1. UV/VIS Software
Gamal A. Hamid

2. Thanks
To everyone who has helped us with support, new books, hard / soft ware And over the internet Special thanks for Thermo

3. Contents Introduction Software Menus Toolbar Data Store Status Bar
Reporting
Applications

4. Introduction

5. UV/VIS
An analytical technique for measuring 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. UV/VIS Region
The UV is the electromagnetic spectrum  shorter than those of ordinary,  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. Spectrometer Single beam instrument. Double beam instrument.
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.

8. Instrument Components
Light Source
Sample Chamber
Optical System
Detector

9. Software

10. Main window

11. Menus

12. 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.

13. 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.

14. 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. 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

16. 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.

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

18. 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. 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. 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

21. 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. 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. 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.

24. Toolbars

25. 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. The toolbars groups File operation group Application group
Analysis group
Window management group
Window group
Graph group

27. 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. 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)

29. 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

30. 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)

31. 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

32. 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

33. Data Store

34. 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

35. Status Bar

36. 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

37. Reporting

38. 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.

39. Applications

40. Applications
Scan
Fixed
Quant
Rate
MCA
DNA

41. 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. Scan Parameters

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 .

44. Display Parameters
( Scan and MCA) methods – display Parameters – results table, enables you to choose from a number of ways of reporting and at run-time
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.

45. 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.

46. FTIR
Fixed Parameters
Meslo-Misr

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.

48. Quant. Parameters

49. FTIR
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.
Meslo-Misr

50. Rate Parameters

51. 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.

52. MCA Parameters

53. 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. DNA Parameters

55. Accessories Software

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 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.

57. 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. 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.

59. 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.

60. 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.

61. 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.

62. 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.

63. 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.

64. Thanks 64