Uv Probe

Getting Started with

UVProbe Tutorial Version 1.1

Read the instruction manual thoroughly before you use the product. Save this instruction manual with care so that you can use it any time you need it.

206-94459C


A Tutorial for the Spectrum, Photometric, Kinetics, and Report Generator Modules

P/N 220-92901-00


UV Probe

Tutorial Version 1.0

Shimadzu Scientific Instruments, Inc. 7102 Riverwood Drive Columbia, MD U.S.A. 21046-2502 410/381-1227

First Edition: September 1999 Copyright Shimadzu Corporation, 1998-2000. All rights are reserved, including those to reproduce this publication or parts thereof in any form, without the express written permission of Shimadzu Corporation. Shimadzu Corporation Provides this publication "As Is" without warranty of any kind, either express or implied, including, but not limited to, the implied warranties of merchantability or fitness for a particular purpose. Some states do not allow disclaimer of express or implied warranties in certain transactions, therefore this statement may not apply to you. Any technical inaccuracies, omissions, or typographical errors in this publication will be corrected as soon as feasible. Changes are periodically made to the information herein and incorporated into new editions of the publication. Shimadzu may make improvements and/or changes in the product(s) and/or the program(s) described in this publication at any time. It is possible that this publication may contain reference to, or information about, Shimadzu products (instruments and programs), programming, or services that are not announced in your country. Such references or information must not be construed to mean that Shimadzu intends to announce such products, programming, or services in your country. This document and the software described in it are furnished under license from Shimadzu Corporation and may be copied only in accordance with the terms of such license. Shimadzu may use or distribute any of the information which you supply in any way it believes appropriate without incurring any obligations whatsoever. The following registered trademarks are used throughout this document: IBM, PC DOS and PS/2 are registered trademarks of International Business Machines, Inc. Microsoft and MS-DOS are registered trademarks and Microsoft Windows is a trademark of Microsoft Corporation.

Table of Contents

UV Probe Manual i

Table of Contents CHAPTER 1 INTRODUCTION .................................................................................................................. 1-1

INTRODUCING UVPROBE .................................................................................................................................. 1-1 ABOUT THIS MANUAL ....................................................................................................................................... 1-1 UVPROBE INSTALLATION REQUIREMENTS........................................................................................................ 1-1

Minimum Computer Hardware Requirements ......................................................................................... 1-1 Minimum Software Requirements ........................................................................................................... 1-2 Installing UVPROBE ................................................................................................................................. 1-2 Step 1 Installing Shimadzu User Authentication Tool .......................................................................... 1-2 Step 2 Installing UVPROBE................................................................................................................... 1-2 Uninstalling UVPROBE............................................................................................................................. 1-3

APPLICATION MODE .......................................................................................................................................... 1-3 ABOUT UVPROBE ............................................................................................................................................. 1-5 STARTING UVPROBE ........................................................................................................................................ 1-5 UVPROBE THE BASIC INTERFACE.................................................................................................................. 1-6

Output Window........................................................................................................................................ 1-7 Instrument Bar.......................................................................................................................................... 1-7 Photometer Status Bar.............................................................................................................................. 1-7 Standard Toolbar...................................................................................................................................... 1-7

SYSTEM ADMINISTRATION ................................................................................................................................ 1-8 Assign user's rights................................................................................................................................... 1-8 Rights ....................................................................................................................................................... 1-9 Add a group............................................................................................................................................ 1-15 Assign group rights ................................................................................................................................ 1-16 Remove a group ..................................................................................................................................... 1-17 Add a user .............................................................................................................................................. 1-18 Edit a user............................................................................................................................................... 1-19 Enabling / disabling user ........................................................................................................................ 1-19 Change a password................................................................................................................................. 1-20

USING THE MODULES ...................................................................................................................................... 1-21 Panes that vary between modules........................................................................................................... 1-21 Unique menus and toolbars .................................................................................................................... 1-22

UVPROBE FUNCTIONS .................................................................................................................................... 1-22 Communicating with the Spectrophotometer ......................................................................................... 1-22 Shortcut Menus and Properties Pages .................................................................................................... 1-24 Graph Modes.......................................................................................................................................... 1-25 File Properties, Storages, and Data Sets................................................................................................. 1-26 Precision of Internal Data Processing .................................................................................................... 1-27

THE UVPROBE TUTORIAL............................................................................................................................... 1-28 Lesson 1 The Spectrum Module.......................................................................................................... 1-28 Lesson 2 The Photometric Module ..................................................................................................... 1-28 Lesson 3 The Kinetics Module............................................................................................................ 1-29 Lesson 4 The Report Generator........................................................................................................... 1-29

CHAPTER 2 THE SPECTRUM MODULE, LESSON 1 ........................................................................... 2-1 SPECTRUM WINDOW.......................................................................................................................................... 2-2 SPECTRUM TOOLBAR......................................................................................................................................... 2-2 EXERCISE 1 BASIC MEASUREMENTS............................................................................................................... 2-3

Step 1 Perform a Baseline Correction................................................................................................... 2-3 Step 2 Create a Data Collection Method............................................................................................... 2-4 Step 3 Save a Data Collection Method.................................................................................................. 2-5 Step 4 Collect the Data.......................................................................................................................... 2-5 Step 5 Save the Data ............................................................................................................................. 2-7

EXERCISE 2 BASIC SPECTRUM OPERATIONS................................................................................................... 2-8 Step 1 Adjust the Parameters of a Peak Pick Table .............................................................................. 2-8 Step 2 Create a Peak Area Table......................................................................................................... 2-13 Step 3 Manipulate a Peak Area Table and Graph ............................................................................... 2-14 Step 4 Create a New Region ............................................................................................................... 2-15 Step 5 Manipulate a Data Set .............................................................................................................. 2-16

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EXERCISE 3 ADVANCED TECHNIQUES .......................................................................................................... 2-18 Part 1 Acquire Data with a Cell Positioner.............................................................................................. 2-18

Step 1 Load and Modify a Saved Data Collection Method................................................................. 2-18 Step 2 Configure the Positioner .......................................................................................................... 2-20 Step 3 Remove Data from Memory .................................................................................................... 2-20 Step 4 Collect the Data........................................................................................................................ 2-21

Part 2 Use UVProbe with Windows WordPad ........................................................................................ 2-22 Step 1 Copy and Paste a Bitmap to WordPad ..................................................................................... 2-22 Step 2 Copy and Paste a Table to WordPad........................................................................................ 2-23

CHAPTER 3 THE PHOTOMETRIC MODULE, LESSON 2................................................................... 3-1 PHOTOMETRIC WINDOW.................................................................................................................................... 3-2 PHOTOMETRIC TOOLBAR ................................................................................................................................... 3-2 SET AND EDITO PHOTOMETRICB METHOD ......................................................................................................... 3-3 EXERCISE 1 BASIC MEASUREMENTS............................................................................................................... 3-6

Part 1 Create a Standard Curve ................................................................................................................. 3-6 Step 1 Create a Data Collection Method............................................................................................... 3-6 Step 2 Save a Data Collection Method.................................................................................................. 3-8

Part 2 Measure Standard Samples ............................................................................................................. 3-8 Step 1 Entering File Information........................................................................................................... 3-9 Step 2 Populate a Standard Table.......................................................................................................... 3-9 Step 3 Read the Standard Samples...................................................................................................... 3-10 Step 4 View the Standard Curve ......................................................................................................... 3-11 Step 5 Save the Standard Table........................................................................................................... 3-11

Part 2 Read Unknown Samples ............................................................................................................... 3-12 Step 1 Create a Sample Table ............................................................................................................. 3-12 Step 2 Read the Unknown Sample...................................................................................................... 3-12 Step 3 Manually Enter Sample Table Data ......................................................................................... 3-13 Step 4 View the Sample Graph ........................................................................................................... 3-13 Step 5 Save the Data ........................................................................................................................... 3-14

EXERCISE 2 BASIC PHOTOMETRIC OPERATIONS ........................................................................................... 3-15 Step 1 Use Auto Fill to Build a Standard Table .................................................................................. 3-15 Step 2 Use Repetition to Populate a Standard Table........................................................................... 3-16 Step 3 Use Various Standard Curves to Calculate Unknown Concentrations..................................... 3-17 Step 4 Show Statistics ......................................................................................................................... 3-19 Step 5 Perform a Reciprocal Transformation on the Data .................................................................. 3-20

EXERCISE 3 ADVANCED PHOTOMETRIC TECHNIQUES .................................................................................. 3-22 Part 1 Custom Equations ......................................................................................................................... 3-22

Step 1 Create a Data Collection Method using Custom Equations ..................................................... 3-23 Step 2 Save a Data Collection Method................................................................................................ 3-26 Step 3 Populate the Sample Table....................................................................................................... 3-26 Step 4 Verify the Calculation Results ................................................................................................. 3-27 Step 5 Display Necessary Columns .................................................................................................... 3-27

Part 2 Use a Sipper to Collect Data ......................................................................................................... 3-28 Step 1 Install a Sipper Attachment...................................................................................................... 3-28 Step 2 Modify a Data Collection Method to Use the Sipper ............................................................... 3-29 Step 3 Collect the Unknown Data ....................................................................................................... 3-29

CHAPTER 4 THE KINETICS MODULE, LESSON 3.............................................................................. 4-1 KINETICS WINDOW............................................................................................................................................ 4-2 KINETICS TOOLBAR ........................................................................................................................................... 4-3 EXERCISE 1 BASIC MEASUREMENTS............................................................................................................... 4-4

Step 1 Create a Data Collection Method............................................................................................... 4-4 Step 2 Prepare a Powder Sample .......................................................................................................... 4-5 Step 3 Perform a Time Course Reading................................................................................................ 4-5

EXERCISE 2 BASIC KINETICS OPERATIONS ..................................................................................................... 4-6 Step 1 Perform a Point Pick .................................................................................................................. 4-7 Step 2 Save the Point Pick Table as a Template ................................................................................... 4-7

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Step 3 Perform a Cell Blank Operation................................................................................................. 4-8 Step 4 Collect a Second Set of Data...................................................................................................... 4-8 Step 5 Open a Previously Saved Point Pick Template .......................................................................... 4-9 Step 6 Modify the Main Table .............................................................................................................. 4-9

EXERCISE 3 ADVANCED KINETICS TECHNIQUES .......................................................................................... 4-11 Step 1 Perform a Michaelis-Menten Calculation ................................................................................ 4-11 Step 2 Configure a Custom Kinetics Graph ........................................................................................ 4-13 Step 3 Create and Populate an Inhibitor Table.................................................................................... 4-15

CHAPTER 5 THE REPORT GENERATOR, LESSON 4 ......................................................................... 5-1 OBJECT MODES OF OPERATION (SELECTING OBJECTS) ...................................................................................... 5-1

Edit Mode................................................................................................................................................. 5-1 Selected Mode.......................................................................................................................................... 5-1 Unselected Mode...................................................................................................................................... 5-2

EMBEDDED VS. LINKED OBJECTS ...................................................................................................................... 5-2 Embedded Objects ................................................................................................................................... 5-2 Linked Objects ......................................................................................................................................... 5-2

REPORT GENERATOR MAIN WINDOW................................................................................................................ 5-3 REPORT GENERATOR TOOLBAR......................................................................................................................... 5-3 REPORT GENERATOR OBJECT TOOLBAR............................................................................................................ 5-4

Text Objects ............................................................................................................................................. 5-4 Kinetics Objects ....................................................................................................................................... 5-4 Photometric Objects ................................................................................................................................. 5-5 Spectrum Objects ..................................................................................................................................... 5-5

EXERCISE 1 CREATE A BASIC REPORT WITH EMBEDDED OBJECTS ................................................................. 5-6 Step 1 Configure the Grid and Set Page Margins ................................................................................. 5-6 Step 2 Embed a Graph .......................................................................................................................... 5-6 Step 3 Create a Report Title .................................................................................................................. 5-7 Step 4 Print and Save a Report.............................................................................................................. 5-9

EXERCISE 2 CREATE A BASIC REPORT WITH LINKED OBJECTS..................................................................... 5-10 Step 1 Link a Graph to the Active Spectrum ...................................................................................... 5-10 Step 2 Link a Peak Pick Table to the Active Spectrum....................................................................... 5-11 Step 3 Create a Title and Print a Report.............................................................................................. 5-12

EXERCISE 3 ADVANCED REPORTING TECHNIQUES ....................................................................................... 5-13 Step 1 Insert Text Object and Repeat on Each Page ........................................................................... 5-13 Step 2 Configure the Quick Print Function......................................................................................... 5-14

Introduction

UVProbe Manual 1-1

Chapter 1 Introduction

Introducing UVProbe

Welcome to the UVProbe personal software package. UVProbes modular approach to data collection, analysis, and reporting provides a rare combination of simplicity and power.

UVProbe includes four basic components.

A Spectrum module for wavelength scanning and analysis. A Kinetics module for Time Course measurement and Michaelis-Menten calculations. A Photometric module for quantitative data analysis. A powerful and flexible Report Generator that is used to create and print custom reports with

linked or embedded data, which can be instantly printed from within any module. Other features include: An intuitive screen layout that can be customized for simple layouts with just a graph and

Photometer control buttons to more complex layouts with Instrument History and status displays, as well as multiple graphs and tables.

Instant machine control with real-time feedback, including onscreen readings of absorbance, transmittance, energy, or reflectance values.

Flexible output to files and printers. Various tables used to display, collect, and control data. Three graph modes to display data while being collected or after it is collected. Numerous other post-processing procedures, such as Point Pick, Peak Pick, and Peak Area. Import and export features used to share data with other Windows applications. Comprehensive Online Help, including context-sensitive Help for each dialog box.

About this Manual

The purpose of this manual is to help the user become familiar with UVProbe. It briefly introduces key concepts, explains the layout of the software, then guides you through the basics with a four lesson tutorial.

The tutorial contains important basic procedures for each module and some advanced techniques. Before beginning the tutorial, read the preliminary information contained in the following sections. For more detailed explanations of features or procedures, refer to Online Help.

UVProbe Installation Requirements

This section describes the minimum hardware and software necessary to run UVProbe, as well as how to install and remove the software from the system.

Minimum Computer Hardware Requirements

An IBM PC or PC compatible with a Pentium (200MHz) processor; a Pentium II (300MHz) is recommended.

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Approximately 128 MB RAM. Approximately 35 MB free hard disk space. SVGA video adapter and monitor: 800x600 resolution required, 1024x768 recommended. Parallel and serial adapters. Graphic printer or plotter (recommended for printing data). Mouse or a similar pointing device. CD ROM.

Minimum Software Requirements

Microsoft Windows XP/NT4.0/2000 operating system

Installing UVProbe

Install UVProbe as follows:

Install Shimadzu Authentication Tool and UVProbe following the procedures from Step 1 to Step 2.

If you install the optional software, UVPC Validation Software, you are required to click Help button and follow the viewed procedure to install Support files for UVPC validation.

Step 1 Installing Shimadzu User Authentication Tool 1 Click Shimadzu User Authentication Tool.

2 Welcome dialog box appears. Read the description well and click the Next button.

3 When installation starts, the next window will appear. If it is the first installation, click Yes. In the case of reinstallation or ADO has been already installed by Office and the equivalent, click No.

4 When installation is complete, Setup Complete dialog box appears. If you restart the PC immediately, click Finish. If you restart the PC later, click No, I will restart the PC later first, and then click Finish.

Step 2 Installing UVProbe 1 Start up the setup file from the CD-ROM. Then click the [UVProbe] button.

NOTE : The install program can be started using the Run command in MS-Windows/NT/2000/XP. Choose [Start] -> [Run] to open the Run dialog box. Click the [Browse] button and choose the SETUP.EXE program from the root folder on the CDROM. Click the [OK] button to run the setup program. 2 Please read the information in the Welcome box and click Next.

3 Please read the software license agreement and click Yes to accept.

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4 Enter your Name, Company, and Product ID Number in the User Information Box. Click Next. (The Product ID number is on the front cover of this tutorial.)

5 In the Choose Destination Location dialog box, use the Browse key to choose a folder for UVProbe, or accept the default folder (Program FilesShimadzuUVProbe). Click Next.

6 In the Option Selection dialog box, select the application mode of the UVProbe you wish to install and click Next. For the details of each mode, see Application Mode in this document, UVProbe Help.

7 In the Create Shortcut box, click the check box to place an icon on the desktop, then click Next.

8 When the software has finished loading, click in the box to view the ReadMe file. Click Finish to complete the setup.

9 Restart the computer. The Shimadzu icon should appear on the Windows desktop.

Uninstalling UVProbe

1 Select Windows Start > Settings > Control Panel.

2 Double-click Add/Remove Programs.

3 Select UVProbe from the list of programs, then click the Add/Remove button.

4 Click Yes to confirm deletion of the program.

NOTE: When UVProbe is uninstalled, all sample data files are removed with the program. However, uninstalling does not remove any files that have been created and saved to disk. 5 Click OK when the process has finished.

Application mode

Application modes are provided in three types: Normal, Security, and GLP.

The available functions differ depending on each mode.

Function Normal Security GLP function

Security function Disabled Enabled Enabled

GLP function Disabled Disabled Enabled

Security function

When security function is disabled, entering User Name and Password is necessary at the time of log-in to the system, and this will limit access to the system. Assigning rights to each user limits the available UVProbe functions. Also, the user name of the log-in user is automatically used as analyst name. The analyst name cannot be changed.

For the details, see UVProbe Functions and System Administration in the Introduction chapter.

NOTE : When security function is valid, the right to overwrite the files in photometric module does not exist in the default state.

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GLP function

GLP function supports the system to cope with GXP (GLP: Good Laboratory Practices, GMP: Good Manufacturing Practices, etc) When the GLP function is enabled, the following limitations apply in the operation of each module.

Common

UVProbe system can be locked using Windows > Lock command. Information of Instrument History can be transmitted to the database. The unsaved file is automatically saved in the disk at the exit of UVProbe or at the printing. Kinetics / Spectrum module

Newly measured and created by data calculation data sets are automatically saved to disk. The Sewing Box feature is disabled. Renaming of data files, storage names, and data set names is prohibited, except for Enzyme

files. Deletion of storages and data sets contained in data files is prohibited, except for Enzyme

files. Saving at the existing file name is prohibited. Photometric module

Deletion of samples rows and standards rows is prohibited, only excluded. Deletion of samples columns and standards columns is prohibited. A User Entry cannot be chosen as a data acquisition method of a sample table. Saving at the existing file name is prohibited. After Saved file, it cannot change the factor on a standard table and a sample table. Verification and changing the application mode

The installed UVProbe application mode cannot be verified in Option of the Edit menu. It is also possible to toggle the Normal mode and the Security mode.

Switching over from the Normal mode to the Security mode

1 Select Option from the Edit menu of UVProbe.

2 Click the Security Mode button and give a checkmark.

3 Click the OK button to close the dialog box.

4 A message telling mode selection is displayed from the next start-up.

5 When UVProbe is restarted after it is closed once, a log-in dialog box is displayed and it is requested to enter the user ID and the password.

6 Administrator that owns every right is already registered as User ID. Password is not set. Enter admin for User ID and click the OK button.

NOTE: It is not possible to change from the other mode to the GLP mode and vice versa. In this case, UVProbe must be reinstalled after it is uninstalled once.

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UVProbe Manual 1-5

About UVProbe

Although UVProbe is a unified software package with a shared set of capabilities, it can be viewed as four programs in one, with the Spectrum module, Photometric module, Kinetics module, and Report Generator comprising the four programs. Each opens in its own window within the larger UVProbe window, and each has a unique purpose and capabilities. They also have similar, yet differing interfaces, with their own toolbars, menus, tables, graphs, and screen arrangements.

The following information guides you through the basics from the common to the unique. For a more precise explanation of the procedures, refer to UVProbe Functions on page 1-2.

Starting UVProbe

When UVProbe is started, the window is displayed in the same configuration as when the program was exited. For example, the toolbars and windows are restored to the same position; however, no data is displayed.

1 Turn on the monitor, computer, and spectrophotometer.

2 Select Windows Start > Programs > Shimadzu > UVProbe, or double-click the UVProbe icon on the desktop.

3 Enter the User Name and Password into the User Login dialog box when Security is enabled, then click OK. When Security is not enabled, this dialog box will not appear.

NOTE: When the system starts for the first time after installation, the user ID of the administrator is admin. It is not necessary to input password.

Open a module

On the Window menu, click on a module.

Double-click tostart UVProbe

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All modules can be open at the same time. Use the Window menu to quickly switch from module to module, or to arrange multiple modules using the Cascade and Tile choices. Modules can also be dragged and sized.

UVProbe The Basic Interface

Menu Bar Standard Toolbar

Photometer Status Bar Instrument Bar Output Window

This is an example of the basic UVProbe window with no open modules. Notice that it includes a Menu bar, a Standard toolbar, an Output window, an Instrument bar, and a Photometer Status bar. The following capabilities are available before either a module or the Report Generator is opened.

Set options Perform system administration functions Add, configure, and remove instruments Add custom tools to the Tools menu For details on performing the above procedures, refer to Online Help.

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Output Window

The Output window is dockable and can be positioned anywhere within the UVProbe workspace. It displays useful system information at the bottom of the UVProbe window and contains two tabs Output and Instrument History.

Output displays general messages while the software is running. This is temporary information that will be cleared the next time the system is started.

Instrument History displays information related to the currently active instrument, such as initialization time, baseline information, etc. The information changes when switching between instruments to display information specific to the currently active instrument.

Neither Output nor Instrument History information can be printed or saved.

Instrument Bar

The Instrument bar is a dockable toolbar that can be positioned anywhere within the UVProbe workspace. It displays a button for each available instrument. To switch between the instruments, click the desired instrument.

Photometer Status Bar

The Photometer Status bar is a dockable status and control bar that can be positioned anywhere within the UVProbe workspace. Using the Photometer Status bar, any number of machine manipulation functions can be performed. The appearance of the Photometer Status bar can be configured to control the font style, size, and color, and the background color for the status display. Right-click the Photometer Status bar and choose Properties. See UVProbe Help for more details.

Standard Toolbar

New Tool Print Tool Spectrum Module

Open File Tool Print Preview Tool

Save File Tool Undo Tool

Redo Tool

Cut Tool Report Generator

Copy Tool Kinetics Module

Paste Tool Photometric Module

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1-8 UVProbe Manual

System Administration

This section explains basic system administration. When security is disabled, and will not be used, skip to Communicating with the Spectrophotometer on page 1-15. Basically, security enables a system administrator to determine the access privileges of everyone authorized to use the system. There are three procedures to master: adding groups, assigning group privileges, and adding users.

When UVProbe is first installed, there are only four groups Administrator,Developer,Operator and Guest. The Administrator group controls all access privileges, i.e., when a user is added to this group, that user receives unrestricted access to UVProbe.

To effectively control system access, create groups for each level of access that is to be granted, then assign users to the appropriate groups. For example, a group can be restricted from using the Peak Area table or the Report Generator. Groups cannot be restricted from individual modules.

Use security to control access to the system, track users, and the operations that are performed by individual users. When security is enabled, the User Name is automatically entered into the analyst field that is saved with the data (in the New Data Set Information dialog box). View user and operation information on the Instrument History tab in the Output window, or in the File Properties dialog box History tab. In the Report Generator, the logged-in user can be printed on the report.

Click Security in the Edit menu to display the Administrative dialog box. System control is performed using this dialog box.

The tabs (pages) other than Change Password tab are available for the users registered in the Administrator group.

Assign users rights

For convenience and ease of administration,every user must belong to a group. Group users carefully to control their rights within the system. The following rules apply to users and groups.

A group is a collection of users. Each user must belong to a group,and cannot belong to more than one group. Groups have rights. All members of a group acquire the rights of the group.

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Rights

The rights that can limit the operation are divided in 18 components. The rights contained in each components and the ones already made available in UVProbe are described as follows:

Also, no operation right of the UVProbe is given to the Guest group.

Shimadzu Activity table Control Kinetics Module

Right Description Administrator Developer OperatorClipboard Operations

A function to copy the rows or columns of the activity table to the clipboard.

Shimadzu Command Container

Right Description Administrator Developer OperatorAccess Report Generator

A right to use report generator module. It is a function to create/save/read the report files and report template in which objects are arbitrary lay out.

Edit Options A right to use Option in the Edit menu. It is the function to toggle UVProbes application modes (Normal mode and Security mode only).

Modify Tools Menu

A right to use the Tools menu. It is a function to add the other application software in the UVProbe menu command Adding a program in the Tools menu.

Shimadzu Data print Control SpectrumKinetics Module


A right to copy the rows or columns of the Data Print table to the clipboard.

Shimadzu Kinetics Main Table Control


A right to copy the rows or columns of the main table to the clipboard.

Modify A right to enter Edit, Coefficient/Comment to the main table. The right to toggle display/non-display of the columns on the table is also included.

Shimadzu Kinetics Module

Right Description Administrator Developer OperatorAcquire Data A right to perform measurement Activity Table A right to create activity table. Cell Blank A right to use cell blank function Data Print A right to use data print function Edit Method A right to use the Method function in the Edit

menu. It is the function to create/edit the measurement method.

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Right Description Administrator Developer OperatorEdit Settings A right to use the Settings function in the View

menu. It is the function to set the number of digits of the data to be displayed, link setting of the report and template, whether message is displayed or not, display format of the dataset names, setting of the delimiters used at the time of saving text, etc

Enzyme Table A right to create Enzyme file. File Properties A right to use File Property. File Property is a

function to confirm the file loaded on RAM and to change the names such as file names, storage names, and dataset names.

Go to Wavelength A right to perform wavelength transfer Load File A right to use the Open function in the File menu.

It is a function to read Kinetics files, Enzyme files, Measurement Methods, and various templates.

Main Table A right to create Main Table Manipulation A right to use data manipulation. Peak Area A right to create the Peak Area table. Peak Pick A right to use the Peak Pick function of the

Operation menu.

Perform Auto Zero

A right to use auto-zero function

Perform Baseline A right to use baseline correction function. Point Pick A right to use Point Pick function. Print Report A right to use Print Preview and Print functions in

the File menu. They are the functions to perform printing using the report template linked to each pane.

Properties A right to use the Properties function in the View menu. It is the function to edit or set the display of graphs and tables in each pane.

Save File A right to use the Open function in the File menu. It is a function to open Kinetics files, Enzyme files, Method files, and various templates.

Sewing Box A right to use the sewing box function.

NOTE : The data operation function is disabled in the GLP mode.

NOTE : File names, Storage names, and Dataset names cannot be changed in the GLP mode.

Shimadzu Manipulation Control SpectrumKinetics Module

Right Description Administrator Developer OperatorArithmetic A right to use the Blank Subtract function that is

one of Manipulate in the Operations menu. It is a function to create a new dataset by performing four operations of calculation of the constant number to the specified data sets.

Blank Subtract A right to use the Blank Subtract function that is one of Manipulate in the Operations menu. It is a function to create a new dataset by performing blank corrections on the specified data set.

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Right Description Administrator Developer OperatorEnsemble Average A right to use the Ensemble Average function that

is one of Manipulate in the Operations menu. It is a function to create one dataset using the average value per point with regard to the specified two or more data sets.

Data Set A right to use the Data Set function that is one of Manipulate in the Operations menu. It is a function to create a new dataset using four operations of calculation among data sets.

Interpolation A right to use the Interpolation function that is one of Manipulate in the Operations menu. It is a function to interpolate datasets in arbitrary pitch and to create a new data set.

Normalization A right to use the Normalization function that is one of Manipulate in the Operations menu. This function enables easier view of the datasets with different kinds of measurement values on the overlay graph.

Transformations A right to use the Transformation function that is one of Manipulate in the Operations menu. It is a function to create a new dataset using differential transformation, reciprocal transformation, and Abs/T% transformation.

Shimadzu Michaelis-Menten Control Kinetics Module


A right to copy the rows and columns of Michaelis-Menten Table to the clipboard.

Create New Data A right to newly create of Michaelis-Menten Table.

Delete Row(s) A right to delete (cut out) the columns of Michaelis-Menten Table.

Edit A right to change the numerical value in Michaelis-Menten Table.

Shimadzu Peak Area Control SpectrumKinetics Module


A right to copy the rows and columns of the Peak Area table.

Edit A right to change the numerical values and comments in the Peak Area table.

Delete Region A right to delete the areas in the Peak Area table.

Shimadzu Peak Pick Control SpectrumKinetics Module


A right to copy the rows or the columns of the peak pick table.

Edit A right to change the comment of the peak pick table.

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Shimadzu Photometric Module Right Description Administrator Developer Operator

Acquire data A right to perform measurement. Cell Blank A right to use the Cell Blank function. Edit Method A right to use the Method function in the Edit

menu. It is a function to create/edit the measurement method.

Edit Settings A right to use the Settings function in the View menu. It is a function to perform settings such as link settings of report template, whether to display messages, dataset name display format, and delimiters used at the time of text saving.

Go to Wavelength A right to perform wavelength movement. Load File A right to use the Open function in the File menu.

It is a function to load the photometric files, standard files, method files, etc

Make Standard A right to use the Make Standard function of the Operation menu. It is a function to move the data on the table to the standard sample table.

Manipulation A right to use the Manipulate function in the Operations menu.

Overwrite File A right to use the Save function in the File menu. Perform Auto Zero

A right to use Auto-Zero function

Perform Baseline A right to use baseline correction function. Print Report A right to use the Print Preview and Print

functions in the File menu. It is the function to perform printing using the report template linked to each pane.

Properties A right to use the Properties function in the View menu. It is a function to perform edit/display setting of the graphs and table on each pane.

Save File A right to use Save and Save as functions in the File menu. It is a function to save/overwrite the photometric files, standard files, ASCII files, method files, etc

Statistical Analysis

A right to use the Statistical Analysis function in the Operations menu. It is a function to add the column to display the calculation results of the statistical analysis (standard deviation and average) on the sample table.

Shimadzu Point Pick Control SpectrumKinetics Module


A right to copy the rows or columns of the Point Pick table to the clipboard.

Edit A right to change the wavelength and comment of the Point Pick table.

Remove Points A right to delete the rows within the Point Pick table.

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Shimadzu Report Generator Right Description Administrator Developer Operator

Modify A right to create/edit the report files. It is a function to insert objects onto the report or change the positions of objects.

Print A right to use Print Preview and Print functions in the File menu. They are functions to print reports from the report generator.

Save File A right to use Save and Save as functions in the File menu. It is a function to save the created report files.

Shimadzu Sample Table Control Photometric Module


A right to copy the rows or columns of the Sample table to the clipboard.

Delete rows A right to delete the rows within the Sample table.

NOTE : The rows of the Sample table cannot be deleted in the GLP mode.

Shimadzu SEP Table Control Photometric Module


Right to copy the rows or columns of S.E.P table to the clipboard.

Delete rows A right to delete the rows within the S.E.P table.

NOTE : The rows of the S.E.P table cannot be deleted in the GLP mode.

Shimadzu Sewing Box Control SpectrumKinetics Module

Right Description Administrator Developer OperatorShear A right to use the Shear function that is one of

Sewing Box in the Operations menu. It is a function to cut out a part of the selected data set.

Stitch A right to use the Stitch function that is one of Sewing Box in the Operations menu. It is the function to connect two data sets to create a new data set.

Shimadzu Spectroscopy Instrument Bar

Right Description Administrator Developer OperatorAdd Instrument A right to use the Add function in the Instrument

menu. It is a function to add instruments to be used for the system.

Configure Instrument

A right to use the Configure function in the Instrument menu. It is the function to perform the COM port change and instrument baseline correction (with UV-1600/1700 series only) of the registered instruments.

Remove Instrument

A right to use the Configure function in the Instrument menu. It is the function to perform the COM port change and instrument baseline correction (with UV-1600/1700 series only) of the registered instruments.

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Shimadzu Spectrum Module Right Description Administrator Developer Operator

Acquire Data A right to perform measurement.

Data Print A right to use data print function Edit Method A right to use the Method function in the Edit

menu. It is the function to create/edit the measurement method.

Edit Settings A right to use the Settings function in the View menu. It is the function to set the number of digits of the data to be displayed, link setting of the report and template, whether message is displayed or not, display format of the dataset names, setting of the delimiters used at the time of saving text, etc

File Properties A right to use File Property. File Property is a function to confirm the file loaded on RAM and to change the names such as file names, storage names, and dataset names.

Go to Wavelength A right to perform wavelength transfer Load File A right to use the Open function in the File menu.

It is a function to read ASCII files, Measurement Methods, and various templates.

Manipulation A right to use data manipulation function. Peak Area A right to create the Peak Area table on the

Spectrum module.

Peak Pick A right to use the Peak Pick function of the Operation menu.

Perform Auto Zero

A right to use auto-zero function

Perform Baseline A right to use baseline correction function. Point Pick A right to use Point Pick function. Print Report A right to use Print Preview and Print functions in

the File menu. They are the functions to perform printing using the report template linked to each pane.

Properties A right to use the Properties function in the View menu. It is the function to edit or set the display of graphs and tables in each pane.

Save File A right to use Save, Save All, and Save as functions in the file menu. It is a function to save/overwrite Spectrum files, Measurement Methods, various templates, and various files.

Sewing Box A right to use the Sewing Box function.

NOTE : The data operation function is disabled in the GLP mode.

NOTE : File names, Storage names, and Dataset names cannot be changed in the GLP mode.

Introduction

UVProbe Manual 1-15

Shimadzu Standard Table Control Photometoric module


A right to copy the rows and columns of the standard table.

Delete Rows A right to delete the rows of the standard table.

NOTE : In the GLP mode, the rows of the standard sample table cannot be deleted.

Add a group

Groups are added in the Group page of the Administrative dialog box.

Groups can be added in addition to the existing user group. Two methods to add groups are available: one that creates new groups and the other that refers to the rights of the existing groups.

Creating a new group:

1 Click the Add button of the Group page to open the Edit Group dialog box.

2 Enter the group name you wish to add in the Group dialog box and the groups description in the Description edit box.

3 (To Procedure 3 in Group right setting ? Using Edit Group dialog box.)[TM3]

Referring to the right of the existing groups

1 Click the group to refer to in the group list in the Group page.

2 Click the Copy button to view the Edit Group dialog box.

3 Enter the group name you wish to add in the Group dialog box and the groups description in the Description edit box.

4 (To Procedure 3 in Group right setting ? Using Edit Group dialog box.)

Introduction

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Assign group rights

Rights of the group are set in the Group page of the Administrative dialog box.

Two methods to set group rights are available: one that uses the dialog box and the other that uses the Current Right list.

Using the Edit Group dialog box

1 Click the group you wish to set rights in the group list in the Group page.

2 Click the Properties button to open the Edit Group dialog box.

3 Select the target component from the Object combo box.

4 Click the target right, and then click the arrow button to transfer the right between the Available Functions list and the Selected Functions list.

5 Repeat steps 3 and 4 to set the rights.

6 When setting of the right is complete, click the Close button to confirm the setting.

Using the Administrative dialog box

1 Click the group you wish to set rights in the group list in the Group page.

2 Click the + mark next to the target module or object in the Current Rights list.

3 Give check marks to the boxes next to the each right and assign the right as shown in the figure.

4 Repeat steps 2 and 3 to set the rights.

5 When setting of the right is complete, click the Close button to confirm the setting.

Introduction

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Remove a group

A group is deleted in the Group page of the Administrative dialog box.

1 Click the group you wish to delete in the group list of the Group page.

2 Click the Remove button and confirm that the target group is deleted from the group list.

3 Click the Close button to confirm that it has been deleted.

NOTE : When users exist within the group, that group cannot be deleted. The registered groups cannot be deleted. Administrator group cannot be deleted.

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Add a user

A user can be added in the User page of the Administrative dialog box.

You can add a new user in addition to the existing user.

1 Click the Add button in the above User page to view the Add a User dialog box.

2 Enter User ID, User Name, and Password of the user you wish to register now.

3 Select the group into which the new user is registered from the Group Combo Box.


5 Click the Close button to confirm that the user has been added. NOTE : Once registered, the user cannot be deleted.

Introduction

UVProbe Manual 1-19

Edit user

User can be edited in the Users page in the Administrative dialog box.

The group to register the user and the password can be changed here.

1 In the user list of the Users page, click the user whose contents you wish to edit.

2 Click the Properties button to open the Edit User dialog box.

3 Edit the items you wish to change. Select the group to register the user into from the Group Combo box. To change the user password, enter a new password.

4 Click the OK button.

5 Click the Close button to close the Administrative dialog box.

NOTE : User Name and Full Name cannot be changed when UVProbe is set to the GLP mode. Only a system administrator can use this function. The same user cannot be registered in two or more groups.

Enabling/disabling user

To enable/disable user is toggled in the Users page of the Administrative dialog box.

Here, the registered users can be disabled or the disabled users can be enabled.

NOTE : The registered users cannot be deleted. To toggle user enabled/disabled, it is necessary to enter the reason. 1 Click the user you wish to disable/enable in the user list of the User page.

2 Click the Enable (Disable) button to open the Input a Reason dialog box.

3 Enter the reason to enable or disable the user in the Edit Dialog box.


5 Confirm that the target user is enabled or disabled, and then click the Close button to confirm the change.

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Changing a password

Password is changed in the Change Password page in the Administrative dialog box.

1 Enter the current password that the user is using.

2 Enter a new password.

3 Enter the password that has been entered in 2 in the Confirm edit box.

4 Click the Change button to confirm the password change.

NOTE : The minimum number of lower-case letters for a password is set by Shimadzu authentication tool. A password requires combination of numbers and alphabetical letters. A password differentiates upper-case letters and lower-case letters.

Introduction

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Using the Modules

Peak Pick Table in Operation Pane Spectrum Toolbar

Method Pane Photometer Button Bar Graph Pane

This is a graphic of the UVProbe window with an open Spectrum module. The Spectrum module is in its own window within the larger UVProbe window, and includes a Menu bar, a Standard toolbar, a Spectrum toolbar, an Instrument bar, a Photometer Button bar, and a Photometer Status bar. Use the View menu to enable/disable any of the toolbars or display elements.

Panes that vary between modules

The Spectrum window is divided into panes, with the Operation pane in the upper left, the Graph pane to the right, and the Method pane in the bottom left. The Kinetics and Photometric modules also contain panes.

Each pane has a specific function or set of functions. For example, the Spectrum module Graph pane displays three different types of graphs. The Method pane displays the data collection method information for the current data set, and the Operation pane displays data collected or manipulated by various operations, such as Peak Pick or Peak Area.

Use the View menu to enable/disable the panes. Resize panes by dragging the horizontal and vertical splitter bars.

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Unique menus and toolbars

Although the modules share some menus, the available menus change from module to module and the choices within the menus also change. For example, the Spectrum and Kinetics modules each have a Graph menu, while the Photometric module does not. However, the Graph menu provides different choices depending on whether the Spectrum or Kinetics module is active.

The modules also have their own toolbars, once again with both shared and unique capabilities.

For a detailed depiction of a module and a description of its purpose, see the introduction to the lesson for that module.

UVProbe Functions

This section describes some of the functions that must be understood before starting the tutorial, including:

Communicating with the spectrophotometer Shortcut menus and Properties pages Graph modes

Communicating with the Spectrophotometer

Once the PC is physically connected to the spectrophotometer (refer to the Instrument Installation Manual), and UVProbe had been installed and started, the software is almost ready to take measurements. The final step is to add and configure the instrument to work with UVProbe.

Add and configure an instrument 1 Select View > Instrument Bar.

2 Select Instrument > Add to initiate the Add Instrument Wizard.

3 Click Next to view a list of instruments.

Introduction

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4 Click the instrument model, then click Next.

5 In the Instrument name box, enter a name for the instrument. This will appear on the Instrument bar button.

6 Click Configure, then select the communications port for the instrument, usually COM1 or COM2. (When uncertain, look at the back of the computer. When the communication ports are not labeled, refer to the PC hardware manual.) Click OK.

7 Click Next.

8 Enter the model name and the serial number of the instrument. Be sure to enter them as each is recorded as one piece of data set information (summary).

NOTE: The serial number cannot be changed after it has been entered. When the serial number is incorrect, remove the instrument and add it again.

Some instruments contain internal serial numbers. When this is the case, UVProbe will automatically enter this information. 9 Click Finish to display a button on the Instrument Bar with the name of the installed

spectrophotometer will display. The screen should resemble the following.

Instrument Name

NOTE: Move the mouse along the button on the Instrument bar to display a ToolTip to identify the type of the instrument.

Connect to the spectrophotometer 1 Select Window > Spectrum, Kinetics, or Photometric. A module must be active before the

spectrophotometer can be connected.

2 On the Instrument bar, select the instrument button. When only one instrument is installed, it is automatically selected.

3 Ensure that the spectrophotometer is on, then click the Connect button.

When connected to the instrument, the Connect button changes to Start and the Photometer buttons become active, as shown in the next figure. Now create a data collection method for any module and begin taking readings.

If instrument initialization has not yet completed when connecting to the spectrophotometer, a window similar to the following may appear.

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NOTE: On some instruments, initialization is performed when the power is turned on. If the initialization has completed before the software is connected to the instrument, this screen will not display, and Instrument History is not stored. To ensure that instrument history is stored, connect to the instrument immediately after turning it on.

When necessary, click OK when initialization is complete. UVProbe stores the initialization information in the Instrument History for future use.

Shortcut Menus and Properties Pages

A Shortcut menu is a context-sensitive menu that can be accessed by right-clicking the mouse. A Properties page is a pane-specific dialog box used to set features or perform actions specific to the current pane and the current situation.

For example, right-click the Spectrum graph to display a Shortcut menu with options specific to the Spectrum graph. Or, right-click a Spectrum Operation pane containing an active Peak Pick table to display a Shortcut menu with options unique to Peak Pick, and select Properties to display the Peak Pick Properties page.

Manipulating a Properties page

The Properties page can be pinned so that it is always visible. Click in the upper left corner of the page to pin it. When moving from pane to pane, or module to module, the Properties page remains visible and dynamically updates with new choices and new information, depending on the contents of the active pane.

The Properties page can be moved like any other window or dialog box. Close the Properties page by clicking , or, when it is not pinned, click outside the box to close it. When data is entered into a Properties page, the entry takes effect when either the Return or Tab key is pressed or the mouse is clicked outside the Properties page.

Introduction

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Graph Modes

Each module contains graphs for tracking data. There are three graph modes for the Spectrum and Kinetics modules: Active, Overlay, and Stacked. In the Kinetics module there is also a Custom graph mode. The Photometric module has only two graphs: the Standard Curve and the Sample Graph.

Active Graph Mode

The Active graph mode displays a single line of data that represents the currently active data set. The data does not show in this mode until after it has been collected. To watch the graph update as UVProbe collects data, switch to the Overlay or Stacked mode. The Active mode is for viewing or manipulating data that is already in memory.

Overlay Graph Mode

The Overlay graph mode simultaneously displays all of the data sets in memory. For example, when there are three data sets in memory, this graph will display a line for each. It may be necessary to use the Auto Scale function on the Shortcut menu to fit all of the data into the graph. The Overlay mode also includes a graph legend to help distinguish between different lines on the graph. The legend can be hidden when not in use and is accessed on the Shortcut menu.

Whenever data is collected with the spectrophotometer, UVProbe automatically switches to Overlay mode and displays the data in real-time as it is collected.

Stacked Graph Mode

The Stacked graph mode displays a separate graph for each data set in memory. The graphs are stacked on top of one another. As more data sets are loaded into memory, each graph becomes smaller, until a scroll bar appears to the right. At that time, it becomes necessary to scroll to see the graphs. This scrolling option may be disabled to compress the graphs to fit within the plotting area. The X-axis labels disappear to conserve space. See Online Help for more information.

Custom Graph Mode

The Custom graph mode displays a custom graph arrangement only in the Enzyme graph pane of the Kinetics module. Its basic purpose is to simultaneously view Michaelis-Menten data acquired with several linear transform types.

Standard Curve

The Standard Curve is based on data in the Standard table. UVProbe uses points from the Standard table to calculate the curve and then uses the curve to determine the concentration value of the unknown samples in the Sample table. The Y-axis displays absorbance values and the X-axis displays concentration values. The Y-axis can also display transmittance, energy, or reflectance values, depending on the Measuring Mode set in Photometric > Method > Instrument Parameters.

Sample Graph

The Sample graph displays a point for each entry in the Sample table. The X-axis contains one point for each value in the table, and the Y-axis displays concentration values for each point. From the Graph menu, the graph can be changed to display absorbance values for each point on the Y-axis.

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File Properties, Storages, and Data Sets

Data is saved into a file that is divided into collection units called storages. Each storage contains one or more data sets. The data sets contain the actual data as well as all Method, History, and Summary information.

The basic data container is a file, and all data is stored in files that are subdivided into collection units called storages, and storages are further subdivided into data sets. Each file contains at least one storage, and each storage contains at least one data set.

For better understanding, see the following example which shows the File Properties dialog box displaying one file with multiple storages and multiple data sets.

File Storage Data Set

File Properties

On the File menu, Properties refers to the File Properties dialog box. (This is different from a Properties page.) Refer to Online Help for more information.

From this dialog box:

Determine which Spectrum files are loaded. List each storage and data set in a file. View method, history, and summary information. Rename a storage or data set. Hide a data set. Show a hidden data set. Store all data in a single file. Delete files, storages, or data sets from memory.

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Storage

A storage is a data unit contained within a file. There is one storage for each scan, and each storage contains one or more data sets, including the RawData set (the data collected in the scan) and any data sets created when manipulating the data.

Data Set

A data set is that part of a file that contains data collected in a scan or created in some other way, such as manipulating the scanned data. Data sets are grouped into storages.

Advantages

The advantages of the File, Storage, Data Set architecture becomes apparent when the Store All Data in a Single File feature is enabled. When this feature is enabled several options are possible:

Measurements taken using a cell positioner can be stored together. Every measurement for a given day can be stored in a single file under a different storage thus

reducing the total number of files that reside on disk. Measurements of similar samples can be stored together in one disk file.

Precision of Internal Data Processing

Calculations in UVProbe are performed using double-precision floating-point values. The data stored in a file also retains the same precision.

The data, either shown on-screen or printed, is rounded to either the user-specified or the default number of digits. This rounding process applies only to the on-screen or printed image and does not affect the precision of the stored data or any subsequent calculations. For example, a manually calculated calibration curve that is based upon on-screen or printed tabular data and the curve that is calculated by UVProbe using double-precision floating-point values may appear to be different.

NOTE: Double-precision Floating Point:

Compliant to IEEE. Mantissa: 53bit, Exponent: 11bit.

Equivalent decimal system: 16 digit * 10308

Rounding Process: The number is rounded up when it is five and above and any number under five is rounded down.

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The UVProbe Tutorial

After the software is installed, you are ready to begin the tutorial which includes four lessons, one each for the Spectrum, Photometric, and Kinetics modules, and one for the Report Generator. We recommend that lessons be completed in order; however, you can also skip to the lesson for a specific module. It is important to note that Lesson 4 on the Report Generator makes use of files created in Lesson 1; therefore, Lesson 4 cannot be completed without Lesson 1.

It is also important that the UVProbe Functions section be read and understood (see page 22), as certain procedures are explained that must be understood to successfully complete the tutorial.

All data files required by the tutorial can be located in the data subdirectory from which UVProbe was installed, e.g.,

C:Program FilesShimadzuUVProbeData

NOTE: All procedures in this tutorial are performed with GLP and security disabled.

Lesson 1 The Spectrum Module

Basic Measurements

In Exercise 1, perform a Baseline Correction, create and save a data collection method, and collect and save spectral data.

Basic Spectrum Operations

Exercise 2 contains basic Spectrum operations, including how to display and configure a Peak Pick table, how to create and manipulate a Peak Area table, and how to perform basic arithmetic operations on Spectrum data sets.

Advanced Spectrum Techniques

In Exercise 3, data is acquired with a cell positioner. Also, bitmap graphics are copied from the Spectrum module and pasted into WordPad.

Lesson 2 The Photometric Module

Basic Measurements

In Exercise 1, create a Standard table and a Standard Curve by taking readings with the spectrophotometer or by manually entering data into a Standard table.

Basic Photometric Operations

In Exercise 2, calculate unknown concentrations using various Standard Curves. Also, use Auto Fill to build a Standard table and perform a reciprocal operation on the data.

Advanced Photometric Techniques

In Exercise 3, create custom equations by performing a Hops Acid analysis, and use the sipper attachment to measure unknown samples.

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Lesson 3 The Kinetics Module

Basic Measurements

In Exercise 1, create a Kinetics data collection method and collect Time Course data with the Kinetics module.

Basic Kinetics Operations

In Exercise 2, create a Point Pick table, save the Point Pick data as a template, then open the template. Also, perform a cell blank operation, and interpret and control both the Activity and Main Kinetics tables.

Advanced Kinetics Techniques

In Exercise 3, create a Michaelis-Menten table to calculate Km and Vmax, create an Inhibitor table based on the calculated Km and Vmax values, and create a custom Kinetics graph configuration.

Lesson 4 The Report Generator

Create a Basic Report with Embedded Objects

In Exercise 1, create a report using embedded objects. The report will include an Overlay graph from the Spectrum module and a report title. Also save and print reports.

Create a Basic Report with Linked Objects

In Exercise 2, create a report using linked objects. The report will include a graph object and a Peak Pick table object linked to the active spectrum.

Advanced Reporting Techniques

In Exercise 3, add a linked object with custom settings, and insert various text objects into a report. Also, configure Quick Print in the Spectrum module.

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Chapter 2 The Spectrum Module, Lesson 1 The basic purpose of the Spectrum module is to control the spectrophotometer and scan through a range of wavelengths, while recording absorbance, transmittance, reflectance, or energy readings at each wavelength in the scanned range.

The module is easy to use and flexible, allowing design of simple or complex methods for collecting data. The instrument and attachment types can be configured for data collection. The user can save collection parameters, view collected data on graphs in various ways, manipulate the data with features such as Data Print and Peak Pick, save the data, and print it directly from within the module.

The module includes three panes: Operation, Method, and Graph.

The Operation pane is positioned in the upper left and contains all the data viewing and manipulation functions, such as Data Print, Peak Area, and Peak Pick.

The Method pane is positioned below the Operation pane and displays the data collection method information for the active data set.

The Graph pane is positioned on the right and contains the Active, Overlay, and Stacked graphs.

This lesson includes the following exercises:

Basic Measurements Basic Spectrum Operations Advanced Spectrum Techniques

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Spectrum Window

Operation Pane Spectrum Toolbar

Method Pane Graph Pane

Spectrum Toolbar

View Graph Tool Edit Method Tool Sewing Box Tool

View Operation Tool Data Print Tool

View Method Tool Manipulation Tool

File Properties Tool Peak Pick Tool

Settings Tool Point Pick Tool

Properties Tool Peak Area Tool

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Exercise 1 Basic Measurements

In this exercise:

Perform a Baseline Correction Create a data collection method Save a data collection method Collect the data Save the data Before beginning, maximize the UVProbe window and ensure that the Photometer Status bar, Photometer buttons, Instrument bar, and Output window are displayed. When necessary, select these items on the View menu.

NOTE: If an instrument was not added and configured as described in the Introduction, please do so now. See page 1-15, Communicating with the Spectrophotometer.

Step 1 Perform a Baseline Correction Baseline Correction sets the background to zero over the currently selected wavelength range and affects all subsequent readings within that range. This ensures a good reference point before collecting data.

NOTE: Perform a Baseline Correction periodically to compensate for drift.

After a Baseline Correction completes, UVProbe stores information about the Baseline Correction in the Instrument History, including the analyst, date and time.

NOTE: Before starting the Baseline Correction, ensure that neither the sample nor the reference beam is obstructed and that there are no samples in the sample compartment. Refer to the instrument manual for help in identifying the sample or reference beam.

Perform a Baseline Correction and view instrument history 1 Select Window > Spectrum to open the Spectrum module.

NOTE: When more than one instrument is installed, click the button on the Instrument bar that represents the desired instrument.

2 Click Connect on the Photometer Button bar to connect to the instrument.

3 Click Baseline on the Photometer Button bar to initiate the baseline operation.

4 When the Baseline Parameters dialog box appears, enter 700 as the Start and 300 as the End baseline parameters.

5 Click OK. Notice the reading in the Photometer Status window as it performs the baseline procedure.

6 When the scan is completed, click the Instrument History tab on the Output Window and notice that the Baseline Correction is listed.

Baseline Correction Listing

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Step 2 Create a Data Collection Method A data collection method will be created using a wavelength range of 600 to 450, a medium scan speed, and a sampling interval of 1.0 nm. The absorbance of a didymium filter will be measured. (Any available filter or sample may be used as a substitute.)

1 Select Edit > Method, or click the Method icon to display the Spectrum Method dialog box.

2 To set the Wavelength Range, enter 600 in the Start box and 450 in the End box.

3 Select Medium in the Scan Speed list.

4 Select 1.0 in the Sampling Interval list. This will set the machine to take a reading every 1.0 nm.

5 Click Single under Scan mode to take a single reading across the selected Wavelength Range.

6 Click the Instrument Parameters tab.

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7 Select Absorbance in the Measuring Mode list.

8 Click OK to send the parameters to the instrument. Notice the Photometer Setup message in the Photometer Status display. (This displays very briefly.) Leave all other method settings in their default state. Please refer to Online Help for more information about these settings. To access context-sensitive Help, right-click an item on the dialog box, then click Whats This?

Step 3 Save a Data Collection Method Sometimes it is useful to save a data collection method so that it can be used later to collect new data. Save the current method as an .smd file to be used in Exercise 3 of this lesson.

1 Select File > Save As.

2 In the File Name box, enter SpecMeth.

3 In the Save As Type list, click Method File (*.smd) and then click Save.

Step 4 Collect the Data The absorbance of the didymium filter will now be measured using the method above. First, configure the Y-axis of the Overlay graph to display the data as it is collected. Whenever a reading is initiated, UVProbe automatically switches to the Overlay graph and sets the X-axis to the wavelength range in the method. However, the Y-axis may have to be manually set to properly display data.

Configure the Overlay graph 1 Click the Overlay tab to place the graph in Overlay mode.

2 Click the minimum absorbance value on the Y-axis, and change it to -1.

3 Click the maximum absorbance value on the Y-axis, and change it to 3.

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Click on the Abs.values to change the range

NOTE: Either of the following techniques can be used after a scan completes. To ensure that all the collected data displays properly on the graph, use the Auto Scale function. After the

scan completes, right-click and select Auto Scale on the Shortcut menu to adjust the graph coordinates to fit the data.

To zoom in on a region of the graph, hold down the left mouse button and drag it to form a box around the area to be viewed. The graph will adjust immediately when the mouse key is released.

Perform a spectral scan 1 Place the didymium filter into the sample compartment of the spectrophotometer. For

additional information, refer to the instrument manual.

2 Click the Start button on the Instrument bar to initiate the scan.

3 When the scan is complete, enter Didymium as the file name in the New Data Set dialog box that appears onscreen.

4 Enter Data1 as the name of the data storage and click OK.

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Step 5 Save the Data At this point, data has been collected and named, but the data is stored in memory only; it is not saved to disk. If UVProbe is closed at this point, the data would be lost. To preserve the data, save it in a file.

When saving a Spectrum file, UVProbe stores the following for each data set in the file:

Peak Area table Point Pick table Peak Pick table Method information Summary information History information Save the data 1 Select File > Save As.

2 Select the appropriate data directory in the Save In box at the top of the dialog box.

3 Enter Didymium for the file name.

4 Select .spc in the Save As Type list.

5 Click Save.

NOTE: Select File > Save to save the file; however, Save As must be used to save the file to a specific data directory.

NOTE: We have two ways to show parameter of the data set.

1. Open File Property dialog box and select Data Set Icon. Parameter will be displayed in the Method tab.

2. On the Legend Window, double click on the data set. Parameter will be displayed in the Method pane.

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Exercise 2 Basic Spectrum Operations

In this exercise:

Open a Peak Pick table, adjust the threshold, and modify the table to annotate the graph. Create a Peak Area table. Manipulate a data set using Arithmetic and Transformations manipulation types to create two

new data sets.

Step 1 Adjust the Parameters of a Peak Pick Table Peak Pick is displayed in the Operation pane and is used to display all of the peaks and valleys in a data set, as well as the wavelength, absorbance, transmittance, or reflectance of the data at each peak and valley.

In this exercise, a Peak Pick table is viewed, the threshold value is adjusted, and the graph labeling is enabled and disabled to annotate a graph using the Peak Pick table Properties page.

Open the file and display it in the Active graph 1 Click the Active graph tab in the graph pane.

2 Select File > Open.

3 Double-click the file Holm_ox.spc located in the Data directory.

4 Right-click on the graph and choose Auto Scale to set the graph to display all of the data. Notice that each peak and valley on the graph is numbered.

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Display a Peak Pick table 1 Select Operations > Peak Pick.

When necessary, use the View menu to hide the Method pane and Output window to create more room onscreen for the Peak Pick table. The screen should resemble the following.

2 Right-click on the Peak Pick table and select Mark Peaks on the Shortcut menu. Repeat the

above step and select Mark Valleys. Notice that the peaks and valleys are no longer labeled on the graph, as in the following figure.

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Change the Peak Pick threshold value 1 Right-click on the Peak Pick table and select Properties on the Shortcut menu.

2 Click on the Properties page to pin it.

3 Enter 10 into the Threshold box and press Enter. Observe the change in the Peak Pick table. The table should resemble the following.

4 Enter 20 into the Threshold box and press Enter. Notice that the number of entries in the table decreases as the threshold value is increased. This is because the higher the threshold value, the fewer the number of peaks and valleys detected. For additional explanation of the Peak Pick threshold algorithm, see Online Help.

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Label each peak and valley on the graph 1 Drag the Properties page beneath the Peak Pick table to view the table.

2 In the Description column of the Peak Pick table, enter the following information. When Mark Peaks and Mark Valleys are enabled, these entries will appear on the graph.

No. Peaks No. Valleys 1 2 3 4 5 6 7 8 9 10 11 12

Peak A Peak B Peak C Peak D Peak E Peak F Peak G Peak H Peak I Peak J Peak K Peak L

13141516171819202122

Valley A Valley B Valley C Valley D Valley E Valley F Valley G Valley H Valley I Valley J

3 Click the Peaks tab on the Peak Pick Properties page.

4 Click in the Description check box. Notice that the entered descriptions are displayed on the graph peaks.

5 Click in the Number check box. Notice that the number above each peak is no longer displayed on the graph.

Spectrum

2-12 UVProbe Manual

6 Click the Valleys tab on the Peak Pick Properties page.

7 Click in the Description check box. Notice that the entered descriptions are displayed on the graph valleys.

8 Click in the Number check box. Notice that the number below each valley is no longer displayed on the graph.

The screen should now resemble the following figure. Noti

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