skanit for multiskan go user manual.pdf

8/19/2019 SkanIt For Multiskan GO User Manual.pdf

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Thermo Scientific

SkanIt Software 3.2

for Multiskan®GO

User Manual

R ev. 1.0


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Thermo Scientific

SkanIt® Software 3.2

for Multiskan® GO

User Manual

Rev. 1.0, Cat no. N10597


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Copyright

Copyright © 2010 Thermo Fisher Scientific. All rights reserved. Reproduction of the accompanying userdocumentation in whole or in part is prohibited.

Trademarks

“SkanIt” and “Multiskan” are registered trademarks of Thermo Fisher Scientific.

All other trademarks and registered trademarks are the property of their respective holders.

Remarks on screenshots

Screenshots may be slightly different on your system depending on the SkanIt Software and operating systemversions.

Disclaimer

Thermo Fisher Scientific reserves the right to change its products and services at any time to incorporate technologicaldevelopments. This manual is subject to change without prior notice as part of continuous product development.

Although this manual has been prepared with every precaution to ensure accuracy, Thermo Fisher Scientific assumesno liability for any errors or omissions, nor for any damages resulting from the application or use of this information.This manual supersedes all previous editions.

No liability for consequential damages

Thermo Fisher Scientific shall not be liable for any damages whatsoever arising out of the use or inability to use

this product.


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ContentsIntroduction ......................................................................................... 17Chapter 1

Installing SkanIt®

Software ................................................................ 21Chapter 2

Getting Started .................................................................................... 31Chapter 3User Interface ..................................................................................... 33Chapter 4

Session ................................................................................................ 43Chapter 5

Layout .................................................................................................. 53Chapter 6

Protocols ............................................................................................. 69Chapter 7

Step Parameters .................................................................................. 73Chapter 8

Starting a Session ............................................................................... 83Chapter 9

Results ................................................................................................. 87Chapter 10

Calculations ........................................................................................ 95Chapter 11Pathlength Correction ....................................................................... 145Chapter 12

Reports .............................................................................................. 151Chapter 13

Settings ............................................................................................. 159Chapter 14

Using Help ......................................................................................... 183Chapter 15

Multiskan GO Simulator .................................................................... 185Chapter 16

Troubleshooting Guide ...................................................................... 187Chapter 17

Database Maintenance ..................................................................... 189Appendix A

Registering SkanIt Software ........ ........ ......... ........ ........ ........ ........ .... 197Appendix BGlossary ............................................................................................. 199

Index .................................................................................................. 201

3Thermo Scientific SkanIt®

Software 3.2 for Multiskan®

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ContentsAbout the User Manual ....................................................................... 15Intended users ..................................................................................... 15For more information .......................................................................... 15Language versions of the Brief User's Guide ........................................ 15

Warnings and other markings used in the documentation ................... 16

Introduction ......................................................................................... 17Chapter 1SkanIt Software ................................................................................... 17Language versions of SkanIt Software .................................................. 17

Multiskan GO ..................................................................................... 17 Automation Interface ........................................................................... 18

Installing SkanIt®

Software ................................................................ 21Chapter 2Registering SkanIt Software ................................................................. 21Checking the PC requirements ............................................................ 21Microsoft Windows settings ................................................................ 22Starting the installation ........................................................................ 23Installing the software .......................................................................... 24Connecting an instrument ................................................................... 27Installing SkanIt Software for different instrument types ..................... 29

Uninstalling SkanIt Software ............................................................... 29Uninstalling the database engine .......................................................... 29Reinstalling (repairing) the software ..................................................... 30Technical description for system administrators ................................... 30

Getting Started .................................................................................... 31Chapter 3General operating procedure ................................................................ 31Starting SkanIt Software ...................................................................... 31Changing the language ........................................................................ 32

Working with demo sessions ............................................................... 32

User Interface ..................................................................................... 33Chapter 4

Navigating the software ....................................................................... 33Home view .......................................................................................... 35Layout view ......................................................................................... 37Protocol view ....................................................................................... 38Results view ......................................................................................... 39Reports view ........................................................................................ 40Effective use of the software ................................................................. 41

Context menus .................................................................................. 41Shortcuts ........................................................................................... 41

Session ................................................................................................ 43Chapter 5

Session structure .................................................................................. 43Creating a new session ......................................................................... 44





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Editing and saving a session ................................................................. 44Opening an existing session ................................................................. 46Deleting a session from the database .................................................... 47Exporting and importing sessions ........................................................ 47

Exporting sessions ............................................................................. 47

Importing sessions ............................................................................. 50Importing instrument sessions ........................................................... 50

Managing folders ................................................................................ 51

Layout .................................................................................................. 53Chapter 6Structure of a layout ............................................................................ 53Selecting a template ............................................................................. 54

Adding samples to a layout .................................................................. 54 Adding samples with the Fill With function ...................................... 55 Adding samples with the Fill Wizard function ................................... 60Example of adding a concentration series .......................................... 64

Editing samples ................................................................................... 65Clearing the layout .............................................................................. 66Copying a sample ................................................................................ 66

Adding a new plate .............................................................................. 66Renaming a plate ................................................................................. 66Deleting a plate ................................................................................... 66Viewing the original layout .................................................................. 67Printing the current layout .................................................................. 67

Protocols ............................................................................................. 69Chapter 7Defining a protocol ............................................................................. 69

Adding new protocol steps ................................................................ 70Renaming a protocol step .................................................................. 71Deleting protocol steps ..................................................................... 71

Step Parameters .................................................................................. 73Chapter 8Photometric measurement ................................................................... 73Spectrum measurement ....................................................................... 74Kinetic Loop ........................................................................................ 75

Area definition .................................................................................... 76Pause ................................................................................................... 77Shake ................................................................................................... 78

Incubate .............................................................................................. 80Plate In / Plate Out ............................................................................. 81

Starting a Session ............................................................................... 83Chapter 9Starting a plate session ......................................................................... 83Starting a cuvette session ...................................................................... 85

Results ................................................................................................. 87Chapter 10Measurement results ............................................................................ 87Calculation results ............................................................................... 87Viewing kinetic curves or spectra ......................................................... 88Disabling values from measurement data ............................................. 89

Arranging a list ................................................................................... 89Exporting measurement and calculation data ....................................... 92

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Exporting manually ........................................................................... 92Open in Excel ................................................................................. 92Exporting data ................................................................................ 93

Exporting automatically .................................................................... 93Presenting results as a report .............................................................. 94

Calculations ........................................................................................ 95Chapter 11 Adding calculations ............................................................................. 95Deleting calculations ........................................................................... 96Note on sample names ......................................................................... 96Blank subtraction ................................................................................ 97

Examples of blank subtraction ........................................................... 97Blank subtraction in kinetic measurements ........................................ 98

Basic statistics ...................................................................................... 99Pathlength correction ........................................................................ 101Spectral analysis ................................................................................. 102

Spectral peak search ......................................................................... 102Spectral maximum .......................................................................... 104Spectral minimum ........................................................................... 104Ratio within spectrum ..................................................................... 104Ratio between spectra ...................................................................... 105Select wavelength range ................................................................... 105Select single wavelength ................................................................... 105

Kinetics ............................................................................................. 106 Average rate ..................................................................................... 106Maximum rate ................................................................................ 107

Time to maximum rate ................................................................... 109Time to maximum rate / 2 .............................................................. 111Time to change ............................................................................... 111Maximum of well (Peak) ................................................................. 112Maximum - Minimum (Change) .................................................... 113Time to maximum (Peak) ............................................................... 113Time to maximum (Peak) / 2 .......................................................... 113Select reading .................................................................................. 113Ignore readings ................................................................................ 113Integral ............................................................................................ 114Sum ................................................................................................ 114

Average value .................................................................................. 115Baseline subtraction ......................................................................... 115

Precalculation .................................................................................... 117Merge data ......................................................................................... 118Graph ................................................................................................ 118

Viewing results as a graph ................................................................ 120Quality control (QC) ........................................................................ 122

Example of a Quality Control calculation ........................................ 123User-defined equation ....................................................................... 124Quantitative curve fit ......................................................................... 127

Quantitative curve fit definition ...................................................... 128Polynomial fit types ......................................................................... 130




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Point to point .................................................................................. 131Cubic spline .................................................................................... 131Four parameter logistic and Log-Logit ............................................. 131Quantitative curve fit results ........................................................... 132Multiple roots ................................................................................. 134

Effective dose ..................................................................................... 134Data normalization ............................................................................ 138Qualitative classification .................................................................... 139Parallel Line Analysis ......................................................................... 140

Performing a PLA calculation .......................................................... 141Results of the PLA ........................................................................... 142

Pathlength Correction ....................................................................... 145Chapter 12Microwell pathlength ......................................................................... 145Creating a K-factor ............................................................................ 146Pathlength correction with microplates .............................................. 147

Pathlength correction with cuvettes ................................................... 148

Reports .............................................................................................. 151Chapter 13Measurement and calculation reports ................................................. 151Creating a report ............................................................................... 151Editing a report ................................................................................. 152Editing a report item ......................................................................... 153Exporting the report .......................................................................... 154

Exporting manually ......................................................................... 154Open in Excel ............................................................................... 154Exporting data .............................................................................. 154

Exporting automatically .................................................................. 154Printing a report ............................................................................... 157

Printing a report manually .............................................................. 157Printing a report automatically ........................................................ 157Sending a report via email ............................................................... 157

Settings ............................................................................................. 159Chapter 14Options ............................................................................................. 159

General ........................................................................................... 159Database ......................................................................................... 160Results ............................................................................................. 161

Reporting ........................................................................................ 162Colors ............................................................................................. 163Plate Template ................................................................................ 163

Setting a plate template as default ................................................. 164Creating a new plate template ....................................................... 164Editing a plate template ................................................................ 165Deleting a plate template .............................................................. 166

Saved curves .................................................................................... 166K-Factors ........................................................................................ 168

Instruments ....................................................................................... 169

Instrument Setup ............................................................................ 169Setting the default instrument ....................................................... 170 Adding an instrument to the SkanIt Software database manually ... 170



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Creating an instrument report ....................................................... 171Instrument Settings ......................................................................... 172

Instrument temperature ................................................................ 172Power Save .................................................................................... 173

User Management ............................................................................. 173

Password Options ........................................................................... 174Users ............................................................................................... 175 Adding a new user ......................................................................... 175Viewing and editing user information ........................................... 177Changing the login password ........................................................ 177

Groups ............................................................................................ 179 Adding a new user group .............................................................. 179Viewing and editing group information ........................................ 180

Laboratory information ................................................................... 181

Using Help ......................................................................................... 183Chapter 15

Multiskan GO Simulator .................................................................... 185Chapter 16

Troubleshooting Guide ...................................................................... 187Chapter 17

Database Maintenance ..................................................................... 189Appendix ASelecting the database in SkanIt Software .......................................... 189Starting Database Maintenance ......................................................... 189Creating a backup file ........................................................................ 190Restoring a backup file ...................................................................... 190

Archiving sessions .............................................................................. 191Creating a new database ..................................................................... 192

Deleting the database ......................................................................... 193 Attaching the database ....................................................................... 194

Registering SkanIt Software ........ ........ ......... ........ ........ ........ ........ .... 197Appendix B

Glossary ............................................................................................. 199

Index .................................................................................................. 201




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FiguresMultiskan GO with cuvette spectrophotometer ....... ......... .. 18Figure 1-1Determining the maximum rate with window value 2 .... ... 107Figure 11-1Determining the time to maximum rate ....... ......... ........ ... 109Figure 11-2Integral calculation ....................................................... 114Figure 11-3Example of an absorbance curve ........ ........ ........ ........ ..... 115Figure 11-4Determining the average value of a kinetic measurement .. 115Figure 11-5Determining the baseline subtracted kinetic curve ........ ... 116Figure 11-6An example of a graph with photometric measurement

results ......................................................................... 120

Figure 11-7

Effective dose (ED) determination ......... ........ ........ ........ .. 135Figure 11-8





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Figures


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TablesMinimum PC requirements ........ ........ ........ ........ ......... ...... 22Table 2-1Keyboard shortcuts ......................................................... 41Table 4-1Function key shortcuts ..................................................... 42Table 4-2The minimum number of calibrators required in different curve

fit types ....................................................................... 129

Table 11-1

Rights of the different security groups ........ ........ ........ ..... 174Table 14-1





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Tables


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About the User Manual

Intended users The user manual has been written for the users of the Thermo ScientificMultiskan GO spectrophotometer and provides information on ThermoScientific SkanIt Software 3.2 for Thermo Scientific Multiskan GO. Themanual contains the operating instructions for Thermo Scientific SkanItSoftware 3.2 Research Edition (RE).

Read the manual in its entirety before using the software.

For more information For instrument-related issues, refer to the Thermo Scientific Multiskan GO User Manual (Cat. no. N10588). The instrument and software user manualscan be found in PDF format on the Thermo Scientific SkanIt Softwareinstallation CD. After installation, the user manuals open at the samelocation as the software itself:

Start > All Programs > Thermo SkanIt Software > SkanIt for Multiskan GO> SkanIt for Multiskan GO 3.2 User Manual.

For the latest information on products and services, visit our website on theInternet at:

http://www.thermoscientific.com

http://www.thermoscientific.com/readingroom

In an effort to produce useful and appropriate documentation, we appreciateyour comments on this user manual to your local Thermo Fisher Scientificrepresentative.

Language versions of the Brief User's Guide

The language versions of the Thermo Scientific SkanIt Software MultiskanGO Brief User's Guide can be found on the SkanIt Software installation CDin the Manuals folder.




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Warnings and other

markings used in thedocumentation

The following symbols and markings appear in this manual.

Caution Risk of damage to the instrument, other equipment orloss of performance or function in a specific application.

Note Marks a tip, important information that is useful in theoptimum operation of the system, or an item of interest.

TipGives a helpful hint for getting the most out of the softwarefunctionality.



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Chapter 1

Introduction

SkanIt Software SkanIt Software 3.2 for Multiskan GO is used to control all of theinstrument functions, and it provides data processing as well as reporting functions.

The information that is needed to define and run an assay is saved in anentity called a session. SkanIt Software enables you to build sessions for yourown applications and to run or modify ready-made sessions.

With SkanIt Software you can:

• Create and edit sessions

• Perform calculations and export data

• Create and print measurement and calculation reports

• Export and import sessions between SkanIt Software databases on

different PCs

• Import sessions exported from the instrument's internal software.

The sessions are made and stored in a database on the PC by using SkanItSoftware. Once you have created a session, you can run it directly from thesoftware.

Language versions of

SkanIt Software

The SkanIt Software user interface language can be freely chosen from theSettings. The following languages are available: English (default), German,French, Spanish, Portuguese, Japanese, Chinese and Russian.

For more information on changing the language, see Chapter 14: “Settings ”.

Note The online help is available only in English.

Multiskan GO The Multiskan GO is a high-quality monochromator-based UV/VISspectrophotometer. It is used in spectral scanning, end-point and kinetic

measurements to measure absorbance in the 200–1000 nm wavelengthrange from appropriate 96- or 384-well microplates with and without lids





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and various types of cuvettes (only with the cuvette version). The instrumentallows incubation up to 45°C and shaking of the microplate.

The instrument can be used by itself with the internal software for quick and simple plate and cuvette measurements or by controlling it with SkanItSoftware 3.2. The Multiskan GO is robotic compatible and can be connectedto plate handling devices such as stackers. The unique Power Save functionlowers its energy consumption. The Multiskan GO can be used in a variety of applications, including nucleic acid and protein analysis, ELISA assays,enzyme assays, cytotoxicity and cell proliferation assays as well as apoptosisassays.

Figure 1-1. Multiskan GO with cuvette spectrophotometer

The Multiskan GO is available in the following configurations:

• Multiskan GO 100–240 V – Cat. no. 51119200 and 51119250 (Japan)

• 96- and 384-well plate reading, shaking and incubation

• Multiskan GO with cuvette 100–240 V – Cat. no. 51119300 and51119350 (Japan)

• 96- and 384-well plate reading, shaking, incubation, and cuvette

reading with incubation

For more information, see the Multiskan GO User Manual (Cat. no.N10588).

Note This manual covers the operation SkanIt Software with theMultiskan GO with the cuvette port. If you have the MultiskanGO without the cuvette port, you can ignore the references tocuvette use.

Automation Interface SkanIt Software 3.2 can be integrated with and controlled via an automationenvironment. This can be done by incorporating MIB Automation Interface



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to the SkanIt installation. The required version is MIB Automation Interface3.0.0.6. For details, refer to the Thermo Scientific MIB Automation Interface Version 3.0 User Manual (Cat. no. N08444).






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Chapter 2

Installing SkanItThis chapter contains information that is necessary for a successfulinstallation of SkanIt Software. Read these instructions before you start toinstall SkanIt Software.

Note Failure to follow these instructions may lead to anunsuccessful installation of SkanIt Software.

Registering SkanItSoftware

You need an installation code for SkanIt Software. To receive the code, youhave to register SkanIt Software by filling out the registration form on our

website at:

www.thermoscientific.com/skanit

For more information, see Appendix B: “Registering SkanIt Software ”.

During software registration you will need the instrument serial numberand the CD serial number that is printed on the installation CD package.

The code that you receive as a result of the registration is sent to the emailaddress that you enter on the registration page. When you log in for thefirst time, the software asks you to enter the code (see Enter the InstallationCode in “Connecting an instrument” on page 27).

Note You can also install SkanIt Software without registering itfirst. The Software will work for 30 days without the installationcode. During this period, the code is asked every time you log in.

Checking the PC

requirements

Check that the PC meets the requirements that are needed for using SkanIt

Software.

The table below lists the minimum PC requirements for SkanIt Softwareversion 3.2.




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Table 2-1. Minimum PC requirements

Minimum PC requirements

Microsoft Windows 7

Microsoft Windows Vista with Service Pack 2 (or later)

Microsoft Windows XP Professional with Service Pack 3

(or later)

Supported operating systems

5 GB free hard disk spaceDisk space

Dual-core processorProcessor

2 GB RAMMemory

1Available USB port

Mouse or equivalent is necessaryPointing device

1CD-ROM drive

XGA monitor with 1024 x 768 resolutionMonitor and color settings

Microsoft Internet Explorer 6.0 (or later)Browser

If you do not have the correct Service Packs installed, you can downloadthem from the Microsoft website at:

www.microsoft.com

Microsoft WindowssettingsIn the Power Options Properties , ensure that the Turn off hard disks , Systemstandby and System hibernates settings are set to Never . In long kinetic sessionsthe computer is seemingly in an idle state, as the data flow is not monitored.Therefore, if the power option setting is not set to Never , the computer may turn off the power in the middle of a measurement. The power optionssettings can be checked and changed in the Power Options Properties

window:

Windows XP :

Start > Settings > Control Panel > Power Options > Power Schemes > Turn

off hard disk/System standby/System hibernates > Never

Windows Vista or Windows 7 :

Start > Control Panel > Power Options > Change when the computer sleeps> Change advanced power settings > Turn off hard disk after > Never

Start > Control Panel > Power Options > Change when the computer sleeps> Put the computer to sleep > Never



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Start > Control Panel > Power Options > Change when the computer sleeps> Change advanced power settings > Sleep > Hibernate after > Never

Starting theinstallation

To start the SkanIt Software 3.2 for Multiskan GO installation, follow thesesteps:

Note SkanIt Software cannot be installed on a network drive.

Note You have to be logged on to your computer withadministrator privileges to install SkanIt Software.

Note You can stop the installation procedure at any stage by clicking Cancel. The setup returns your system to the previousstate.

1. Check that the PC requirements in Table 2-1 are met.

2. Insert the SkanIt Software installation CD into the CD-ROM driveof your PC.

3. The Welcome to ThermoFisher Software Setup dialog opensautomatically. If the dialog does not open, start the installation from

the CD by double-clicking the Setup.exe file.

The SkanIt Software Setup checks that all the software and systemrequirements are met. The setup installs the required components:

• SkanIt Software 3.2, always installed

• Microsoft SQL Server 2008 R2 Express, installed if not found onyour PC

• Microsoft .NET Framework 3.5 SP1, installed if not found on

your PC

• Microsoft Visual C++ 2005 SP1

• Windows Installer 4.5, installed if not found on your PC.

4. Close all other programs on your computer and click Next .




Installing SkanItStarting the installation

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5. Click Install Software Prerequisites to install the software requiredbefore installing SkanIt Software.

If a restart is requested during the installation of software prerequisites, it

should be confirmed. After the restart, click Install Software Prerequisitesto continue the installation.

After all the prerequisites have been installed, you can proceed with theactual software installation.

Installing the software When the prerequisites have been installed, the SkanIt for Multiskan GOSetup will proceed with the actual SkanIt Software installation.

1. In the SkanIt for Multiskan GO 3.2 dialog, click Install Software to

start the Setup Wizard.



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The wizard guides you through the entire installation procedure. Inthe Setup Wizard dialog, click Next .

2. Read the Licence Agreement and click I Agree to accept it and proceed

with the installation. Click Next .

3. Fill in your customer information and click Next .

4. Select the installation location and click Next .

The Setup Wizard suggests a location for the program files. Changethe suggested location only if absolutely necessary. Click Browse toselect another folder or drive.

Click Disk Cost to view the available disk space on the available drives.

The recommended minimum free disk space for SkanIt Software is 5GB.

5. The Setup Wizard is now ready to install SkanIt Software for MultiskanGO on your computer. Click Next to start the installation.

6. Accept or modify the information in the SkanIt Database Configuration.






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• Create a new database. SkanIt Software is connected to an existing database engine (the one that was installed in the prerequisites)and a new SkanIt Software database will be created.

• Use an existing database. If you have previously created a database,SkanIt Software is connected to an existing database engine andan existing SkanIt Software database will be used.

• Server Name. This is the name of the database engine (SQL Server)in which the SkanIt Software database will be created. The databaseengine has the instance name THERMO, separated by a backslash(\).

• DB Name. The name of the SkanIt Software database which you want to create. The default name is Skanit_GO_RE . If the database with the defined name already exists, an error message is displayed.The existing database will not be overwritten.

Click Configure.

The installation proceeds with the database configuration. Wait untilit has finished even if the installation seems not to respond. This may take several minutes.

7. You will receive a confirmation message when the installation iscomplete. Click Close.

Click OK in the Thermo Fisher Scientific Software Setup dialog indicating that the installation is complete.

8. In the SkanIt for Multiskan GO 3.2 dialog, click Exit to finish theinstallation.



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Note The installation of a new database engine does not affectany other installed database engines.

Note If the installation fails, SkanIt will be removed but thirdparty components (SQL server and Microsoft .NET) may remaininstalled. When reinstalling SkanIt Software, the installation detectsthis and takes it into account.

After the installation, the setup directly proceeds with connecting aninstrument to the software. If you want to make a connection to aninstrument, proceed with “Connecting an instrument” on page 27. If youdo not want to make a connection to an instrument, proceed with Step 4in section “Connecting an instrument“.

If you do not set up a connection to any instrument at this point, thesimulator will be set as a default instrument.

Connecting aninstrument

After installing the software (see “Installing the software” on page 24), youcan connect the instrument to the software.

1. Ensure that the instrument is switched off.

2. Connect the instrument to the computer by using a USB cable.

3. Switch on the instrument. Wait for the instrument to finish initializing.

In the ThermoFisher Scientific Software Setup dialog, click OK .

4. Log in to SkanIt Software. Use admin as your Username and leave thePassword field empty. Click Login.

5. Enter the CD Serial number and Installation Code .




Installing SkanItConnecting an instrument

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The CD serial number is printed on the cover of the SkanIt SoftwareCD. You receive the installation code from:http://www.thermoscientific.com/skanit

Note You must enter the CD serial number, but SkanIt Softwarecan be used for 30 days without entering the installation code. If you do not enter the code, the software will ask for the code every time when you log in. If the code is not entered in 30 days, you

can open the software but sessions cannot be run.

Click OK .

After you have logged in, the software searches for new instrumentsand makes the connection automatically.



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6. Select an instrument from the list. The selected instrument is set asthe default instrument. Click OK .

If no instruments are found, the software reminds you to check thatthe cables are connected and the instrument is switched on.

If no instrument is available, click Cancel. The simulator will be set

as the default instrument if you have not connected any instrumentsearlier. You can also connect an instrument to the software later (formore information, see “Starting SkanIt Software” on page 31 and“ Adding an instrument to the SkanIt Software database manually ” onpage 170).

Installing SkanItSoftware for different

instrument types

SkanIt Software is published separately for different instrument types. If you want to use the same PC to operate several instruments, such asVarioskan Flash, Multiskan FC and Appliskan, you need to install separateversions of SkanIt Software onto your PC.

Uninstalling SkanItSoftware

You can uninstall SkanIt Software by clicking Add or Remove Programsin the Windows Control Panel.

Click Remove. You are asked to confirm the removal of the program. Click Yes. The SkanIt Software is uninstalled.

Removing SkanIt Software will not remove the database engine or theMicrosoft .NET Framework, because they may be used by other softwareapplications.

Uninstalling the

database engine

Backup the database with a database maintenance tool, if you choose todelete the SkanIt database engine. The following files will remain in the

installation folder after the uninstallation: SkanIt_GO_RE.mdf andSkanIt_GO_RE.ldf .




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You can delete these files, make a backup copy of them, or attach them toa database engine (Microsoft SQL Server 2008 R2 Express) using DatabaseMaintenance (see Appendix A: “Database Maintenance ”).

The database engine can be uninstalled by clicking Add or RemovePrograms in the Windows Control Panel.

Caution Do not delete the database engine if any of your othersoftware applications uses it.

Reinstalling (repairing) the software

The repairing mode is not supported. You have to uninstall SkanIt Softwareand then install a fresh copy.

Technical descriptionfor system

administrators

The system does not open any communication ports on the target computer.Communication with Multiskan GO is handled via a USB port. Installationconfigures the SQL Server to accept only local connections.

The installation grants the Windows Users group full privileges to the SkanItconfiguration files in the installation folder (default c:\ProgramFiles\Thermo\SkanIt for GO 3.2\). The installation also grants the WindowsNetwork Service user full privileges to the data folder located in the

installation folder.



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Installing SkanItTechnical description for system administrators

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Chapter 3

Getting StartedThis chapter contains information that helps you get started with thesoftware after the installation.

General operatingprocedure

The general operating procedure with SkanIt Software is as follows:

• Start SkanIt Software.

• Open an existing session or create a new one.

• Edit the session (protocol, layout and calculations) if necessary and saveit.

• Start the session.

• Perform calculations.

• Create a report.

• Export the results.

Starting SkanItSoftware

1. Start the software from the Start menu:

Start > Programs > Thermo SkanIt Software > SkanIt for MultiskanGO > SkanIt for Multiskan GO 3.2.

or double-click the Skanit for Multiskan GO 3.2 shortcut icon onyour desktop.

2. The SkanIt Login dialog opens.




http://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_LaunchingSkanItSoftware.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_OpeningAnExistingSession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_CreatingANewSession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_SavingASession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_ExecutingASession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Calculations_AddingCalculations.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Reports_CreatingAReport.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Results_MeasurementAndCalculationReports.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Results_MeasurementAndCalculationReports.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Reports_CreatingAReport.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Calculations_AddingCalculations.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_ExecutingASession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_SavingASession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_CreatingANewSession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_OpeningAnExistingSession.htmlhttp://localhost/var/www/apps/conversion/tmp/scratch_3/Sessions_LaunchingSkanItSoftware.html


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Note When you log in for the first time, enter “ admin” in theUser name field and leave the Password field empty. Use SkanIt

User Management to create new users (see “ Adding a new user”on page 175) and to change the administrator password to protectdata security (see “Changing the login password” on page 177).

3. Type your user name and password and click Login. The softwarestarts to load. The software will try to connect to the default instrumentif the Connect to default instrument at startup setting is selected inthe Settings > Options > General menu.

When the software is ready for use, the main window opens. You can now create a new session (see “Creating a new session” on page 44), open anexisting session (see “Opening an existing session” on page 46) or open a demo session (see next section “ Working with Demo Sessions”).

Changing the language To change the user interface language of SkanIt Software:

1. Click Settings in the Home view.

2. In the General dialog, select the desired language from the list.

3. Click Close and restart SkanIt Software for the change to take effect.

Working with demosessions

SkanIt Software provides demo sessions in the Recent Sessions list of theHome view. More demo sessions are available in the Thermo FisherScientific > Demo Sessions folder.

To open a demo session, click the session in question and follow theinstructions in the Protocol view of each session. You can freely edit a demosession, save it with a new name, perform calculations and create reports.

The original demo sessions cannot be deleted.



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Chapter 4

User InterfaceThis chapter describes the functionality of the user interface. It providesinformation on its features, the toolbars and functions and tells you how you can use them effectively.

Navigating thesoftware

When you log into SkanIt Software for Multiskan GO, the main (Home)view opens.

The SkanIt Software user interface is divided into five views: Home, Layout ,Protocol, Results and Reports. You can easily navigate from view to view by clicking the desired tab on the navigation bar. The tabs are visible inevery view of the software, and they become active after you open a new oran existing session.

Toolbar (1)

The toolbar contains the most frequently used functions. The toolbar alsoshows the currently open session, and the name and the version of thesoftware. The toolbar is displayed in every view.

New creates a new session.





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Open launches the Open Session dialog for opening an existing session.

Save saves the session that is currently open.

Show Help opens the SkanIt Software Help.

Application menu (2)

Open the Application menu by clicking the SkanIt Software icon.

The New , Open and Save buttons function as on the toolbar.

Save As saves a session with a new name.

Lock locks the software to prevent unauthorized use. Only a user whohas locked the software or an administrator can unlock the software.

Help opens the SkanIt Software Help.

About provides information on the SkanIt Software application.

Exit closes SkanIt Software.

Navigation bar (3)

The navigation bar displays the tabs for the Home, Layout , Protocol,Results and Reports views.

Action panels (4)

Action panels include the available functions that differ in each view.

If the window is too small, all action panels and function buttons are notdisplayed. In this case, black arrows indicate the missing buttons. Otherpossible unavailable action panels and buttons become available by enlarging the window size.

Status bar (5)

The status bar at the bottom of the view displays the following information:

• The connected instrument. When the software is connected to an

instrument, the icon is displayed with instrument information, and

the Disconnect and the Plate In and Plate Out buttons are



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active. When an instrument is not connected, the icon, instrumentinformation and the Connect button are displayed.

If the Disconnect/Connect and the Plate In/Plate Out buttons arenot visible, you have to enlarge the window size.

• The temperature of the instrument's plate measurement chamber andcuvette port (if an instrument is connected) as well as the targettemperature if set.

• The logged-in user (for example, admin)

Home view The Home view opens every time you log into SkanIt Software. In theHome view, you can perform basic functions that concern sessions andinstrument operation, and access the software settings.

The Home view includes the following parts and functions:

Recent Sessions (1)

Recent Sessions lists the recently used and pinned sessions.

You can set the number of sessions that are displayed in the list (for more

information, see “General” on page 159). You can also click the pin besidethe session name to pin or unpin the session. If a session is pinned, it is




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always shown in the list regardless of use. If a session is not pinned, it willdrop off the list if you do not use it frequently.

Session action panel (2)

New creates a new session (see “Creating a new session” on page 44).

New K-factor creates a new K-factor (see Chapter 12: “PathlengthCorrection”).

Open launches the Open Session dialog for opening an existing session

(see “Opening an existing session” on page 46).

Save saves the current session in the database (see “Editing and saving a session” on page 44).

Save As opens the Save As dialog for saving the current session with a new name (see “Editing and saving a session” on page 44).

Import imports sessions that are exported from another SkanIt Softwarefor Multiskan GO database or from the instrument's internal software (see“Exporting and importing sessions” on page 47).

Export exports selected sessions as a separate file (*.msz ) that can beimported to another SkanIt Software for Multiskan GO database (see“Exporting and importing sessions” on page 47).

System action panel (3)

Settings opens a dialog for defining the instrument andsoftware-related settings.

Help opens the SkanIt Software Help.

Instrument action panel (4)

Connect opens the connection to the instrument that is selected from

the list. This icon is visible when the software is not connected to aninstrument.



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Disconnect closes the connection to the instrument. This icon isvisible when the software is connected to an instrument.

Set Temperature opens a dialog for setting the instrument temperature.This button is displayed only when an instrument is connected.

Plate In runs the plate into the instrument. This function is active if an instrument is connected.

Plate Out runs the plate out of the instrument. This function is activeif an instrument is connected.

Start begins the measurement (see Chapter 9: “Starting a Session”).

Layout view In the Layout view, you can define the sample layout for the session.

The Layout view includes the following parts and functions:

The Action panels (1) include the functions that are available in the Layout view.

For more information on the button functions, see Chapter 6: “Layout ”.




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The Current template (2) shows either the selected plate type or cuvette.

The Plate tabs (3) show the plates that are added to the plate layout. Click

a tab to select the plate.

The Layout pane (4) shows the plate or cuvette set and its contents.

The Zoom slider (5) enables you to increase or decrease the magnificationof the layout.

The Description field (6) shows the optional description that the user candefine for the layout.

Protocol view In the Protocol view, you can add and define the protocol steps for thesession.

The Protocol steps (1) tree view shows the added steps in hierarchical order.

The Main pane (2) shows the protocol properties of a session or if you click a protocol step, the pane shows the parameters of the protocol step inquestion.

The Action panels (3) include the functions that are available in theProtocol view.

For more information on the function of the buttons, see Chapter 8: “StepParameters ”.



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Results view In the Results view, you can view the results after the measurement. Youcan also add calculations to measurement data and view these results here.

The Results tree (1) shows the measurement and calculation steps inhierarchical order.

The Main pane (2) shows the measurement or calculation results as a tableor list. You can choose the display format with the tabs (3).

The Toolbar (4) includes functions for editing steps.

The Action panels (5) include the calculations and other functions that are

available in the Results view.

For more information on the functions of the buttons, see “Exporting measurement and calculation data ” on page 92 and Chapter 11:“Calculations ”.




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Reports view In the Reports view, you can create a report to which you can add themeasurement and calculation results of your choice.

The Reports tree (1) shows the individual measurement and calculationresults that have been added to the report in hierarchical order.

The Toolbar (2) includes functions for editing the report.

For more information, see “Editing a report” on page 152.

The Main pane (3) shows the selected measurement or calculation resultsin the report.

The Action panels (4) include functions that are available in the Reportsview. For more information on the action panel buttons, see “Creating a report” on page 151, “Exporting the report” on page 154 and “Printing a report ” on page 157.



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Effective use of the

software

You can speed up the use of SkanIt Software by using context menus and

shortcut keys as described below.

Context menus When using the software, you can often open a context sensitive menu by right-clicking the mouse. For example, in the Protocol and Results views,you can also edit and add steps by right-clicking in the tree view and selecting the function from the context menu. Context menus allow quick access tofunctions that are relevant to the situation. Some functions, such as advancedgraph properties and enabling or disabling values from measurement data in the Results list view, are available only from the context menu.

Context menus are available in all measurement result lists, in the platelayout view, and in the protocol and result trees.

Shortcuts You can select menus by pressing Alt and the underlined letter; for example,Settings is selected by pressing Alt+S.

Some of the operations have keyboard shortcuts. These are presented inTable 4-1.

Table 4-1. Keyboard shortcuts

Keyboard shortcutOperation

Ctrl+NCreate a new session

Ctrl+OOpen an existing session

Ctrl+SSave a session

Ctrl+Shift+SSave a session with a new name

DelDelete a step or result

Alt+HOpen the Home view

Alt+LOpen the Layout view

Alt+POpen the Protocol view

Alt+ROpen the Results view

Alt+EOpen the Reports view

Alt+SOpen the Settings menu

Alt+IOpen the Import dialog

Alt+XOpen the Export dialog

Some of the operations have function key shortcuts. These are presented inTable 4-2.




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Table 4-2. Function key shortcuts

Function key shortcutOperation

F1Open the help application

F2Rename a protocol step or result

F5Run a session

F9Run the plate in

F10Run the plate out

F11Connect to the default instrument

F12Disconnect from the default instrument



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Chapter 5

SessionThis chapter describes the structure of a session and how you can create andedit the sessions.

Session structure A session includes all the definitions that are required for successfulmeasurement and result data processing. You can create a new session, savethe current session and open an existing one. Only one session can be openat a time.

The structure of a session:

• Layout defines the plate type or cuvette set and the samples in each wellor cuvette. Sample properties, such as concentrations or dilutions, canalso be defined.

• Protocol defines the protocol steps and parameters which are requiredfor the instrument to perform actions.

•

Results shows the raw measurement data and the defined calculations with the results.

• Reports presents the selected measurement and calculation results as a report.

Running a session produces measurement data. The measurement data is processed with the calculations that you define in the results. You canrun a session several times and each execution produces new measurement data. The executed sessions are saved automatically andthey can be opened or exported separately.

The functions of the Session action panel in the Home view are describedin the following sections.





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Creating a new

sessionIn the Home view, click the New icon on the toolbar. A new session is now created and the Layout view opens.

You can start creating a session by defining the layout and adding protocolsteps (see Chapter 6: “Layout ” and Chapter 7: “Protocols ”).

Editing and saving asession

1. In the Home view, click Save or Save As on the toolbar or on theSession action panel.

Note If you use the Save As command for an executed session,the new session, which is created, does not contain any measureddata of the original session.



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2. Enter a name for the session in the Session name field. You can savethe session in an existing folder or create a new folder for the sessionin the tree view. Click New Folder or right-click the parent tree tocreate a new folder under it. Click OK to save the changes.

If a new session is saved before starting the measurement, a separate session without measurement data is created. This session is marked with in thesession list. You can always edit this session for new measurements, and itnever contains any measurement data.

When you start a session, an executed session is created. This session, whichhas been run and includes measurement data, is marked with . You canedit the layout, calculations and reports of an executed session. Any changesmade after the measurement must be saved separately.

When you edit a protocol of a session that includes measurement data, thesoftware informs you that a new session has to be created. If you accept this,the software will automatically create an identical new session but withoutresults.

If a new session is not saved before starting the measurement, only anexecuted session is created and automatically saved in the SkanIt Software folder.




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Opening an existing

sessionIn the Home view, click Open on the Session action panel.

The Open Session dialog shows all the sessions that are currently in thedatabase in a hierarchical tree view. In this dialog you can create new folders,rename folders, move sessions between folders, and delete folders and

sessions. The sessions without measurement data are marked with , theexecuted sessions with measurement data are marked with .

You can open a session with no measurement data or a particular executedsession that includes the measurement data of the session that has been run.

To open an existing session:

1. Click a session in an appropriate folder in the tree view.

2. Click Open or double-click the session.



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Deleting a session

from the databaseTo delete a session from the database on the PC:

1. In the Home view, click Open.

2. In the Open Session dialog, select the desired session from the tree view.

3. Click Delete, or right-click the session and click Delete. You can selectmultiple sessions by pressing the Ctrl key while selecting the sessions.If the session is currently open, you cannot delete it unless you first

close it.

Exporting andimporting sessions

SkanIt Software does not save sessions to separate files, but uses a databaseinstead. Sessions can be exported as a separate file (*.msz ) that can beimported to another SkanIt Software for Multiskan GO database.

It is also possible to import plate measurement sessions directly from theMultiskan GO instrument using a USB memory device.

Exporting sessions

1. In the Home view, click Export . The Export Data dialog opens.




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2. In the hierarchical tree, select the checkbox beside the sessions thatyou want to export.

3. Click Browse to select the file path.

4. Select a location for the SkanIt data file (*.msz ).

5. Enter a name for the file.

6. Click Save. The “_GO ” suffix is added to the filename to distinguish

it from data that is exported from other instruments.

7. Click OK .

You will receive a message which informs you whether the exportprocedure was successful.

Importing sessions

1. In the Home view, click Import . The Import Data/Import Options dialog opens.



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3. Select the SkanIt data file (*.msz ) by browsing in the Open dialog.

4. Click Open. The file path appears in the File location field in the Import Options dialog.

5. Click Next .

In the Import Data/Definitions done dialog, you can view the sessionsthat are imported. If there are already sessions with the same name inthe database, the sessions in the database will not be overwritten. Thesoftware automatically adds a new number to the file name of the new,imported sessions to distinguish them from previously imported

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6. Select a folder to which you want to import the selected sessions. You

can also create a new folder.

7. Click Finish.

You will receive a message which informs you whether the importprocedure was successful.

The imported session is shown in the folder tree with the text [import] infront of it.

Importing instrumentsessions

To import an instrument session, you must first export the session from theMultiskan GO internal software. You can import only microplate sessionsthis way. Cuvette sessions exported from the instrument cannot be importedto SkanIt Software.

1. In the Home view, click Import . The Import Data/Import Options dialog opens.


3. Select the session file (*.txt ) by browsing in the Open dialog. Set the

file type to Multiskan GO Data File .

4. Click Open. The file path appears in the File location field in the Import Options dialog.

5. Click Next .

6. Select a folder to which you want to import the selected sessions. Youcan also create a new folder.

7. Click Finish.

You will receive a message which informs you whether the importprocedure was successful.

The imported session is shown in the folder tree with the text [Imported from instrument] in front of it.

SkanIt Software automatically adds unknown samples to the layout basedon the wells measured with the instrument session. You can edit the sample



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types in the layout, for example, by changing the unknown samples to

blanks, calibrators or controls to be able to perform calculations.

Managing folders Sessions are managed by using a tree view.

The root folder in the tree view is SkanIt Software under which you cancreate new folders. A new session is stored in the root folder by default. TheThermo Fisher Scientific folder has demonstration sessions created by ThermoFisher Scientific. It is not possible to remove the root folder or the ThermoFisher Scientific folder and its sessions, but you can move the sessions toanother folder.

Sessions can be organized and stored in folders that you can easily create,move, rename or delete in the Open Session dialog.

To create, rename or delete a folder, click the appropriate button on thetoolbar, or right-click the folder in question and select the action from the

menu.

To move a folder or a session, drag it to the correct folder in the tree view.




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Chapter 6

LayoutThis chapter describes how to define samples on the layout.

Structure of a layout The layout defines the plate template or cuvette set and the samples in thesession. Internal calculations on the measured data are made based on thelayout.

The following sample types can be used in a layout:

• Unknown samples are the samples under investigation.

• Blank samples are used for blank subtraction.

• Calibrators are samples with known concentrations used for quantitativeanalysis (see “Quantitative curve fit” on page 127).

• Control samples are used for quality control (see “Quality control (QC)”on page 122) and for qualitative analysis (see “Qualitative classification”on page 139).

• Empty wells remain empty and are not measured.

If there are no samples in the layout when you start the measurement, thesoftware asks you if you want to fill the layout with unknown samples.





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Selecting a template After you click New in the Home view to create a new session, the Layout view opens.

You can now define the layout.

Select the appropriate 96-well or 384-well plate or cuvette template for thelayout from the list.

You can define several plate layouts, but only a single cuvette set with upto 32 cuvettes.

Adding samples to alayout

You can add samples to a layout in two ways:

• Use the Fill With function. It allows you to perform most layoutdefining actions, except adding specific blanks and dilutions forunknowns or loading sample IDs from a text file.

• Use the more advanced Fill Wizard for microplates. This feature is notavailable for cuvette sets.



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Adding samples with the

Fill With functionThe Fill With function is an easy way to create a layout. You can use it toadd blanks, unknowns, controls and calibrators with possible concentrationsand replicates to the layout.

To add samples to the layout:

1. Paint the wells or cuvettes with the left mouse button.

2. Right-click or click the Fill With icon.

3. Select the desired sample type from the menu and define its parameters

4. Click OK to add the samples to the layout.






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Filling in sample type information UNKNOWNS :

Samples :

• Name. The sample name is suggested automatically. The name consistsof an abbreviation of the sample and of running numbers, for example,Un_0001, Un_0002, and so on. You can change the name, but therunning numbers after the abbreviation cannot be deleted.

If you select several plate wells for a sample type, you have to define theorder in which the wells are filled with individual samples and their possiblereplicates:

Fill as ...

• Individual samples. All selected wells or cuvettes have individualsamples without replicates.

• All replicates. All selected wells or cuvettes have replicates of one sample.

• Horizontal samples with replicates. Individual samples are placedhorizontally and replicates are added below each individual sample.(Not for cuvettes.)

• Vertical samples with replicates. Individual samples are added vertically and replicates are added next to each individual sample. (Not forcuvettes.)



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CALIBRATORS :

You have to define concentrations for calibrators:

Concentrations :

• Single. When Single is selected, all the selected wells or cuvettes havethe same concentration.

• Value. The concentration value.

• Unit . The unit for the concentration.






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• Series. When Series is selected, a mathematically regularly-changing concentration series is created.

• Initial value. The initial concentration value.

• Op. Defines the mathematical operator in the formula for the series.The choices are multiplication (*), division (/), subtraction (-) andaddition (+). The concentrations increase or decrease from the initialvalue by the steps defined in the Step by field.

• Step by . The factor for the concentration series.

• Unit . The unit for a concentration.



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• Values. When Values is selected, the concentration series is created by entering the values one by one.

• Add. Adds the selected value to the list.

• Remove. Removes the value that you select from the list.

• Clear. Clears all values from the list.

• Unit . The unit for a concentration.

• Use the arrow keys to move the order of the values.






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Adding samples with theFill Wizard function

The Fill Wizard allows you to create a plate layout with more advancedfeatures. The Fill wizard is available only for defining plate layouts.

Click the Fill Wizard icon in the Layout view to open the Fill Wizard dialog.

Select the desired Samples , Replicates , and Concentrations or Dilutions , and

click Add or Add and Close to confirm the selection.

The Fill Wizard dialog includes the following functions:

Samples :



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• Type. Select the type of sample from the list. The available types are:

Blank , Calibrator , Control , Empty and Unknown.

• Name. The sample name is suggested automatically. The name consistsof an abbreviation of the sample and of running numbers, for example,Un_0001, Un_0002, and so on. You can change the name, but therunning numbers after the abbreviation cannot be deleted.

• Group. The name of the sample group. The default group is Assay .Different group names can be used when several sets of samples mustbe separated from each other. When samples are defined to differentgroups, certain result calculations can be performed separately for eachgroup. For example, two different calibrator series with their ownunknown samples can be added to the same plate by defining the samplesto different groups (for example, Assay1 and Assay2). Therefore, thecorrect calibrator group for each set of unknown samples can be selectedby the group name when calculating the concentrations with theQuantitative curve fit step.

• No. of samples/No. of unknowns. The number of samples of theselected type.

• Ask number of unknowns at start . Lets you define the layout withouthaving to know the number of unknown samples. When this option isselected, you can define the starting point, filling directions for samplesand replicates, but not dilutions or specific blanks. The layout showsthe first unknown sample and its replicates, as well as an arrow depicting the filling direction of the following unknowns. The number of samplesis asked when you start the session.

• Primary filling direction. Selects the filling direction of the samples

in the plate layout.

Replicates :

• No. of replicates. Enter the number of replicates for each sample of theselected type.

• Specific blanks. Select the number of specific blanks (individual sample

blanks) in use: none , one or two. Specific blanks can be used if differentsamples have somewhat different blank characteristics and all sample

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