• Check waste pipe for blockages
3.3.1.2. Sample being pumped right through Flowcell
• Check air gap and reset to correct value
3.3.1.3. Bubbles in Flowcell
• Check Flowcell connectors are tightened
• Clean Flowcell with detergent solution
3.3.1.4. Inconsistent readings
• Check volume being sipped – try increasing the volume
• Adjust air gap so the end of the sample is closer to the Flowcell inlet - more of
the sample flushes the previous sample out of the Flowcell
3.3.1.5. Wrong volume being sipped
• Check Sipper calibration

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 4. INSTALLING THE
INTERNAL PRINTER
Ensure that the instrument is unplugged before installing the internal printer.
1. Before the internal printer can be installed the printer blanking panel must be
removed. This is accessed from the back of the unit.

2. Remove the screw securing the printer blanking panel.

3. Lift off the printer blanking panel to reveal the connector for the internal
printer.

4. Connect the printer to the ribbon cable.

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 5. Slide the front legs of the printer in place and lower into the correct position.

6. Secure to the instrument by screwing into place. Reconnect the instrument to

the mains and switch on. Once installed the internal printer will appear in the
list

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