This document provides information about UV/VIS spectroscopy software. It discusses the various components and features of the software, including the main window, menus, toolbars, data store, status bar, and reporting capabilities. It also describes the different application modes like scan, fixed, quantitative, rate, MCA, and DNA analysis. Parameters for these applications and accessories like rapid mixing, stirrer, temperature control, cell changer, and sipper are outlined as well.

1. GamalA.Hamid

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3. 3 Gamal A. Hamid
Contents
 Introduction
 Software
 Menus
 Toolbar
 Data Store
 Status Bar
 Reporting
 Applications

5. 5 Gamal A. Hamid
UV/VIS
 An analytical for measure the concentration
of samples or samples components according
to Beer’s lambert Law depending on the ratio
between incident and transmitted light
through the cuvette.
 Absorbance is expressed as
A = εbc
where ε is a constant called absorptivity
Absorbance is directly proportional to the path
length, b, and the concentration, c, of the
absorbing molecule.

6. 6 Gamal A. Hamid
UV/VIS Region
 The UV is the electromagnetic
spectrum shorter than those of ordina
ry, visible violet light but longer than
those of x-rays.
 The human eye is only sensitive
between approximately 380 and 780
nm and within this area we perceive
the colors of the rainbow from violet
through to red.

7. 7 Gamal A. Hamid
Spectrometer
 A spectrophotometer is an instrument for
measuring the transmittance or
absorbance of a sample as a function of
the wavelength of electromagnetic
radiation.
 Single beam instrument.
 Double beam instrument.

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Instrument Components
1. Light Source
2. Sample Chamber
3. Optical System
4. Detector

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Main window

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Menus
 File
 View
 Tools
 Application
 Command
 Quant
 Data Store
 Table
 Window
 The Main Menu Bar gives you access to all of the
operations needed to obtain, process, store and
retrieve data.
 Each pull-down menu gives you access to one or
more sub-menus.
 The most frequently-used operations may also be
accessed directly via icons on the toolbar.

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File menu
 The File Menu is used for all
operations connected with creating,
opening, saving and printing files.
 The File Menu is used for all operations
connected with creating, opening, saving
and printing files.

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View menu
Customize
 This opens a tabbed dialog which
gives you control over which
toolbar icons are displayed and
how they are grouped.
 You also have some choices about
the appearance of the toolbar
buttons.

15. 15 Gamal A. Hamid
Tools menu
 The Tools Menu enables you to configure
the software to suit your preferences.
Options
 This item opens a tabbed dialog through
which you can control the following:
 File Load/Save Behavior
 System Settings
 Batch Information Printout
 Environment Information

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Application menu
 The Applications Toolbar enables you to
move between one application and
another with a single mouse click,
instead of accessing the applications via
the Application Menu.

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Command menu
 The available options in the Command
Menu will depend on which instrument
you are using and on the current context.

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Baseline
 100%T Baseline
Causes the instrument to do a Baseline
Scan over the Wavelength Range and Data
Interval specified in the current method.
 This is used to compensate for introduced
differences between the sample and
reference beams other than the presence
of the sample (e.g., differences in
absorption between the Reference
position or sample and the Sample
position or sample).

19. 19 Gamal A. Hamid
Math menu
 The Math Menu contains all the commands
needed to process your data post-run.
 If you are going to repeat the manipulation
on a number of batches of results, the
window can be left open and other batches
dragged to it.
 The Math Manipulation window will
remain on top on the work area all the
time it is open.

20. 20 Gamal A. Hamid
Quant menu
 No curve fit
 Select all curve fits
 Select Linear fit
 Select Linear through zero fit
 Select Quadratic fit
 Select Quadratic fit through zero

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Data Store menu
 The Data Store menu gives you access to
commands that operate on data in the
Data Store.
 Not all commands will be applicable in all
circumstances.
 Commands not available in the current
context will be grayed out.

22. 22 Gamal A. Hamid
Table- Graph- Report menus
 When the Results Table has the
focus Table is added to the Main
Menu Bar.
 When the Graph window has the
focus Graph is added to the Main
Menu Bar.
 When a Report window exists and
has the focus Report is added to
the Main Menu Bar.

23. 23 Gamal A. Hamid
Window menu
 The options in the Window Menu give
you control over the way in which
windows are displayed on the program
work area and enable you to transfer
the focus from one window to another.
 Clicking on your selected window will
transfer the focus to that window and
re-open it if that window has
previously been closed or minimized.

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25. 25 Gamal A. Hamid
The toolbars
 The toolbars contain icons for the most
commonly used operations, enabling them
to be accessed with a single mouse click
rather than via the pull-down menus on
the Main Menu Bar.

26. 26 Gamal A. Hamid
The toolbars groups
 File operation group
 Application group
 Analysis group
 Window management group
 Window group
 Graph group

27. 27 Gamal A. Hamid
File operation group
 Create a new method in the current application
 Load a method for the current application from disk
 Save the Sample Method to disk using its current name
 Load a result file for the current application from disk
 Save the file currently selected in the Data Store to disk using its current name

28. 28 Gamal A. Hamid
Application group
 Starts the Scan Application (shows the appearance of the button for the active application)
 Starts the Fixed Application
 Starts the Quant Application
 Starts the Rate Application (available only if VISIONlife is installed)
 Starts the MCA (Multicomponent Analysis) Application
 Starts the DNA Melting Application (available only if VISIONlife and suitable accessories are
installed)

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Analysis group
 Starts a run in the current application using the current Application and Accessory Method
parameters.
 Toggle to pause start/stop data collection.
 Start a Zero measurement or a baseline scan as applicable using the current Application
Method parameters.
 Stop the current run
 Access this Help system

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Window management group
 Remember the Current Window Layout
 Restore the remembered window layout
 Arrange the windows as non-overlapping tiles
 Cascade the Windows
 Load a Window arrangement from disk. (Window arrangements can be saved via the
Save/Window Layout command in the File Menu)

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Window group
 Restores the Method window
 Restores the Graph window
 Restores the Results window
 Restores the Calibration window
 Restores the Kinetics window
 Restores the Data Store
 Restores the Report Composer window

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Graph group
 Cancels Tracking
 Sets tracking
 Clears the graph, without clearing the axes (Use the Graph Menu to clear axes)
 Steps through grid displays (dots, lines, no grid)
 Sets up Axes
 Toggles display of the legend
 Toggles display of selected labels
 Toggles Graph background between white and gray
 Toggles Graph Line Type between Solid and Points

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Data Store
 The Data Store lists all of the batches of
results that are currently held in memory.
 When a batch of results has been run it will
appear in the Data Store.
 When a results file is loaded from disk it
will be placed in the Data Store.
 A batch is represented by
 A sample is represented by
 A cycle is represented by

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36. 36 Gamal A. Hamid
Status Bar
The following will be displayed on the status bar when appropriate:
 The effect of a left mouse-click at the current cursor position (e.g., reminders of the action of
toolbar icons)
 Icons for currently active accessories (e.g., sipper, Cell Changer, temperature control, stirrer)
 The status of active accessories (e.g., current cell, cell temperature, equilibration status)
 The presence of any Performance Verification accessory
 Lamp status
 The current absorbance reading
 The current wavelength
 The status of the instrument
 Zero or user Baseline status

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Report
 The Report Menu only appears on the Main Menu Bar when the Report Composer
window has the focus.
Click on the item you require to select it, Move the cursor into the Report window.

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Applications
 Scan
 Fixed
 Quant
 Rate
 MCA
 DNA

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1.Scan
 Spectrum recording.
 The spectrophotometer measures the amount
of light that passes through the sample over a
continuous range of wavelengths and plots a
graph of the resulting spectrum.
 The starting and finishing wavelengths of the
scan are both set .
 Select the appropriate Baseline Correction you
wish to perform.
 Maximum wavelength range is determined by
the working range of the spectrophotometer.

42. 42
Scan Parameters

43. 43
Definitions
No. Item Definition
1 Data Mode
The Data Mode enables you to select what will be used as the vertical
axis when the spectrum is first plotted.
2 Bandwidth The Effective Spectral Slit width of the monochromator.
3 Scan speed
A measure of how fast the monochromator changes the wavelength
of the light falling on the sample.
4 Data interval
The Data Interval is the difference in wavelength between successive
measurement points.
5 Lamp change
Control an instrument with a deuterium lamp installed to cover the
UV wavelengths and a tungsten lamp to cover the visible range.
It will not be available if the instrument has a xenon lamp installed,
6 Cycle Single measurement on a sample
7
Baseline
correction
The standard User Baseline Correction selection will be the 100%T .

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Display Parameters
Off No results will appear in the Results Table
Manual
The Results Table will contain the values of the Y-axis
variable at up to 100 specified wavelengths.
Peak Pick
The Results Table will contain the wavelengths and Y-
axis variable values of up to 100 peaks, valleys or zero-
crossings.
Peak Area
The Results Table will report the area of a selected
peak.
Peak
Height
The Results Table will report the height of a selected
peak.
( Scan and MCA) methods – display Parameters – results table, enables
you to choose from a number of ways of reporting and at run-time

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2. Fixed
 Recording spectrometer readings at
different dedicated wavelengths and
performing simple calculations
 In the Fixed application the instrument
measures the amount of light passing
through the sample at one or more
wavelengths.
 Set the wavelengths at which the
instrument will make measurements.

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Fixed Parameters

47. 47
3. Quantitative
 Quantifying sample concentrations via
calibration, based on Lambert- Beers law
 The Quantification application is used to obtain
quantitative concentration data on a single
component from absorbance measurements.
 A valid calibration must be present before
samples can be measured.
 Enter the number of standards that will be used.
 Once a calibration has been performed it can be
saved as part of the method and will be available
for use next time the method is loaded.

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Quant. Parameters

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4. Rate
 The Rate application is used to measure the
change in concentration of a reactant or product
with time.
 The absorbance of the sample is measured
repeatedly at a fixed wavelength over a period of
time appropriate to the reaction being studied.
The software then offers a variety of methods to
calculate the rate of reaction from the variation of
absorbance with time.
 Recording time dependent readings at a fixed
wavelength and is dedicated for measuring rate
curves.

50. 50
Rate Parameters

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5. MCA
 It provides the ability to perform
simultaneous quantitative analysis on
samples for up to 20 components
 Standards and components are scanned,
and each data point of the scan
contributes to the calculation.
 A series of Standards, in which the
concentrations of the components are
known, is prepared and scanned.
 There must be at least as many standards
as there are components to be analyzed.

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MCA Parameters

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6. DNA
 During a DNA experiment, the sample is
heated and Absorbance v Temperature
data are collected at a suitable
wavelength.
 Tm, the "melting point" of the DNA, may
be calculated at run-time, or post-run via
the Math menu.

54. 54
DNA Parameters

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56. 56
Rapid Mixing Accessory
 The Rapid Mixing accessory provides a very low
dead time of 8 ms, giving you access to reactions
that occur up to 1000 times faster than those
visible to manual mixing experiments.
 The Rapid Mixing accessory provides a very low
dead time of 8 ms, giving you access to reactions
that occur up to 1000 times faster than those
visible to manual mixing experiments.
 The Anaerobic accessory consists of a manifold,
which is mounted over the base of the drive
syringes and is purged with a steady stream of
inert gas.

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Stirrer Parameters
 Off The stirrer is off
 Continuous The cell is stirred
continuously
 Off Before Measurement The stirrer is normally
on but is switch off prior to and during
measurement.
 A programmable settling time elapses before the
measurement is made.

58. 58
Air-Cooled Peltier
 The Air-cooled Peltier Accessory allows the cell to be
thermostatted during measurements. It comprises a
dedicated cell holder and an electronic control device,
which is connected to the PC.
 The Air-cooled Peltier accessory delivers reliable
temperature control .
 Wider temperature range from 0 to 110 °C
 Multiple cell efficiency for higher sample throughput.
 Designed for biologically relevant assays that require
temperature control at 25°, 37°, 40° and 50 °C, the Air-
cooled Peltier accessory is ideal for the life science
laboratory.

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Temp. Control Parameters
 Method off not selected
 Tolerance Target Temperature ±
Tolerance
 Start on using block or probe
 The Equilibration Time permitted
range and start a measurement.
 The Equilibrate Using sample or
sample and reference.

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Cell Changer
 Using a cell changer, you load the system
with a batch of samples before starting
the measurement.
 During the measurement the cell changer
moves the required sample automatically
into the sample beam of the
spectrophotometer.
 This type of measurement procedure is
advisable for time consuming analyses,
e.g. rate measurements.

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Cell Changer Parameters
 Method off not selected
 Cell changer type. When an instrument
with a cell changer installed is connected,
this field will automatically show the
correct type.
 Each cell can contain a Sample (green) or
a Reference (red), or not be used.

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Sipper
 In sipper operation the sipper pump
transports the sample to the flow cell
located in the sample beam. Then the
measurement starts automatically.
 Therefore, there is no need to change and
clean the cells.
 This operation mode is recommended for
high sample throughput in routine
analyses.

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Sipper Parameters
 Method off not selected
 Sipper Mode. Choose between Sip Only, Sip and
Run, Continuous.
 Sample Direction. When Waste is selected the
sample is pumped to waste after it has been
measured. Return sample is returned to the
sample container .
 Sample Delay.
 The Sample time between the end of pumping the
air gap and the start of sample measurement.
 The purpose of the Sample Delay is to allow time
for the sample to settle down in the flowcell.

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