Thermo Scientific

SkanIt Software for

Microplate Readers
Technical Manual
Software Version 4.1
Cat. No. N16046 Rev 1.1 June 2015
 2015 Thermo Fisher Scientific Inc. All rights reserved.

Thermo Fisher Scientific Inc. provides this document to its customers with a product purchase to use in the
product operation. This document is copyright protected and any reproduction of the whole or any part of this
document is strictly prohibited, except with the written authorization of Thermo Fisher Scientific Inc.

The contents of this document are subject to change without notice. All technical information in this
document is for reference purposes only. System configurations and specifications in this document supersede
all previous information received by the purchaser.
Thermo Fisher Scientific Inc. makes no representations that this document is complete, accurate or error-
free and assumes no responsibility and will not be liable for any errors, omissions, damage or loss that
might result from any use of this document, even if the information in the document is followed
properly.
This document is not part of any sales contract between Thermo Fisher Scientific Inc. and a purchaser. This
document shall in no way govern or modify any Terms and Conditions of Sale, which Terms and Conditions of
Sale shall govern all conflicting information between the two documents.

Release history:

For Research Use Only. Not for use in diagnostic procedures.

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Contents

Preface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
About This Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Related Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Software Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Safety and Special Notices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i
Contacting Us. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ii

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1

Chapter 2 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Installation Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Connect the Software to the Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Update the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Firmware update for Varioskan LUX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Uninstall the Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6

Chapter 3 Main Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Application Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Session Tree. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Task Ribbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Software Language. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Chapter 4 Instrument Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

Default Instrument . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Instrument Status Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
Multi-instrument Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Simulator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Run the Plate In / Out. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Set the Instrument Temperature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Set the Gas Atmosphere. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Dispense . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Dispensing Tips. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Dispensing Positions F and L. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Prime the Dispensers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Empty the Dispensers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Thermo Fisher Scientific Thermo Scientific SkanIt Software Technical Manual iii
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Plate Trays and Plate Adapters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Plate Trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Plate Adapters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Install Filters to Varioskan LUX . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Install Filters to Multiskan FC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Chapter 5 Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Save a Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Open a Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
View Multiple Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Search for a Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Export a Session. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Import a Session . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Import Sessions from the On-Board Software of Multiskan GO . . . . . . . . . . 31

Chapter 6 Using SkanIt Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Sessions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Plate Layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Start a Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Calculations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Chapter 7 Plate Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Plate Layout Ribbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Defining the Plate Layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Plate Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
Define Pipette Content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Using the Virtual Pipette . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Adding Samples Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42

Chapter 8 Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Protocol Ribbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Protocol Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Define a Protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
Protocol Main Pane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Absorbance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
Absorbance Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Fluorescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Fluorescence Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
Luminescence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Luminescence Spectrum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
AlphaScreen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
TRF. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
TRF Spectrum. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Kinetic Loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Well Loop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Area Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

iv Thermo Scientific SkanIt Software Technical Manual Thermo Fisher Scientific

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Shake . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Pause . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Dispense . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Dispensing in a Kinetic Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Run Plate Out / Run Plate In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64

Chapter 9 Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Results Ribbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Start a Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Print Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
View Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
Measurement signal units . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Number Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Disable a Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Saturated Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Run Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Customize List View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68

Chapter 10 Export Results and Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Export Results of a Single Result Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Export Results of Several Result Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

Chapter 11 Calculations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Results Ribbon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Calculation Actions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Blank Subtraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Average, SD, CV% . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Basic Calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Dilution Factor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
Pathlength Correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
Standard Curve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Dose Response. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Kinetic. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Spectral . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Multipoint. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Classification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
Quality Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
Custom Formula . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100

Chapter 12 Result Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Create a Data Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Export a Result Report Manually. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Export a Result Report Automatically . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Email Report Automatically. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Print Report Automatically . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
Result Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Thermo Fisher Scientific Thermo Scientific SkanIt Software Technical Manual v

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Chapter 13 Settings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107

General . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Saved Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
K-Factors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Instruments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Edit Instrument Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 113
Plate Adapters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
Plate Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

Chapter 14 Drug Discover Edition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Windows Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Export Session History . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Digital Signatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Software Audit Trail . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
FDA 21 CFR Part 11 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128

vi Thermo Scientific SkanIt Software Technical Manual Thermo Fisher Scientific

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Preface

About This Guide

This guide explains how to install and use Thermo Scientific SkanIt Software for Microplate Readers
version 4.0. You can find information on the software features and operations. The software is used
with different types of instruments, and there may be information that may not be relevant to the
instrument you are using.

Thermo Scientific SkanIt Software for Microplate Readers controls Thermo Scientific microplate
readers. The software is used with:
Thermo Scientific Varioskan LUX
Thermo Scientific Multiskan FC
Thermo Scientific Multiskan GO

Related Documentation
In addition to the SkanIt Software for Microplate Readers Technical Manual, Thermo Fisher Scientific
provides the following electronic documents for SkanIt Software:
Thermo Scientific SkanIt Software for Microplate Readers User Manual (Cat. No. N16243)

Software Help
The software Help includes the same information as the SkanIt Software for Microplate Readers
Technical Manual. To open Help, click the Help icon or press F1 on your keyboard.

Use the Help search to find information on specific topics. Write the keyword of the topic you are
searching for, click List Topics, or press Enter.

Safety and Special Notices

Make sure you follow the precautionary statements presented in this guide. The safety and other
special notices appear in boxes.

Safety and special notices include the following:

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Preface

CAUTION Highlights hazards to humans, property, or the environment. Each CAUTION notice is
accompanied by an appropriate CAUTION symbol.

IMPORTANT Highlights information necessary to prevent damage to software, loss of data, or

invalid test results; or may contain information that is critical for optimal performance of the
system.

Note Highlights information of general interest.

Tip Highlights helpful information that can make a task easier.

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

www.thermoscientific.com/platereaders

ii Thermo Scientific SkanIt Software Technical Manual Thermo Fisher Scientific

 1

Introduction
Thermo Scientific SkanIt Software for Microplate Readers controls the instruments:
Thermo Scientific Varioskan LUX Multimode Reader
Thermo Scientific Multiskan FC Photometer
Thermo Scientific Multiskan GO Spectrophotometer

Note The software automatically detects how the instrument is configured and shows only those
features that are available.

The software is available in two editions, Research Edition (RE) and Drug Discovery Edition (DDE).
In addition to having the same features as RE, the DDE edition offers features for compliance with
FDA 21 CFR Part 11.

SkanIt Software for Microplate Readers is available in French, German, Italian, Japanese, Portuguese,
Russian, Simplified Chinese and Spanish.

With SkanIt Software you can:

Control instrument actions.
Create measurement sessions and start measurements.
View measurement results and perform calculations with the data.
Create comprehensive result reports.
Print or export result reports in different file formats (e.g., Microsoft Excel).
Export and import sessions between SkanIt Software databases in different PCs.

All measurement and calculation data is stored in the SkanIt Software database.

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1 Introduction

2 Thermo Scientific SkanIt Software Technical Manual Thermo Fisher Scientific

 2

Installation
To install SkanIt Software you need:
Administrator rights to the PC.
To register at http://www.thermoscientific.com/skanit to receive the installation code by email.
The installation CD.
To make sure your PC meets the minimum requirements.

Table 1. PC requirements.
System Minimum requirements Recommended requirements
Supported operating systems Microsoft Windows 7 with Service 64-bit edition of Microsoft Windows
Pack 1, or Microsoft Windows 8.1 7 with Service Pack 1, or 64-bit edition
of Microsoft Windows 8.1
Disk space 14 GB free disk space Solid-state drive with 14 GB free disk
space
Processor Dual-core processors, 2 GHz or faster Quad-core (or dual-core with four
logical processors), 2 GHz or faster
Memory 4 GB RAM 8 GB RAM
USB port available 1 (one) 1 (one)
CD-ROM drive 1 (one) 1 (one)
Graphics Processing Unit Dedicated Dedicated
Monitor SXGA monitor with 1280 x 1024 SXGA monitor with 1280 x 1024
resolution resolution

Note We strongly recommend using a computer that fulfills the recommended requirements,
especially if you process sessions with more than total of 150 000 individual measurements or with
complex calculations.

Installation Steps
1. Insert the installation CD into the CD-ROM drive.

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2 Installation
Installation Steps

If the installation window does not open automatically, open the Setup file from the CD.
2. In the components list dialog, verify the selected the components, and click Install.
3. Click Finish.
4. The Setup Wizard will take you through the software installation. Click Next.
Figure 1. Setup Wizard.

5. Read and accept the End User License Agreement and click Next to continue.
If you do not accept the License Agreement, the installation does not continue.
6. Select the destination folder where the software is installed. Click Next.
7. Click Install to start the installation.
8. The Setup Wizard shows a Application installed successfully! message. Click Finish.
9. Click the software icon on the desktop to start the software.
10. Enter the serial number that is on the installation CD.
11. Enter the installation code you received after you registered.
Note You can use SkanIt Software for 30 days without entering the installation code. During those
30 days, the software asks for the code each time it starts.

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 2 Installation
Connect the Software to the Instrument

Figure 2. Serial number and installation code.

12. Click OK.

The software opens on your screen.

Connect the Software to the Instrument

Connect the software to the instrument by plugging the USB cable from the PC to the instrument.
Switch the instrument on and start SkanIt Software. The software finds the instrument automatically.

Update the Software

If you have SkanIt Software 4.0 installed, you do not need to uninstall it first. You can update directly
to SkanIt Software 4.1 while the existing database is also updated. Sessions from SkanIt Software 4.0
remain available also after updating to version 4.1.
Note It is recommended to make a SkanIt database backup before updating the software. For more
information on database backup, refer to Database Backup in Chapter 13, Settings.

1. Insert the installation CD into the CD-ROM drive.

If the installation window does not open automatically, open the Setup file from the CD.
2. In the components list dialog, verify the selected the components, and click Install.
3. The Setup Wizard will take you through the software installation. Click Next.
4. Read and accept the End User License Agreement and click Next to continue.
If you do not accept the License Agreement, the installation does not continue.
5. Select the destination folder where the software is installed. Click Next.

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2 Installation
Uninstall the Software

6. Click Install to start the installation.

7. When the installation is finished, click Finish to exit the Setup Wizard.
Note SkanIt Software 4.1 is otherwise compatible with SkanIt Software 4.0 but sessions exported
from SkanIt Software 4.1 cannot be imported to SkanIt Software 4.0.

Note SkanIt Software 4.1 and SkanIt Software 4.0 cannot be installed in parallel on the same
computer.

Firmware update for Varioskan LUX

If you use a Varioskan LUX instrument and you are updating SkanIt Software from version 4.0 to
version 4.1, it is recommended to update the Varioskan LUX instrument firmware at the same time.
1. After the installation of SkanIt Software 4.1 is finished, click Yes to accept the firmware update.
2. Follow the instructions on the Firmware loader and insert the serial number of the instrument.
The serial number of the instrument is on the VIN plate at the back of the instrument.
Figure 3. Instructions and serial number

3. Click Update.
Note The firmware update can last for hours.

IMPORTANT To avoid instrument damage, do not abort the firmware update.

4. After the firmware update is finished and the system has restarted, click Calibrate.
5. To calibrate another instrument, repeat steps 2-4.
6. After you have updated all your instruments, click Cancel to close the Firmware loader.
7. Click the software icon on the desktop to start the software.

Uninstall the Software

1. Open Control Panel from the Windows Start menu.

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 2 Installation
Uninstall the Software

2. Select Programs and Features.

3. Select SkanIt Software from the program list.
4. Click Uninstall.

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2 Installation
Uninstall the Software

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 3

Main Elements
The main elements in the software are the application menu, the Session tree and the task ribbon.
When you open the software, the application menu opens.

The software automatically detects how the instrument is configured and shows only those features
that are available.
Note Your instrument may not have all of the features presented in this guide.

Application Menu
The application menu is for general tasks. This is where you create new sessions, open saved sessions
and access instrument and software settings. Click the menu icon to open the application menu.
Figure 4. The application menu with New & Recent open.

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3 Main Elements
Session Tree

Session Tree
The Session tree is visible when you have created or opened a session. This is the main area where you
navigate to define which wells to measure, select the protocol, view the measurement results, perform
calculations and create a result report.
Figure 5. The Session tree.

Task Ribbon
The actions in the task ribbon are linked to the section you have selected in the Session tree. When
you select Plate Layout, Protocol, Results or Report in the Session tree, the relevant task ribbon
opens. The task ribbon shows the actions you can select.
Figure 6. The Protocol task ribbon.

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 3 Main Elements
Software Language

Software Language
The default language is English. You can change the language to French, German, Portuguese, Spanish,
Italian, Russian, Japanese, or Simplified Chinese.

1. Click General under

Settings.
2. Select the language under
General settings.
Restart the software to set
the new language.

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3 Main Elements
Software Language

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 4

Instrument Operations
When you connect your PC (with SkanIt Software installed) to an instrument, the software finds the
instrument automatically.

Default Instrument
The default instrument in the software is Multiskan FC. When you connect your PC to the first real
instrument, that becomes the default instrument.

The default instrument is visible on the New Session button in the New & Recent window.

You can change the default instrument without connecting your PC to the instrument:

1. Click Instruments under

Settings.
2. Pin the instrument you want
to set as default.

Note If the instrument your PC is connected to is not listed under Instruments, click Poll now.

Instrument Status Icons

The instrument status icon gives you information about the instrument status. The instrument status
icon is visible both on the Settings > Instruments window and in the instrument selection drop-down
list above the Start button.

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4 Instrument Operations
Instrument Status Icons

Table 2. Instrument status icons.

Icon Description Status

Instrument icon with green dot The instrument is ready and in idle state
symbol.

Instrument icon with yellow warning Failure in the instrument start-up check.
symbol.

Instrument icon with red error Failure in connecting to the instrument.

symbol.

Instrument icon with green arrow The instrument is busy.

symbol.

Instrument icon is gray. The instrument is not connected.

Multi-instrument Run
You can run sessions on different instruments and on the same instrument types. The selection for

Different Instrument Types

You can run sessions on different instruments by selecting the instrument from the Home tab or main
menu.
From the Home tab:
1. Click the Home tab.
2. Click New.
3. Select the instrument from the
drop-down list box.

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 4 Instrument Operations
Run the Plate In / Out

From the main menu:

1. Click the main menu tab.
2. Click New & Recent.
3. Click Other instrument types.

Same Instrument Types

If you are using two instruments that are of the same type, create a new session and select which
instrument to run it on.

Select the instrument from the instrument selection drop-down list above the Start button. The
instruments have their own serial numbers.

Simulator
If you have installed the software on a PC which is not connected to a real instrument, you can use the
software in simulation mode. The simulator has most of the same settings as the instrument.

Select the simulator from the instrument selection drop-down list above the Start button.
Figure 7. Simulator selection.

Run the Plate In / Out

You can run the plate tray in or out from the software.
Note When you start a measurement session and click Start, the instrument automatically runs the
plate in.

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4 Instrument Operations
Set the Instrument Temperature

Click the Run plate in or Run plate out icon below the Start button.
Figure 8. Run plate in (green) and Run plate out (red).

Set the Instrument Temperature

You can set the instrument temperature from the software.
1. When a measurement session is open, click the temperature icon above the Start button.
2. Check the Temperature box and set the temperature.
3. Click OK.
The software shows both the current and target temperatures until the target temperature is
reached.

The temperature stays at the set temperature for as long as the software is connected to the instrument.
Figure 9. The temperature pop-up window.

Tip You can also set the temperature from application menu -> Settings -> Instruments -> Edit
instrument parameters -> General -> Use instrument temperature.

Note The instrument has no cooling system.

Set the Gas Atmosphere

If your Varioskan LUX instrument is equipped with an integrated gas module, you can regulate the
oxygen (O2) and carbon dioxide (CO2) concentrations inside the instrument.
1. Click the gas atmosphere icon above the Start button to open the pop-up window.

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 4 Instrument Operations
Dispense

Figure 10. The gas atmosphere pop-up window.

2. Set the oxygen and carbon dioxide levels as needed and click OK.
You can now see the target gas concentrations above the Start button. If the instrument has not
reached the set level, the current and target levels are shown.

The atmosphere stays as you have set it for as long as the software is connected to the instrument.
Tip You can also set the gas concentrations from application menu -> Settings -> Instruments ->
Edit instrument parameters -> General -> Gas atmosphere control.

Dispense
If your Varioskan LUX instrument is equipped with dispensers, you can use them to add reagents
automatically to a microplate during a run.

Dispensing Tips
There are two dispensing tips:
1. Tip 0.40 ( 0.40 mm) is the default tip for volumes > 5l.
2. Tip 0.25 ( 0.25 mm) is for small volumes ranging from 2 to 20l.
Note If you change the dispenser tip or syringe size, you must update the dispenser settings in the
SkanIt software instrument parameters. Go to Settings -> Instruments -> Edit instrument
parameters -> Dispensers. See Instrument Parameters: Dispensers on page 114.

Figure 11. Tip 0.25 (1) and tip 0.45 (2).

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4 Instrument Operations
Dispense

Dispensing Positions F and L

The Varioskan LUX instrument has two dispensing positions, F (fluorescence) and L (luminescence).
Both positions can be used with dispensers 1 or 2. The instrument recognizes which dispensing
position a dispenser head is inserted into.
Figure 12. Dispensers 1 and 2, dispensing positions F and L.

Table 3. Dispensing positions and the measurement positions they point at.
Position F Position L
Fluorescence (top of the well) Luminescence
Absorbance Fluorescence (bottom of the well)
Spectral TRF TRF
Spectral luminescence AlphaScreen

To start a measurement at the same time as dispensing, place the dispensing head into the dispensing
position (F or L) that points at the correct measurement position. This way there is no delay time
between dispensing and measurement, which is important in fast kinetic reactions.

If you use a dispensing position that does not point at the correct measurement position, the
instrument makes an extra plate movement before the measurement step. This may cause minor time
delays between dispensing and measurement.

Prime the Dispensers

Before you use dispensers in a measurement session, you must prime them. Priming dispensers means
filling the tubing with the dispensing liquid. The aspirate tube is the input tube, which is between the
reagent container and syringe. The dispense tube is the output tube.

You can start the priming from the software or instrument.

1. Insert an empty plate of the same height as the assay plate into the plate tray.

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 4 Instrument Operations
Dispense

2. Place the head of the aspirate tube into the reagent container.
3. Hold the dispensing head in a waste container.
IMPORTANT Do not insert the dispensing head into the dispensing position F or L during
priming.

4. Start the prime

a. From the instrument:
Press the Prime button until the liquid flows out.
b. From the software:
i. Click the Prime dispenser(s) icon to open the Prime window.
ii. Select the dispenser.
iii. Select the volume and speed.
iv. Click Prime.
5. Insert the dispensing head in position F or L.

Dispensing Step in a Measurement Session

After priming the dispensers, you can run a session which includes dispensing. Make sure the
dispensing parameters are correct.

Select the same dispenser (1 or 2) and position (F or L) for both the software and instrument. The
instrument automatically checks that the same positions are selected.
Figure 13. Select the same dispenser (1 or 2) and position (F or L) in the software as you selected in the
instrument.

Empty the Dispensers

You can use the software or instrument button to empty the liquid from the tubes back into the reagent
container.
a. From the software:
i. Click the Empty dispenser(s) icon (below Start) to open the Empty window.
ii. Select the dispenser.

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4 Instrument Operations
Plate Trays and Plate Adapters

iii. Select the volume and speed.

iv. Click Empty.
b. From the instrument:
i. Press the Empty button until the liquid flows back.

Plate Trays and Plate Adapters

Plate Trays
In Varioskan LUX there are two types of plate trays: universal and robotic.

The universal plate tray is for basic use. It is compatible with all plate formats (6 to 1536 well plates).
Always use a plate adapter with a universal tray.

A robotic plate tray is for automation use with robots. It is compatible with 96 to 1536 well plate
formats. Use the special robotic plate adapter when using a plate without a lid. Remove the plate
adapter when using a plate with a lid on a robotic tray.

Plate Adapters
The Varioskan LUX plate adapters are used for adapting plates that are of different heights. Adapters
lift the plates to the optimum height for measuring and dispensing.

Before you run a measurement with Varioskan LUX, check that the correct plate adapter is in the plate
tray. Choose the adapter based on the plate format you have (96, 384,...) and if you are using a lid or
not.

Table 4. Varioskan LUX plate adapters.

Supports
Adapter no Plate adapter
dispensing
2 96-well adapter without lid
3 96-well adapter with lid
4 384-well adapter without lid
5 384-well adapter with lid
6 96-well adapter for PCR plate without lid
48 6-48-well adapter with lid
65 1536-well adapter (10mm) without lid
80 6-48-well adapter without lid
126 Robotic tray with adapter without lid
127 Robotic tray without adapter without lid

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 4 Instrument Operations
Install Filters to Varioskan LUX

Plate Template and Adapter Association in the Software

You need to select the plate template you will use in the measurement:
1. Click on the Plate template drop-down list in the Plate Layout view.
2. Select a template that you will use in a measurement.
The plate templates are automatically associated with the compatible plate adapters. When you
start a measurement, the software checks that the selected plate template and the installed plate
adapter are compatible.

Install Filters to Varioskan LUX

The Varioskan LUX LAT module has built-in AlphaScreen and TRF excitation filters. You need to
install the AlphaScreen, TRF, and luminescence emission filters.

IMPORTANT Do not touch the surfaces of the filters with bare hands.

1. Turn on the instrument and open SkanIt Software.

2. Open the dispenser sliding cover and the LAT module cover.
3. Select the filter position in SkanIt Software:
a. Click Settings on the application menu.
b. Click Instruments.
c. Click the icon (on the right side of the instrument name) to open the Edit instrument
parameters window.
d. Click the Filter definition tab.
e. Click Add.
f. Select a free filter position from the filter wheel and add the new filter information.
g. Click Next.
The filter wheel is now turned to the selected position.

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4 Instrument Operations
Install Filters to Multiskan FC

Figure 14. The define filter pop-up window.

4. Open the blue filter nest lid on the LAT module.

5. Loosen the filter wheel screw on the selected position.
6. Place the filter on a clean, dust free surface with the arrow on the side of the filter pointing
upwards.
7. Use the filter pick-up tool to place the filter into the bottom of the filter nest.
8. Tighten the filter wheel screw.
Figure 15. Filter nest (1) and pick-up tool.

9. Close and fasten the filter nest lid.

10. Click Finish.

Install Filters to Multiskan FC

First install the filter manually to the filter wheel of Multiskan FC. After that enter the filter
information to SkanIt Software.

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 4 Instrument Operations
Install Filters to Multiskan FC

1. Click Settings > Instruments.

a. Click the Edit instrument parameters icon -> Filter definition.
b. Select a free filter position from the filter wheel and click Add.
c. Add the new filter information, click OK -> Apply.
Figure 16. Add new filter pop-up window.

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4 Instrument Operations
Install Filters to Multiskan FC

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 5

Sessions
The information that is needed to define and run an assay is saved in a session. With SkanIt Software
you can build sessions for your own assays and run or modify ready-made sessions.

When you create a session, you define to which wells your samples are pipetted in the microplate and
what you want the instrument to do.

Session tree
The Session tree is the main use area in the software. The Session tree has five main sections:
1. Notes - write notes about a session.
2. Plate Layout - define which wells of the microplate you want to measure.
3. Protocol - define what you want the instrument to do.
4. Results - view the measurement results and choose the calculation methods.
5. Report - create a report of the measurement and calculation results.
6. History - view or export a session audit trail in *.xml format (DDE version only).

Save a Session
There are two different kinds of saved sessions:
a. A session that is saved before you have run it.
A session that you have saved but have not run does not have measurement data. You can edit
all of the content.
b. A session that has been run.
A session that has been run is automatically saved. You cannot edit the protocol, but you can
edit all other content. A green arrowhead icon next to a session name indicates a saved session
with measurement data.

Note If you use Save As to save a session that has been run, the measurement data for the run is not
saved. This makes it possible for you to edit the protocol again.

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5 Sessions
Open a Session

Figure 17. A session with measurement data (green icon) and without measurement data (no icon).

Create and Save a Session

1. Click the application menu icon tab.
2. Click the New session button under New & Recent.
3. Click Save as or Save in the Home ribbon.
4. In the Save as session window, select the folder where you want to save the session.
5. Give the session a name and click Save.

Open a Session
You can open a recent session, or an older session. You can also pin a session to keep it on the recent
sessions list.

Open a Recent Session

1. Click New & Recent in the application menu.
2. Select a recent session from the Open recent session list. A green arrowhead icon indicates a saved
session with measurement data.
The session opens in the Session tree.

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 5 Sessions
Open a Session

Open an Older Session

1. Click Open in the application

menu or Home tab.
2. Select the session from the
Session Browser window, or
3. Use Search sessions or
Advanced search to find an
older session quickly.

Open an Online Session

Online sessions include demo sessions.
1. Open the application menu.
2. Click Open.
The Session Browser window opens.
Figure 18. The Session Browser window.

3. Double-click Online.
4. Select the online session you want and click Open.

Pin Your Favorite Session

The Open recent session list shows the ten (10) most recent sessions. The first session listed is the
most recent. The list moves down when a new session is run.

You can pin a session to keep it permanently on the Open recent session list for quick access.
1. Click New & Recent under the application menu.
2. Move your cursor to the session you want to pin.
3. Click the pin icon at the right end of the session.
The session is pinned and stays on the list.

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5 Sessions
View Multiple Sessions

View Multiple Sessions

You can have several sessions open at the same time. The open sessions have their own tab above the
session tree. You can view them one at a time, side-by-side, or stacked. If you view the sessions one at a
time, you can navigate them by clicking the session tabs above the Session tree.
1. Open the sessions you want to view.
2. Click the View tab.
Figure 19. The View tab options (1.) and the multiple sessions tabs when viewed one at a time (2.).

3. Select Side-by-side or Stack.

4. To view just one session, click Reset.

Search for a Session

Search by session name
1. Click Open in the application menu to open the Session Browser window.
2. Write the session name in the Search sessions box.
A list of found sessions will be shown.

Search by Session Criteria Using Advanced Search

With Advanced Search you can search for sessions based on the session name, description, when it was
executed, who it was created by, when (specific dates), the measurement technology used, the
instrument type used, and the plate template used.
1. Click Open in the application menu to open the Session Browser window.
2. Click Advanced Search on the right-hand side of the Session Browser window.

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 5 Sessions
Export a Session

Figure 20. Advanced search.

3. Write the session details.

4. Click Search.
Figure 21. Advanced search window open.

Export a Session
To copy a session, or multiple sessions, from one SkanIt Software database to another, you need to
export them first. Exporting a session creates a file with an *.ska extension, which you can import to
another PC with SkanIt Software installed. You cannot open the exported session outside SkanIt
Software.

Note Exporting sessions copies sessions, it does not remove them from the database.

1. Open the application menu.

2. Click Export.
The Export session window opens.

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5 Sessions
Import a Session

Figure 22. The selected session and export folder.

3. Check the session(s) you want to export.

4. Click Browse to select the Windows folder you want to export the session(s) to.
5. Select the file name in the Save As window and click Save.
6. Click Ok.

Import a Session
You can import a session that has been exported with SkanIt Software. Files that can be imported have
an *.ska extension.
1. Open the application menu.
2. Click Import. The Import session window opens.
3. Browse to the file location.
4. Select the file and click Open.
5. Click Next.
6. Select the session(s) you want to import.
7. Select the folder you want to import the session(s) to.
8. Click Finish.

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 5 Sessions
Import a Session

Figure 23. The session selection in the Import data window.

If you import one session, the software opens it. The software adds the imported session to the
Open recent session list under New & Recent.
Multiple imported sessions are not opened during import nor added to the Open recent session
list.

Import Sessions from the On-Board Software of Multiskan GO

To import a session which has been run with the on-board software of Multiskan GO, you must first
export the session from the Multiskan GO on-board software. You can import only microplate sessions
this way. Cuvette sessions exported from the Multiskan GO on-board software cannot be imported to
SkanIt Software.
1. Export the session from the Multiskan GO on-board software to a USB stick.
2. Connect the USB stick to your PC.
Copy the session from the USB stick to your PC, or import the session directly from the USB
stick.
3. Click Import in the application menu. The Import session window opens.
4. Browse to the file location.
5. Select the session file (*.txt) and click Open.
6. Click Next.
7. Select the session you want to import and click Finish.
The software adds the imported session to the Open recent session list under New & Recent.

SkanIt Software automatically adds unknown samples to the layout based on the wells measured with
the instrument session. You can edit the sample types in the plate layout to be able to perform
calculations.

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5 Sessions
Import a Session

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 6

Using SkanIt Software

The Session tree is the main part of the software user interface. The Session tree is where you navigate
to create sessions, perform calculations, view and export measurement results, and create data reports.
The Session tree is visible when you have created or opened a session.

The general outline for using the software:

1. Create a new session or open an existing one.
2. Define the plate layout and protocol.
3. Start the session.
4. View the results and perform calculations.
5. Create result reports and export data.

Sessions
You can create new session from the application menu or Home tab.

Create and Save a Session

1. Click the application menu tab.
2. Click the New session button under New & Recent.
If you have multiple instruments, click Other instrument types and to create a session for a
different instrument than the default instrument.
3. Click Save as or Save in the Home ribbon.
4. In the Save as session window, select the folder where you want to save the session.
5. Give the session a name and click Save.

To learn more about sessions, see Sessions.

Plate Layout
In the Plate Layout you define the plate content. You select the plate template, define the sample types
that you have, and tell the software which wells to measure.

If no layout is defined, all wells are measured.

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6 Using SkanIt Software
Protocol

Protocol
In Protocol view you tell the instrument which actions to carry out and in what order.

Start a Measurement
1. Click the Start button.
Figure 24. The Start button.

2. Write a name for the session in the Session Name window.

This step is skipped if you have previously named the session.
3. Click OK.
The software indicates the action it is running.
If you need to stop the run, click Abort. The results measured up to that point are saved.

IMPORTANT To avoid data loss, make sure your computer does not go into hibernation/sleep
during a measurement.

Results
This is where you can view the measurement results and perform calculations. You can also export
measurement and calculation data to use outside SkanIt Software. For more information go to Results.

View the Results

1. Click the measurement step under Results in the Session tree.
2. Click the Plate or List tab to view the results.

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 6 Using SkanIt Software
Calculations

Figure 25. The results of a Fluorescence Spectrum measurement with the Plate view open.

Export Results to Excel

1. In the Results view click on the Export to Excel tab.
2. Save the data.
Tip You can export the data of several steps into the same file by creating a report. You can create
result reports in Excel, PDF, XML and TXT formats.

Calculations
In the Results view the software has built-in calculations that you can use to process data. You can add
calculations either before or after a measurement.

For more information see Calculation Actions.

Report
You can create a result report including both measurement and calculation data. You can export the
result report to Excel, PDF, XML and TXT formats.

A summary table is automatically created under Report. The summary table shows only the
measurement and calculation results of end-point measurements. Kinetic, spectral or multipoint results
are not included in the result summary.

For more information see Result Report.

The next time you start the session, a report is automatically saved in the destination folder you
selected.

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6 Using SkanIt Software
Report

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 7

Plate Layout
In the Plate Layout you define which wells to measure, and what kind of samples you have in the
microplate. You select the sample properties in the Pipette content section, then mark the sample in the
plate wells with the virtual pipette.

Plate Layout Ribbon

Click Plate Layout in the Session tree to open the Plate Layout ribbon.
Figure 26. The Plate Layout ribbon.

Undo: Undo the previous action.

Redo: Redo the action.

Clear all: Remove all of the samples from all of the plates.

Edit samples: Edit content in individual or multiple wells. Click the well(s), then click Edit samples.
Edit the samples in the dialog that opens.

Copy: Copy sample content from selected wells. Click the well(s), then click Copy. With the pipette
cursor select where you want to copy the sample(s). Copying a sample creates a new replicate for it.

Cut: Cut and move sample(s) from selected wells. Click the well(s), then click Cut. With the pipette
cursor select where you want to move the sample(s).

Clear: Remove sample(s) from selected wells. Click the well(s), then click Clear.
Note The Edit Plate Layout functions Edit samples, Copy, Cut, Undo, Redo and Clear are
available in the edit shortcut menu: right-click the well(s) to open the edit shortcut menu, and click
Edit samples.

Preview: Preview layout and then print it, or save it to a document.

Add new: Click to add a new plate. A scrollbar appears on the right side of the plate. Scroll down to
view the new plate. The Plate Layout can consist of more than one plate.

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7 Plate Layout
Defining the Plate Layout

Defining the Plate Layout

1. Click Plate Layout in the Session tree.
2. Select the plate template from the drop-down list.
3. Select the Sample type and sample properties.
4. Click the plate wells with the virtual pipette (your cursor) to add the samples.
Tip You can add multiple samples at a time by dragging the pipette across the wells.

To clear or edit a well, right-click on the well.

You can select a single sample or several samples of the same sample type. Samples of the same type
have the same functionality in the assay, but their concentration/dilution, name, and other parameters
may differ.
Note If you leave the plate empty, the whole plate will be measured automatically.

Figure 27. Plate template drop-down list (1), Pipette content (2.) and marked well (3.).

Plate Templates
The plate templates include the most common plates from different manufacturers. They are grouped
per number of wells in the plate template drop-down list.

Scroll down the list, or write in the Search box to find your template. Click the template to select it.

For instruments that are compatible with cuvettes or the Thermo Scientific Drop Plate, scroll to the
end of the drop-down list to Size: Special.

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 7 Plate Layout
Define Pipette Content

Figure 28. Plate template search box and drop-down list.

Define Pipette Content

In the Pipette content section you set the sample properties before you add samples to the plate. Select
the sample type, name, and if applicable, the replicates, specific blanks, and sample groups.
Figure 29. Pipette content.

Note Use Edit samples if you want to edit the sample properties of a well that you have added to
the plate. Right-click the well you want to edit, then click Edit samples on the shortcut menu.

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7 Plate Layout
Define Pipette Content

Add and edit sample content:

1. Define the sample properties.

2. Add to the well.
3. If you need to edit the samples,
right-click the well(s) you want
to edit to open the shortcut
menu.
Select one of the actions listed.

Sample Types
Blank: A zero sample, which does not include the analyte of interest and is used for blank subtraction.

Standard: Samples with known concentrations used for quantitative analysis (e.g., standard curve).

Control: A sample with known characteristics which you can use for quality control to test that the
assay is valid, or to compare against other samples.

Unknown: Samples that are under investigation.

Sample Names
You have two options for naming samples of the same type:

Auto: Combine a prefix and a running number. Write the prefix in the box. The software adds the
running number.

List: List the unique name for each sample. The names are used in the order written. You can copy &
paste name lists from a document (e.g., Excel) directly to the List box.

Replicates
Select Replicates if the samples have replicates. Sample replicates have the same name. Define the
quantity and positioning of the replicates.

Columns: Select the number of replicates you want to add in a horizontal direction.

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 7 Plate Layout
Using the Virtual Pipette

Rows: Select the number of replicates you want to add in a vertical direction.
Note Blank samples do not have a replicate selection. All blanks of the same sample group are
automatically added as replicates.

Concentrations
Select Concentrations to add concentration values for Standard samples. Select either Series or
Values.

Series: Define mathematically regularly changing concentration values for the whole Standard series at
once. For example, 1, 10, 100, 1000.
First value: Concentration of the first standard
Operator: Mathematical operator in the formula for the series.The concentration increase or
decrease from the initial value by the steps defined in the Step by field.
Step by: The factor for the concentration series.

Values: List the concentration values one by one.

Unit: Add the concentration unit (ng/ml, mM, etc.).

Dilution Factor
You can add dilution factors for unknown samples. For example the factors 1:1 = not diluted, and 1:2
= diluted in half.
Tip You can use the Dilution Factor calculation step in Results to multiply the results with the
dilution factor of each sample.

Use Specific Blank

Select Use specific blank if you need to use individual blanks for each sample. If you perform a blank
subtraction calculation, the specific blanks are then subtracted from their respective samples.

Sample Groups
Define sample groups when you need to separate sets of samples from each other to perform different
result calculations separately to different groups. If all samples are processed in result calculations the
same way, all samples can belong to the same group.

Define groups by entering a new group name in the Group box. Click Add sample group to add a
new group name.

A sample can be in multiple sample groups at the same time.

Using the Virtual Pipette

After you have defined the Pipette content, you can add the samples to the plate.

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7 Plate Layout
Adding Samples Overview

Click the plate wells with the virtual pipette (your cursor) to add the samples.
Tip You can add multiple samples at a time by dragging the pipette across the wells.

To clear or edit a well, right-click on the well to open the edit shortcut menu. Click Edit samples to
open the Edit samples window.

Adding Samples Overview

Add a Blank Sample
1. Select Blank under Sample type.
2. Click the wells with the virtual pipette to add the blanks with its replicates.

Add a Standard Sample

1. Select Standard under Sample type.
2. Select the sample name (Auto or List).
3. Select the number of replicates.
4. Select the concentrations (Series or Values).
5. Click the wells with the virtual pipette to add the samples.

Add a Control Sample

1. Select Control under Sample type.
2. Select the sample name (Auto or List).
3. Select the number of replicates.
4. Click the wells with the virtual pipette to add the samples.

Add an Unknown Sample

1. Select Unknown under Sample type.
2. Select the sample name (Auto or List).
3. Select the number of replicates.
4. Set the Dilution factor, if needed.
5. Click the wells with the virtual pipette to add the samples.

Add Multiple Samples Horizontally or Vertically

You can fill multiple samples in a horizontal or vertical row. Add a sample individually, or drag the
virtual pipette up or down and add multiple samples.

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 7 Plate Layout
Adding Samples Overview

Figure 30. Horizontal and vertical samples, both showing the number of samples being added.

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7 Plate Layout
Adding Samples Overview

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 8

Protocol
In the Protocol view you tell the instrument what actions to perform and in which order. You select an
action from the Protocol ribbon, and it is listed in the Session Tree under Protocol.

Each protocol action has its own parameters that you define. With parameters you can define e.g.,
measurement wavelengths, select fast or precision measurement modes, and set measurement times
Note Your instrument may not have all of the features described here. The software automatically
detects the instrument configuration and shows only those actions that are available.

Protocol Ribbon
Click Protocol in the Session tree to open the Protocol ribbon. Click the protocol action on the
ribbon to add it as a step. The software carries out the steps in the order listed in the Session tree.
Figure 31. The Protocol ribbon for adding actions.

Protocol Actions
You can add multiple actions, and also add an action as a sub-step. Select the protocol action from the
Protocol ribbon.

The software shows only those protocol actions that are available for your instrument.

Table 5. Protocol actions and descriptions.

Action Description
Absorbance Measures absorbance.
Absorbance Spectrum Measures the absorbance spectrum for a wavelength range.
Fluorescence Measures fluorescence intensity.

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8 Protocol
Define a Protocol

Table 5. Protocol actions and descriptions.

Action Description
Fluorescence Spectrum Measures the fluorescence spectrum for a wavelength range.
Luminescence Measures luminescence.
Luminescence Spectrum Measures the luminescence spectrum for a wavelength range.
AlphaScreen Measures the AlphaScreen signal.
TRF Measures time-resolved fluorescence.
TRF Spectrum Measures time-resolved fluorescence spectrum for a wavelength
range.
Kinetic Loop Executes sub-steps several times in defined time intervals in a
kinetic measurement.
Well Loop Executes sub-steps for as many wells at a time as you have
selected as a well count.
Area Selection Executes sub-steps for only part of the defined wells in the plate
layout. Area definition is not necessary when all of the defined
wells in the plate layout are measured.
Shake Shakes the microplate to mix the liquid in the wells.
Dispense Dispenses a given volume of liquid into wells.
Pause Pauses the protocol.
Run Plate Out / In Runs the plate in or out in the middle of a protocol.

Define a Protocol
The general outline for defining protocols:
1. Click Protocol in the Session tree.
2. Select the action from the Protocol ribbon.
3. Define the parameters, e.g., measurement wavelength.

Tip To change the order of the steps in the Session tree, click the step you want to move, then click
the small arrow to move it up or down. You can also use drag-n-drop to change the order.

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 8 Protocol
Protocol Main Pane

Figure 32. To move the action up or down in the Session tree, click the small arrow. To remove the action,
click the x-mark.

Protocol Main Pane

In the protocol main pane you can set certain parameters which apply for the whole protocol. (the
window that opens when you click Protocol in the Session tree).
Figure 33. The Protocol main pane.

Measurement order
Select the direction in which the steps are executed on the plate. The arrow shows the execution order,
and the black dot shows the starting point.

Well interval
Set the time lapse between the starting times of two consecutive wells.

Use settle delay

Define the time delay after the plate has moved to a new reading position before the instrument
performs the next reading. Fast plate movements may cause resonance waves on the liquid surface,
which can in certain cases be seen as noise in measurement signals. Using settle delay helps to minimize
surface wave effect and may thus improve the results.

Settle delay is fixed based on the plate format.

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8 Protocol
Absorbance

Table 6. Settle delay times vs plate formats.

Plate format Settle delay time (ms)
6-well plates 1750
12-well plates 1300
24-well plates 400
48-well plates 200
96-well plates 100
384-well plates 50
1536-well plates 20

Check temperature at start [oC]

You can add a target temperature for the session, which works as a reminder for the user to use a certain
temperature for a specific session.

If the target instrument temperature is different from the set temperature, or if it has not been reached
yet, the instrument will give a warning to ensure whether the measurement shall be executed. The user
can select to measure or cancel the session.
Note The temperature parameter does not affect the instrument temperature.

Check Gas Control at Start

You can add target carbon and oxygen levels for the session, which work as a reminder for the user to
use certain levels for a specific session. If the target is different from the set levels, the instrument will
give a warning to ensure whether the measurement shall be executed. The user can select to measure or
cancel the session.

Absorbance
Measures absorbance.
Figure 34. Absorbance parameters with Advanced parameters open.

Wavelength [nm]: Select the measurement wavelength.

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 8 Protocol
Absorbance

Multiple wavelengths: Select to measure each well at multiple wavelengths.

Check Multiple wavelengths, set the wavelength and click Add. [multiple]
Note When measuring multiple wavelengths with filters, the measurements are done in the order
of the filter position.

Figure 35. Multiple wavelengths selected and two wavelengths added.

Pathlength correction: Select if you want to normalize microplate measurement results to correspond
to a 10 mm pathlength. If you activate the pathlength correction, add the pathlength correction
calculation step to results also.

Measurement mode:
Fast: The measurement head moves over the wells without stopping. This produces fast results
with a slightly narrower linear absorbance range than with the Precision / Normal mode.
Precision / Normal: Precision-optimized mode where the measurement head stops over each
measured well for maximum precision.

Filter (for filter-based instruments): Select the measurement wavelength by selecting the filter. To add,
edit and remove filters, see Instrument Parameters: Filter Definition.
Figure 36. Example of an Absorbance parameters Filter menu open and Measurement mode Normal
selected.

Absorbance: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the measurement step. After the
measurement is performed, the software waits until the entered duration is up before proceeding to the
next step. You can use Step duration to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Measurement time [ms]: Set the light collection time used in the measurement. The wells are
measured with a selected measurement time.

Wavelength interval: Set the interval time between multiple wavelength measurements.

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8 Protocol
Absorbance Spectrum

Absorbance Spectrum
Measure the absorbance spectrum for a specific wavelength range.
Figure 37. Absorbance Spectrum with Advanced parameters open.

Wavelength range: Set the Start [nm] and End [nm] wavelength (200-1000 nm) and the Step [nm]
size (scanning resolution) for the scanning measurement.

Pathlength correction: Select if you want to normalize microplate measurement results to correspond
to a 10 mm pathlength. If you activate the pathlength correction, add the pathlength correction
calculation step to results also.

Measurement mode:
Fast: The measurement head moves over the wells without stopping. This produces fast results
with a slightly narrower linear absorbance range than with the Precision / Normal mode. For the
spectrum this means that the monochromator grating is not stopped for each wavelength.

Precision / Normal: Precision-optimized mode where the measurement head stops over each
measured well for maximum precision. The measurement time takes longer than the Fast mode.
For the spectrum this means that the monochromator grating is stopped for each wavelength.

Absorbance Spectrum: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use Step duration to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Measurement time [ms]: If needed, set the light collection time used in the measurement. The wells
are measured with a selected measurement time.

Fluorescence
Measures fluorescence intensity (FI) at selected excitation and emission wavelengths.

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 8 Protocol
Fluorescence

Figure 38. Fluorescence parameters with Bottom optics selected.

Excitation wavelength [nm]: Set the excitation wavelength. The wavelength range is 200 to 1000 nm.

Emission wavelength [nm]: Set the emission wavelength. The wavelength range is 270 to 840 nm.
Note To prevent any stray light from the excitation light from interfering with the emission light,
the difference between the excitation and emission wavelengths should be at least the sum of the
bandwidths used. If the 5 nm excitation and 12 nm emission (permanent) bandwidths are used, the
difference between excitation and emission wavelengths should be at least 17 nm. With the 12 nm
excitation and emission bandwidths the difference should be at least 24 nm.

Multiple wavelengths: Select if you want to measure each well with multiple wavelength pairs. Select
the excitation and emission wavelengths and click Add. Repeat this for all wavelength pairs.

Measurement time [ms]: Defines the light collection time per well used in the measurement. The
wells are measured with a selected measurement time.

Optics: Select top or bottom.

Top: Measure fluorescence from the top of the plate.
Bottom: Measure fluorescence from the bottom of the plate. Select this when you need to measure
a sample that is at the bottom of the well (e.g., cell samples).

Excitation bandwidth [nm]: Select the bandwidth of the excitation wavelength (5 nm and 12 nm).
The emission bandwidth is permanently set to 12 nm and cannot be changed.

Fluorescence: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use Step duration to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Dynamic range: If needed, select the reading range from the alternatives.
Auto range: The default and recommended setting. Automatically selects the optimal reading
range. Is based on signal intensity in the well and uses the lowest possible reading range for the best
sensitivity.

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8 Protocol
Fluorescence Spectrum

Low range: Produces the highest sensitivity with a limited dynamic range.
Medium low range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards sensitivity.
Medium high range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards dynamic range.
High range: Intended for highest-concentration samples. Covers a wide dynamic range with lower
sensitivity than the other dynamic ranges.

Multiple points per well: Select to define the points in a well that are measured. If you do not select
any of the points, only the center of the well is measured. Select Bottom from the optics options.
Note The Multiple points per well option is for bottom reading 6 to 96 - well plates only.

Figure 39. Multiple points per well with Circle selected.

All: Click to select all points.

Horizontal: Click to select a horizontal point line.
Vertical: Click to select a vertical point line.
Circle: Click to select the outer points in the circle.
Clear: Click to clear your selection.
Note The max number of measurement points per well depends on the selected plate template.

Fluorescence Spectrum
Measures the fluorescence spectrum for a wavelength range.

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 8 Protocol
Fluorescence Spectrum

Figure 40. Fluorescence Spectrum parameters.

Type: Select to measure either excitation or emission spectrum.

Excitation spectrum: Measure excitation spectrum for a selected wavelength range by using a
fixed emission wavelength.
Emission spectrum: Measure emission spectrum for a selected wavelength range by using a fixed
excitation wavelength.

Emission / Excitation wavelength range: Select the Start [nm] and End [nm] wavelengths and the
Step [nm] size (scanning resolution) for the scanning measurement. The available wavelength range is
200 to 1000 nm for excitation and 270 to 840 nm for emission.

Optics: Select top or bottom.

Top: Measure fluorescence from the top of the plate.
Bottom: Measure fluorescence from the bottom of the plate. Select this when you need to measure
a sample that is at the bottom of the well (e.g., cell samples).

Excitation bandwidth [nm]: Select the bandwidth of the excitation wavelength. Bandwidth is selected
using an excitation slit that has 5 nm and 12 nm options. The default value is 12 nm. The emission
bandwidth is permanently set to 12 nm and cannot be changed.
Note To prevent any stray light from the excitation light from interfering with the emission light,
the difference between the excitation and emission wavelengths should be at least the sum of the
bandwidths used. If the 5 nm excitation and 12 nm emission (permanent) bandwidths are used, the
difference between excitation and emission wavelengths should be at least 17 nm. With the 12 nm
excitation and emission bandwidths the difference should be at least 24 nm.

Measurement time [ms]: defines the light collection time used in the measurement. The wells are
measured with a selected measurement time.

Fluorescence Spectrum: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use Step duration to accurately time two protocol steps.

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8 Protocol
Luminescence

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Dynamic range: If needed, select the reading range from the alternatives.
Auto range: The default and recommended setting. Automatically selects the optimal reading
range. Is based on signal intensity in the well and uses the lowest possible reading range for the best
sensitivity.
Low range: Produces the highest sensitivity with a limited dynamic range.
Medium low range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards sensitivity.
Medium high range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards dynamic range.
High range: Intended for highest-concentration samples. Covers a wide dynamic range with lower
sensitivity than the other dynamic ranges.

Luminescence
Measures luminescence.
Figure 41. Luminescence parameters with Advanced parameters open.

Optics: Select normal or filter.

Normal: Measures luminescence by collecting all light without using filters.
Filter: Measures luminescence by using filters. To add, edit and remove filters, see Instrument
Parameters: Filter Definition.

Measurement time [ms]: Defines the light collection time used in the measurement. The wells are
measured with a selected measurement time.

Luminescence: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use this parameter to accurately time two protocol steps.

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 8 Protocol
Luminescence Spectrum

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Dynamic range: If needed, select the reading range from the alternatives.
Auto range: The default and recommended setting. Automatically selects the optimal reading
range. Is based on signal intensity in the well and uses the lowest possible reading range for the best
sensitivity.
Low range: Produces the highest sensitivity with a limited dynamic range.
Medium range: Offers sensitivities and dynamics in between the Low and High ranges.
High range: Intended for highest-concentration samples. Covers a wide dynamic range with lower
sensitivity than the other dynamic ranges.

Use smaller aperture: May help decrease luminescense crosstalk from adjacent wells by decreasing
luminescense signals. The instrument measures the wells by using a smaller measurement aperture than
usual. For example, an aperture that is used for a 384-well plate is used to measure a 96-well plate, and
an aperture that is used for a 1536-well plate is used to measure a 384-well plate.

Luminescence Spectrum
Measures the luminescence spectrum for a wavelength range.
Figure 42. Luminescence Spectrum parameters.

Wavelength range: Set the Start [nm] and End [nm] wavelengths (200-1000 nm) and the Step [nm]
size (scanning resolution) for the scanning measurement.

Measurement time [ms]: defines the light collection time used in the measurement. The wells are
measured with a selected measurement time.

Luminescence Spectrum: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use this parameter to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Dynamic range: If needed, select the reading range from the alternatives.

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8 Protocol
AlphaScreen

Auto range: The default and recommended setting. Automatically selects the optimal reading
range. Is based on signal intensity in the well and uses the lowest possible reading range for the best
sensitivity.
Low range: Produces the highest sensitivity with a limited dynamic range.
Medium low range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards sensitivity.
Medium high range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards dynamic range.
High range: Intended for highest-concentration samples. Covers a wide dynamic range with lower
sensitivity than the other dynamic ranges.

AlphaScreen
Measures the AlphaScreen signal.

Filters: Select the emission filter. Select the measurement wavelength by selecting the emission filter.
To add, edit and remove filters, see Instrument Parameters: Filter Definition.
Multiple filters: Select to measure each well with multiple wavelength pairs.

Excitation wavelength [nm]: The instrument has a built-in 680nm excitation filter.

Excitation time [ms]: Set the time used for excitation.

Delay [ms]: Define the waiting period between the end of the excitation and the beginning of the
emission light measurement.

Integration time [ms]: Define the length of the time the emitted signal is collected.

Measurement time [ms]: The software calculates the sum of the selected excitation / delay /
integration times.

AlphaScreen: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use this parameter to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Use smaller aperture May help decrease luminescense crosstalk from adjacent wells by decreasing
luminescense signals. The instrument measures the wells by using a smaller measurement aperture than
usual. For example, an aperture that is used for a 384-well plate is used to measure a 96-well plate, and
an aperture that is used for a 1536-well plate is used to measure a 384-well plate.

TRF
Measures time-resolved fluorescence.

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 8 Protocol
TRF

Figure 43. Measurement parameters with multiple filters checked and Advanced parameters open.

Filters
Excitation Filter [nm]: The instrument has a built-in 320nm excitation filter.
Emission Filter [nm]: Select the emission filter. To add, edit and remove filters, see Instrument
Parameters: Filter Definition.
Multiple filters: Select to measure each well with multiple wavelength pairs.
Note When measuring multiple wavelengths with filters, the measurements are done in the order
of the filter position.

Delay time [us]: Define the waiting period (TRF delay) between the excitation flash and the
beginning of the emission light measurement

Integration time [us]: Define the length of the measurement window, that is, the time the emitted
signal is collected for each measurement cycle.
Figure 44. TRF principle

The sum of TRF delay time and TRF integration time can be maximum 2400 us,

Measurement time [ms]: Define the light collection time used in the measurement. The wells are
measured with a selected measurement time.

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TRF Spectrum

TRF: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use Step duration to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Dynamic range: If needed, select the reading range from the alternatives.
Auto range: The default and recommended setting. Automatically selects the optimal reading
range. Is based on signal intensity in the well and uses the lowest possible reading range for the best
sensitivity.
Low range: Produces the highest sensitivity with a limited dynamic range.
Medium range: Offers sensitivities and dynamics in between the Low and High ranges.
High range: Intended for highest-concentration samples. Covers a wide dynamic range with lower
sensitivity than the other dynamic ranges.

The measured values are comparable regardless of the dynamic range selection.

TRF Spectrum
Measures time-resolved fluorescence spectrum for a wavelength range.
Figure 45. TRF Spectrum measurement parameters with Emission spectrum selected.

Type: Select to measure either excitation or emission spectrum.

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TRF Spectrum

Excitation spectrum: Measures excitation spectrum for a selected wavelength range by using a
fixed emission wavelength.
Emission spectrum: Measures emission spectrum for a selected wavelength range by using a fixed
excitation wavelength.

Emission / Excitation wavelength range: Select the Start [nm] and End [nm] wavelengths and the
Step [nm] size (scanning resolution) for the scanning measurement. The wavelength range is 200 to
840 nm for excitation and 270 to 840 nm for emission.

Excitation bandwidth [nm]: Select the bandwidth of the excitation wavelength.

5: An excitation slit of 5 nm.
12: An excitation slit of 12 nm. The default value.
The emission bandwidth is permanently set to 12 nm and cannot be changed.

Delay time [us]: Define the waiting period (TRF delay) between the excitation flash and the
beginning of the emission light measurement. See the TRF principle illustration.

Integration time [us]: Define the length of the measurement window, that is, the time the emitted
signal is collected for each measurement cycle.

Measurement time [ms]: Define the light collection time used in the measurement. The wells are
measured with a selected measurement time.

TRF Spectrum: Advanced Parameters

Step duration [hh:mm:ss]: If needed, set the total time for the step. After the measurement is
performed, the software waits until the entered duration is up before proceeding to the next step. You
can use Step duration to accurately time two protocol steps.

Lag time [hh:mm:ss.t]: If needed, set the waiting time for the beginning of the step.

Dynamic range: If needed, select the reading range from the alternatives.
Auto range: The default and recommended setting. Automatically selects the optimal reading
range. Is based on signal intensity in the well and uses the lowest possible reading range for the best
sensitivity.
Low range: Produces the highest sensitivity with a limited dynamic range.
Medium low range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards sensitivity.
Medium high range: Offers sensitivities and dynamics in between the Low and High ranges.
Compromise between dynamic range and sensitivity adjusted more towards dynamic range.
High range: Intended for highest-concentration samples. Covers a wide dynamic range with lower
sensitivity than the other dynamic ranges.

Tip When selecting a fixed gain, the principle for achieving the best sensitivity is to select the lowest
possible range to avoid overrange results.

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Kinetic Loop

The measured values are comparable regardless of the dynamic range selection.

Kinetic Loop
Executes sub-steps several times in defined time intervals in a kinetic measurement. You can set the
number of readings and the interval time.
Note Add the measurement step as a sub-step of the kinetic loop. Click Kinetic Loop in the
Session tree, then add the measurement step.

Figure 46. Kinetic Loop and Fluorescence measurement.

Duration: Set the duration of the kinetic measurement either by the number of readings, or by the
total time.
No. of readings: Set the number of measurements per well. The range is between 2-1000.
Total time: Set the total time (up to 24h). If it is longer than 24 hours, use the No. of readings
setting.
Note Use the number of readings setting for fast kinetic measurements.

Kinetic interval [hh:mm:ss]: Set the time between the starting times of two consecutive loops. If you
choose the default interval (00:00:00) or a shorter interval than the minimum reading time of the
instrument, the instrument measures as fast as possible.

Shake between readings: Select if you want the instrument to shake the plate during the interval times
of a kinetic measurement.
Shaking type
Continuous: Shaking is constant during the shaking time.
Pulsed: Shaking starts and stops at specific times. Set the shaking on and off times
[hh:mm:ss].
Shaking on [hh:mm:ss]: Set how long the shaking time lasts.
Shaking off [hh:mm:ss]: Set how long the pause is between the shaking times.
Speed: Select the shaking speed.

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Well Loop

Force: Select the shaking force of (Varioskan LUX only).

Well Loop
Executes sub-steps for as many wells at a time as you have selected as a well count.

Well count: Define for how many wells at a time you want to perform the steps which are under the
well loop.
Figure 47. Well loop.

Tip Use well loop if you measure a fast kinetic reaction and need to measure all kinetic readings
from one well before proceeding to the next well.

Well Loop: Advanced Parameters

Block interval [hh:mm:ss]: Set how long the well loop execution lasts. Without block intervals, the
instrument performs loops with no delay in between.

Area Selection
Executes sub-steps for a certain area of wells. Use Area Selection when you want to measure / dispense
a limited number of wells defined in the Plate Layout.
Note Area selection is not necessary when all of the defined wells of the plate layout are measured
or dispensed.

Plate: Select the plate from the drop-down list (if you have more than one plate in the layout), then
paint the wells with your cursor to select them. The selected wells are marked in orange.

Note Add the measurement step or dispense step as a sub-step of Area Selection. Click Area
Selection in the Session tree, then add the step(s).

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8 Protocol
Shake

Figure 48. Area Selection

Shake
Shakes the microplate to mix the liquid in the wells.

Duration [hh:mm:ss]: Set the total shaking time (23:59:59).

Shaking type
Continuous: Set the shaking as constant during the shaking time.
Pulsed: Set the shaking to start and stop at specific times.
Shaking on [hh:mm:ss]: Set how long the shaking time lasts in pulsed shaking.
Shaking off [hh:mm:ss]: Set how long the pause is between the shaking times in pulsed
shaking.
End with shaking off: Set the pulsed shaking to end with shaking off.
Speed: Set the shaking speed.
Force: Set the shaking force (Varioskan LUX only).

Note When shaking the plate, do not exceed 50% of the maximum well volume or the plate
manufacturer recommendation, if it is lower.

Note Do not use shaking with the Thermo Scientific Drop plate.

Pause
Pauses the protocol for a specific period. A message is displayed during the pause if you have entered a
message in the Pause parameters. The instrument continues to execute the protocol after the set pause
time expires or through user action.

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Dispense

Continuation
Time expired: Set the duration of the pause. The protocol continues after the time has expired.
User action: Set the pause to stop on user action (the user clicks the Continue button).

Message: Write a message that appears on the screen during the pause.

You can also run the plate out during a pause step.
Figure 49. Pause between running the plate out and plate in steps.

Dispense
Dispenses a given volume of liquid into the wells.

Select the same dispenser and position for both the software and instrument. The instrument
automatically checks that the same positions are selected.

Dispenser: Select the dispenser.

Volume [ul]: Set the liquid volume to dispense to each well.

Position: Select the dispensing position F or L. See Dispensing Positions F and L.

Dispensing speed: Select the dispensing speed based on the liquid volume and viscosity.
Low: For dispensing low viscosity liquids.
Medium Low: For dispensing normal viscosity liquids or low volume dispensing of low viscosity
liquids.
Medium: For low volume (< 15 ul) dispensing of normal viscosity liquids.
Medium High: For dispensing high viscosity liquids.
High: For low volume (< 15 ul) dispensing of high viscosity liquids.

Dispense: Advanced Parameters

Automatic tip prime: The dispenser dispenses a small amount of reagent into the tip priming vessel
every time the instrument fills the dispenser syringe. This makes the volume of the first well equal to
that of the others, thus compensating for the so-called drawback phenomenon. It is recommended to
use the tip priming feature to achieve greater accuracy when the dispensing volumes are small, for
example, 1 to 50 ul.
Note Tip priming is a different procedure from manual priming that must be performed when
reagent bottles are installed into the dispensers and the dispenser tubes are completely empty.

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Run Plate Out / Run Plate In

Step duration [hh:mm:ss]: Set the total step time (23:59:59).

Note When performing dispensing and measurement simultaneously, remarkably high, very rapid
signal peaks even in blank wells can occur. These peaks can be generated by the large static
electricity charges that some microplates can carry. When solution with high conductivity (e.g.
saline) is dispensed into wells, this charge can release as sparks that the instrument detector
measures. To overcome this problem, remove the charge with a de-ionization device before using
the plate, change the plate manufacturer and/or the product to find a plate without static charge or
add 0.1- 0.2 s lag time between dispensing and measurement in the assay allows.

Dispensing in a Kinetic Measurement

To dispense at the beginning, or during a kinetic measurement add the dispense step inside the kinetic
loop step.

Use the Dispense at reading parameter to select at which kinetic reading the dispensing is performed.
The values are from 1 (one) to the number of readings defined for the kinetic loop, the default being 1
(one).
Figure 50. Dispensing in a kinetic measurement.

Run Plate Out / Run Plate In

Runs the plate in or out in the middle of a protocol. This is typically combined with the Pause action.

An example of the procedure would be to: Measure -> Run Plate Out -> Pause -> Run Plate In ->
Measure.
Note When you start a measurement session and click Start, the instrument automatically runs the
plate in.

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Results
In the Results view you can see the measurement results and perform calculations. You can export
measurement and calculation data to use outside SkanIt Software.

You can view results in a Plate or List view, export the results and print the results.

Note To watch the measurement results during a run, click the calculation under Results in the
Session tree.

Results Ribbon
Click Results in the Session tree to open the Results / Add Calculations ribbon (Results ribbon).
Click a calculation to add it as a step in the Session tree. The software carries out the calculations in
the order listed in the Session tree.

Figure 51. Results ribbon.

Calculation Actions
You can add calculations either before or after a measurement. You can add several calculations to a
measurement and also nest calculations. Select the calculation from the Results ribbon.

See Calculations for information.

Start a Measurement
1. Click the Start button.
2. Write a name for the session in the Session Name window.

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Print Results

This step is skipped if you have previously named the session.

3. Click OK.
The software indicates the action it is running.
4. Click the action under Results to watch the measurement results during the run.
If you need to stop the run, click Abort. The results measured up to that point are saved.

Print Results
1. Open the session.
2. Click the measurement step under Results in the Session tree.
3. Click the Print tab in the measurement window.

View Results
You can view the results in Plate or List view. The Plate view shows the measurement result per well in
the plate. The List view shows the measurement results, details, and time.
1. Open the session.
2. Click the measurement step under Results in the Session tree.
3. Click the Plate or List tab to view the results.
Figure 52. List view.

End Point Measurement

Both plate and list views show the numeric measurement results in end point measurements. The
measurement value is shown for each well in end-point measurements.

Kinetic and Spectral

The plate view shows the measurement results as graphs in kinetic or spectral measurements.
right-click on a well to select the graph view. You can paint multiple wells to see curves for multiple
wells.

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 9 Results
Measurement signal units

Figure 53. Kinetic data.

Tip Click Copy to clipboard to copy the picture as a bitmap image for use outside SkanIt
Software.

Multipoint
In the plate view the multipoint measurement results are shown as a heat map. The list view shows the
multipoint measurement results using coordinates indicating where in the well each point was
measured. The center point of the well is defined as origo (0:0) and marked with coordinates x:y.
The unit is 1/100 of mm. For example, coordinates -280:310 means that the measurement point is
2.80 mm left from the well center in horizontal direction and 3.10 mm upwards from well center in
vertical direction.

Measurement signal units

Abs = Absorbance unit

RFU = relative fluorescence unit (Fluorescence intensity and TRF)

RLU = relative luminescence unit (luminescence)

Alpha signal: (AlphaScreen)

Number Formats
Select the number of decimals or significant digits that will be shown for measurement raw data and
calculated data.

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Disable a Sample

1. Click Settings on the application menu.

2. Click Results.
3. Set the decimals or significant digits.

Disable a Sample
You can remove specific wells from results (e.g., outliers). A disabled well is not shown in the results
and is not used in the calculations.
1. Right-click the well that you want to disable.
2. Select Disable in the shortcut menu.
To enable the well, right-click the well and select Enable.

Result disabling is shown as strikethrough and grayed out. Disabling is always traced back to the
original instrument measurement and that particular measurement is never used in calculations.

Saturated Results
Saturated results are shown as strikethrough (data with lines through it). Saturated results are never
used in calculations.

Run Log
A run log has execution information about the session you have run. The log has information about
when a session was started, stopped or aborted, and what steps were started and ended. It also has
information about errors and warnings that may have occurred during a run.

Click Results in the Session tree to view the run log.

Customize List View

You can customize the List view by hiding columns and by grouping the results per column.

Hide a column
1. Open the session.
2. Click the measurement step under Results in the Session tree.
3. Click the List tab in the Results measurement window.
4. Place your cursor on the column header you want to hide.
5. Left-click the column header.
6. Drag the column header down onto its own column.
7. Release the header when a red x-mark appears.

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Run Log

The column is now hidden.

Figure 54. Hiding the Type column.

Undo Hiding a Column

1. Open the session.
2. Click the measurement step under Results in the Session tree.
3. Click the List tab in the Results measurement window.
4. Click Customize.
5. Click Reset list.

Column Grouping
1. Open the session.
2. Click the measurement step under Results in the Session tree.
3. Click the List tab in the Results measurement window.
4. Click Customize.
5. Click Enable column grouping.
6. Place your cursor on the column header you want to group.
7. Left-click the column header.
8. Drag the column header into the grouping area.
9. Release the header.
The view is grouped by the column results.
Figure 55. Column grouping area and Customize menu open.

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Run Log

Undo Column Grouping

1. Click the List tab in the Results measurement window.
2. Click Customize.
3. Click Disable column grouping or Reset list.

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Export Results and Reports

Export Results of a Single Result Step

You can manually export the measurement or calculation data of a particular result step in Microsoft
Excel (*.xls) format.
1. Click the measurement step under Results in the Session tree that contains the data you want to
open.
2. Click the Plate or List tab to select the format in which the data is to be exported.
3. Click Export to Excel. The file is opened in Microsoft Excel or another associated application.
The file can then be saved manually.
Figure 56. Export single step: 1) Click the result, 2) click Plate or List, 3) click Export to Excel.

Export Results of Several Result Steps

If you want to export data from several result steps (e.g. both measurement and calculated data) at once
to the same file, create a result report in the Report view.

You can export the result report either manually or automatically after the run. The available file
formats for result report are PDF, Excel, XML, TXT.

You can also set the software to email the result report automatically after run.

See Result Report for more information.

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Export Results of Several Result Steps

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 11

Calculations
With calculations you can process measurement results. Select a calculation from the Results / Add
Calculations ribbon (Results ribbon), and the calculation appears in the Session Tree under Results.

You can add calculations either before or after a measurement, but not during a run.

Note Your instrument may not support all of the calculations described here.

Results Ribbon
Click Results in the Session tree to open the Results ribbon. Click a calculation on the ribbon to add
it as a step. The software carries out the calculation in the order listed in the Session tree.
Figure 57. The Results / Add Calculations ribbon for adding calculations.

Calculation Actions
You can add calculations either before or after a measurement. You can add several calculations to a
measurement and also nest calculations.

The calculation uses the result data that is directly above it in the Session tree. First select the result
step you want to use as the source data for the calculation, then select the calculation.

Table 7. Calculation actions and descriptions.

Action Description
Blank Subtraction Subtracts the average blank value from all of the samples.
Average, SD, CV% Calculates the average, standard deviation (SD) and the
coefficient of variation (CV%) of sample replicates.

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Blank Subtraction

Table 7. Calculation actions and descriptions.

Action Description
Basic Calculation Performs simple calculations, such as subtractions,
multiplications and divisions.
Dilution Factor Multiplies the results of the unknown samples by dilution
factors defined in the plate layout.
Normalization Normalizes the data of a sample group to a B0 reference
sample. The results are shown in percentages.
Pathlength Correction Normalizes absorbance measurement data to correspond to a
10 mm pathlength (= standard cuvette).
Standard Curve Calculates the concentrations of samples based on a standard
curve generated from a standard sample series.
Dose Response Calculates the concentration at which, e.g., 50% of a
measured sample activity is lost.
Kinetic Offers different kinds of calculations for kinetic data.
Spectral Offers different kinds of calculations for spectral data.
Multipoint Offers different kinds of calculations to reduce multipoint
measurement results in each well to one result per well.
Classification Divides samples into separate categories based on user
defined limit values.
Quality Control Checks the validity of the assay, e.g., against known control
samples.
Custom Formula Lets you create custom calculations.
Graph Creates graphs from the result data.

Blank Subtraction
Use blank subtraction to subtract the average blank value from all of the wells in the Plate Layout.

If samples have specific blanks, these blanks are subtracted from their own samples and no normal
blank average is subtracted from samples with specific blanks.

If you have several sample groups in a Plate Layout, blank subtraction is performed per group.

If you perform blank subtraction to kinetic measurement data, the blank signal at each point in time is
subtracted from sample signals at that specific time.

If you perform blank subtraction to spectral data, the blank signal at each wavelength is subtracted
from sample signals at that wavelength.

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Average, SD, CV%

Average, SD, CV%

If you defined samples to have replicates in the Plate Layout, you can calculate the average (Avg),
standard deviation (SD), and the coefficient of variation (CV%) of the sample replicates.

The standard deviation is calculated using the following formula:

x = the measured value from a single measurement point

m = the average of the measured replicate values
n = the number of replicates.

Basic Calculation
You can perform simple calculations like subtractions, ratios and multiplications. When you select
Basic Calculation, the step goes to the root level under Results. You can use both measurement and
calculation data as source data.

Use basic calculation, e.g., for dual-wavelength measurements to subtract the reference wavelength data
from the assay wavelength data.
Figure 58. Basic Calculation parameters.

Calculation type
Subtraction (A-B): Result data of the second data source is subtracted from the result data of the
first data source.
Ratio (A/B): Result data of the first data source is divided by the result data of the second data
source.
Multiplication (A*x): Result data is multiplied by the determined value.

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Dilution Factor

Division (A/x): Result data is divided by the determined value.

Data source
A: Select the first data source.
B: Select the second data source.

Tip In multiple wavelength measurements, select the wavelength of the source data.

Dilution Factor
The Dilution Factor calculation multiplies the results of unknown samples with the dilution factors
defined in the Plate Layout. The dilution factor calculation does not affect the results of other sample
types, they are multiplied by factor one (1).

Normalization
In normalization the data is normalized to a certain single sample and the results are shown in
percentages.
Figure 59. Normalization parameters.

Calculation type
Ratio B/B0 * 100%: The sample selected as B0 will represent the value 100%.
Inhibition 100%-B/B0 * 100%: The sample selected as B0 will represent the value 0%.

Source
Group: Select the sample group to which the normalization is performed. If you select multiple
groups, you can select the B0 reference only from samples that belong to all selected groups. If you
select Use maximum value, the maximum is selected from each group separately and used in that
groups normalization calculation.
B0: Select which sample is used as B0.

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Pathlength Correction

Use maximum value: Select to use the maximum value of the samples.
Select sample: Select the sample from the drop-down list. The average value of the selected
sample (if replicates are used) will be used in the calculation.

Pathlength Correction
Use pathlength correction to normalize absorbance measurement results to correspond to a 10 mm
liquid pathlength. You can calculate sample concentrations from the absorbance values by using known
concentration factors or extinction coefficient values which are valid for a 10 mm liquid pathlength.
Note Pathlength correction is not applicable to turbidometric measurements.

Pathlength correction in a microplate measurement requires a suitable mathematical K-factor. The

K-factor depends on the microplate and liquid type used in the measurement. SkanIt Software includes
predefined K factors for commonly used liquid and microplate types.

Note To perform pathlength correction in an absorbance measurement, select Pathlength

correction in the Absorbance step before you start the measurement.

Figure 60. Absorbance measurement with Pathlength correction selected.

To perform pathlength correction to measurement results, add the pathlength correction step under
the Absorbance measurement results step.

Define the parameters for the pathlength correction calculation.

Wavelength: Select the measurement data wavelength for which the pathlength correction is
performed.

K-factor (microplate measurement): Select a predefined K-factor from the Select K-factor list (click the
icon to the right of the K-factor box). Select the right K-factor according to the liquid type used in the
assay.

Cuvette pathlength (cuvette measurement): Enter the actual cuvette pathlength (in millimeters).

Calculate concentrations: Select to calculate concentrations from the pathlength corrected absorbance
values. Select the appropriate equation to calculate concentrations and set the value for the coefficient
(x or ).
C=A*x
C=A/

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Pathlength Correction

C refers to concentration, A to absorbance, and x and to the extinction coefficient.

Concentration unit: Enter the concentration unit of the calculated concentrations.
Use in child calculations: If you add a child calculation to the pathlength correction result step,
select which data is used as the source data for the calculation; the corrected absorbance values or
calculated concentrations.

Pathlength Correction Results

The plate view of the results shows the calculated concentrations or the corrected absorbance values
(whichever is selected in the Use in child calculations setting).

The list view shows the following columns:

Blank subtracted: Blank subtracted absorbance values (not pathlength corrected).

Corrected Abs: Absorbance values corrected to correspond to a 10 mm pathlength.

Concentration: Concentrations calculated with the selected equation using the corrected absorbance
values.

Note Pathlength correction automatically performs black subtraction in microplate and cuvette
measurements.

Perform Pathlength Correction in a Microplate Assay

1. Create a new session and define the Plate Layout. Add at least one blank sample to the layout.
2. Click Absorbance on the Protocol ribbon. Select the measurement wavelength(s) and Pathlength
correction.
3. Click Start.
The software automatically adds the 900 & 975 nm measurement step to the protocol to perform
the 900 nm and 975 nm measurements required for pathlength correction.
4. Click the Absorbance step under Results.
5. Click Pathlength Correction on the Results / Add Calculations ribbon to add it under the
Absorbance measurement step
6. Select the wavelength of the source data and the K-factor to be used.
7. Select Calculate concentrations and enter the parameters to calculate the concentrations of the
samples based on the corrected absorbance values.

Perform Pathlength Correction in a Cuvette Assay

Pathlength correction can be used in cuvette measurements when the actual cuvette pathlength is
shorter than 10 mm.

Pathlength correction is not needed if the measurement is performed with a standard 10 mm cuvette.

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Standard Curve

Note K-factors are not used with cuvette measurements.

Pathlength correction in a cuvette measurement:

1. Create a new session and define the cuvette layout. Add at least one blank sample to the layout.
2. Click Absorbance on the Protocol ribbon. Select the measurement wavelength(s).
3. Click Start.
4. After all cuvettes have been measured, click the Absorbance step under Results.
5. Click Pathlength Correction on the Results / Add Calculations ribbon to add it under the
Absorbance measurement step.
6. Enter the actual cuvette pathlength in millimeters.
7. Select Calculate concentrations and enter the parameters to calculate the concentrations of
unknown samples based on the corrected absorbance values.

Standard Curve
Standard curve is used for quantitative analysis. It calculates the concentrations of the unknown and
control samples based on a standard curve that is made from a series of standards with known
concentrations.
Note Standard Curve requires that standards have been defined in the Plate Layout.

Note The standard replicates are automatically averaged prior to curve fitting.

Figure 61. Standard curve parameters with Advanced open.

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Standard Curve

Fit Type
Select the Standard curve fit type.

Linear Regression
The linear regression fit type uses the equation y = ax + b, where
y = signal
x = concentration
a = slope
b = y axis intercept
The coefficients of the functions are solved with matrix calculations by using the linear least
squares (LLS) method. The minimum number of standards is two (2), but at least three (3)
standards should be used to increase the accuracy of the result.
Use extrapolation: Select if you want to enable extrapolation to calculate concentrations to
samples which are outside the concentration of the standard curve. Extrapolation is only available
for the linear regression fit type, as it is not mathematically reliable for other fit types.
Force line through origin: Forces the fitted curve to intercept the origin by following the
equation y = ax. The R2 value is not calculated.

Logistic Fit Types

All logistic fit types use the same fit model:
Figure 62. Logistic fit model.

y = Signal.
x = Concentration.
a = Maximum signal (asymptote above).
d = Minimum signal (asymptote below).
c = Concentration at the inflection point.
b= Slope-related term at the inflection point.
e = Curve asymmetry factor (used only in the 5PL fit).
4PL (Four parameter logistics): The coefficients of the function are solved using the
Levenberg-Marquardt method.
Log-Logit: The a and d coefficients are treated as known, otherwise it is the same as the 4PL fit
type.

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Standard Curve

Custom logistic: The a and d coefficients are treated as known, otherwise it is the same as the 4PL
fit type.
Figure 63. Custom logistic (Fix upper and Fix lower): Enforce fixed value to asymptote when fitting the shape
show in figure X-Y.

5PL (Five parameter logistics): 5PL fit type uses the same fit model as 4PL, but the asymmetry
parameter e is included in the formula.
The minimum number of standards for logistic fit types is three (3).

Polynomial Fit Types

The polynomial fit types are Quadratic polynomial, Cubic polynomial, and Quartic polynomial.

The polynomial fit is determined as: y = a + bx + cx2 ...mxn, where:

n = 1, 2, 3 or 4
a, b, ..., m = Coefficients.
x = Concentration.
y = Signal.

Derived from the above equation:

y = ax2 + bx + c for the quadratic polynomial fit type. The minimum number of standards is three.

y = ax3 + bx2 + cx + d for the cubic polynomial fit type. The minimum number of standards is four.

y = ax4 + bx3 + cx2 + dx + e for the quartic polynomial fit type. The minimum number of standards is
five.

The coefficients of the functions are solved with matrix calculations by using Gauss-Jordan elimination
with a back-substitution algorithm. The roots of the polynomial, that is, the results, are calculated
with an iterative Laguerres method. If more than one root is found in the Standard curve area, the
software produces a warning.

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Standard Curve

Point to Point
The point-to-point method connects the adjacent Standard points together by using a straight line (see
the equation below), which is different for each of the intervals. The results are calculated by first
searching for the correct interval, and then by using the corresponding equation. The minimum
number of standards for this fit type is two.

yi = aixi + bi

Cubic Spline
This method is a smoothed point-to-point method where the adjacent Standard points are connected
together by using cubic polynomials (see the equation below) and by optimizing the connecting points
as smoothly as possible to avoid sharp angles. The results are calculated by first searching for the correct
interval, and then using a bisection method to find the answer in the corresponding equation. The
minimum number of standards for this fit type is three.

yi = aixi 3+ bixi2 +cixi + di

Advanced Options
You can select the type of data transformation for concentration and signal. The transformation means
a change of scale to improve the accuracy of statistical analyses.
Linear: Use linear transformation.
Logarithmic: Use logarithmic transformation.
Tip If the concentration range of the standards is more than four decades, logarithmic
transformation should be used to obtain more precise curve fitting.

Use saved curve: Use a previously measured standard curve. Go to Use the Same Standard Curve
in Several Sessions.

Standard Curve Results

The curve fit equation as well as the correlation coefficient R2 are shown below the curve. The
coefficient of determination, R2, is a statistical measure of how well the curve fit represents the data,
that is, its statistical reliability. The R2 value is not calculated in the following cases: cubic spline fit,
point-to-point fit or linear regression with the force fitted curve through the origin option.

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Standard Curve

Figure 64. Standard curve graph and Results table.

Title: Write the title for the standard curve.

Logarithmic X-axis: Select to display the data on logarithmic X -axis.
Logarithmic Y-axis: Select to display the data on linear Y-axis.
Show replicates: Select to show the individual standard sample replicates in the curve. If this is not
selected, only the averages are shown.
Show unknowns: Show the unknown samples in the curve.

The Standards table below the graph shows the standards used in the curve fit.
Figure 65. Standards table.

Sample: Name of the standard sample.

Concentration: Concentration of the standard sample defined in the Plate Layout.
Average signal: Signal of the standard sample.
CV%: CV% of replicates (if replicates were defined in the Plate Layout).

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Standard Curve

Fitted signal: Signal value calculated using the curve fit function at the given standard
concentration.
Residual: Difference between the average signal (=measured) and the fitted signal (=calculated)
values.

Click the + icon in front of the standard sample name to see the individual replicates.

Tip To remove a standard or its replicate from the standard curve, you can do so directly from the
list under the graph by right-clicking and selecting Disable sample from the menu. The disabled
sample will not be used in the curve fitting and the curve is fit automatically again without disabled
standards. The disabled rows are marked with a strike-through line. To enable the disabled item,
right-click the row, then click Enable sample.

The table under the standard samples shows the calculated concentrations of the unknown and control
samples.
Figure 66. Results table

Well: Well coordinate.

Type: Sample type.
Sample: Sample name.
Signal: Signal of the sample.
Concentration: Concentration of the sample calculated from the standard curve.

If a sample is outside the standard curve, the fitted concentration is shown either as <min (lower than
the lowest standard concentration) or >max (higher than the highest standard concentration).

If you enable extrapolation, the extrapolated samples are shown in orange color in the curves and in
italics in the list.

Tip If you defined dilution factors for unknown samples in the Plate Layout and you want to
multiply the calculated concentration values by the dilution factors, add a Dilution Factor
calculation under standard curve. The Standard Curve calculation does not take the dilution factors
into account.

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Standard Curve

Multiple Roots
With certain fit types and data, the resulting standard curve can be fitted in a way that a measurement
signal hits the curve in two or more points. It means that the signal corresponds to two different
concentration values. This occurs only if there is a maximum or minimum in the curve. In such a case,
a curve is drawn but no concentrations are calculated. The following message is shown in the curve fit
results graph:
The curve contains signal values with multiple possible concentration values (multiple roots).

Multiple roots can occur in all fit types except for Linear Regression (LLS), 4PL and Log-Logit.

If the message is shown, try to disable the standards that cause the curve being shaped in a way that
multiple roots occur.

Use the Same Standard Curve in Several Sessions

You can save a specific standard curve for use in other sessions. This enables you to exclude standard
samples from the assay, and calculate the concentrations of the unknown samples by using a saved
standard curve which you measured earlier.

To save a standard curve to be used in other sessions

1. Click Save curve next to the standard curve.
2. Give a name to the standard curve and a description (optional).
3. Click Save.
The standard curve is now saved in the SkanIt Software database.

To use a saved standard curve in a new measurement session

1. Add a standard curve calculation to results.
2. Click Advanced parameters.
3. Select Use saved curve and select the right curve from the list.
The standard curve calculation step will now show the saved standard curve in the graph view and
calculate the concentrations of the samples based on that curve.

Note Go to application menu -> Settings-> Saved curves to view all the saved standard curves.

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Dose Response

Dose Response
You can use Dose Response calculation to create a curve to calculate, e.g.,the ED50 value. The ED50
value is a concentration value in which 50% of the monitored characteristic of the sample has been
lost. The characteristic can be, e.g., cell death, cell survival, or certain enzymatic activity. The ED value
is used to demonstrate the efficiency (such as toxicity) of the sample.
Note Dose response calculation requires that you have defined a concentration series of standard
samples in the plate layout.

In addition to ED50, other ED (effective dose) values can also be counted, typically ED20 and ED80.
The ED20 value is a concentration where 20% of the activity is lost, and ED80 is the value where 80%
has been lost.
Tip You need to perform a normalization calculation before performing a dose response
calculation. In the normalization calculation define the reference sample/value against which other
samples are normalized. The normalization results can then be used as source data for Dose
response calculation.

Figure 67. Dose Response parameters.

Dose response calculation parameters

Sample groups: Select which sample groups to include in the calculation. If you defined standards
of several sample groups in the Plate Layout, the software displays the curves of all selected sample
groups in the same graph and calculates the ED values separately for each group.
ED values: Enter the ED% to calculate from the curve. You can enter up to three ED% values by
clicking the Add button.
Fit type: Select the fit type to use for fitting the curve. Go to Fit Type for descriptions.

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Kinetic

Dose Response Results

The result view displays the dose response curve according to the selected fitting parameters. The
fitting equation is shown below the curve. If you selected several sample groups to be included in the
calculation, curves of all groups are shown in the same graph.

The table below the graph displays the concentration values of the selected ED%.

Dose Response Calculation Overview

1. Create a measurement session with a standard sample series in the Plate Layout.
2. Add a Normalization calculation to results.
3. Add a Dose Response calculation by using Normalization results as source data.

Kinetic
Use kinetic calculations to reduce data from kinetic measurements.
Figure 68. Kinetic Subtraction parameters with Advanced options open.

Calculation type
Select the calculation type from the list.

Average / SD / CV%
Calculate the average, SD, and CV% value of all kinetic readings.

Click Advanced to exclude kinetic readings from the calculation. Define the Ignore readings settings:
From beginning: ignores a defined number of points (readings), counted from the first reading.

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Kinetic

From end: ignores a defined number of points (readings), counted from the last reading.
If you do not ignore any readings (0 in both), then all readings are included in the calculation.

Integral
Calculate the area under the measurement curve. Click Advanced to limit the range of readings.
Figure 69. Integral calculation

Baseline Subtraction
Transform the measured values to start from 0 by removing the measured baseline before the actual
reaction. It subtracts the average of a defined number of readings from the beginning or end of all other
readings.

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Kinetic

Figure 70. Baseline subtraction calculation with Advanced options open.

Baseline Points
Select the number of kinetic readings used for baseline calculation.
From Beginning: the number of readings is calculated from the beginning of the measurement.
From End: the number of readings is calculated from the end of the measurement.
Readings (0...100): The number of kinetic readings used for baseline calculation. The software
calculates the average value of the readings selected from the baseline. The average equals the
baseline value. If you select End, the change is extrapolated starting from the end of the
measurement.

Click Advanced to exclude kinetic readings from the calculation.

Select Single Reading

Select a specific kinetic measurement point (reading).

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Kinetic

Figure 71. Select single reading calculation.

Reading: The number of the kinetic measurement reading. Select a reading you want to use in
further calculations.

Select reading range

Select specific raange of kinetic measurement points (readings).

Average Rate
The average kinetic rate calculates the slope of the signal vs time. The rate is calculated by linear
regression (linear line squares method or LLS) using all the measurement readings within the selected
data and time range.
Figure 72. Average rate calculation with Advanced options open.

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Kinetic

Select to calculate the rate per second (/s), minute (/min) or hour (/h) depending how fast the reaction
is.

Click Advanced to exclude readings from the calculation:

From beginning: ignores a defined number of points (readings), counted from the first reading.
From end: ignores a defined number of points (readings), counted from the last reading.

Maximum Rate
The software searches the data for the maximum rate (slope of signal vs time) that is found in each well.
To obtain the maximum rate, a series of linear curve fits is performed for different segments of the
measurement value vs time curve.

The first segment starts at the first data point within the selected time and measurement range, the
second segment starts at the second data point, and so on, until all of the data points have been
analyzed.

You can specify the number of data points in a segment with the Window setting.
Figure 73. Maximum rate calculation with Advanced options open.

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Kinetic

Kinetic Rate Unit

Select to calculate the rate per second (/s), minute (/min) or hour (/h).

Window
Select the number of consecutive readings to use for searching for the area of maximum rate.
evaluation.

The window defines how many measurement points are included in the measurement calculations.
The size of this window is given in the Window parameter box.

Example: if the number of kinetic readings is ten, and the Window parameter is three, the software will
calculate the first rate by using measurements 1 to 3, the second rate using measurements 2 to 4, and so
on up to measurements 8 to10. The maximum rate will be the maximum value among these calculated
rates.

Advanced
Click Advanced to exclude readings from the calculation. Define the Ignore readings settings:
From beginning: ignores a defined number of points (readings), counted from the first reading.
From end: ignores a defined number of points (readings), counted from the last reading.

Maximum of Well (Peak)

Use the calculation to search for the maximum measurement value in each well.
Figure 74. Maximum of well (Peak) calculation with Advanced options open.

Click Advanced to exclude readings from the calculation. Define the Ignore readings settings:
From beginning: ignores a defined number of points (readings), counted from the first reading.
From end: ignores a defined number of points (readings), counted from the last reading.

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Kinetic

Time to Change
Calculate the time required to reach a defined change in the signal (in each well).
Figure 75. The Time to change calculation with Advanced options open.

Baseline Points
The baseline parameter is the number of initial readings that are used for the baseline calculation.
Select the value from which the change in the signal is calculated.
Use zero: The comparison is made against zero.
From Beginning: The number of initial readings is calculated from the beginning of the
measurement.
From End: The number of initial readings is calculated from the end of the measurement.
Readings (0...10): The number of readings used for baseline calculation. The software calculates
the average value of the readings selected from the baseline. The average equals the baseline value.
If you select End the change is extrapolated starting from the end of the measurement.

Change (+/-)
The change from the baseline as a relative or absolute change. The change in signal is specified in the
Change parameter and is compared to the baseline. The change can be positive or negative. The value
is negative when the signal decreases from the baseline. The Window parameter defines the number of
consecutive measurements which should reach the change before the result is accepted.

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Spectral

Select if the signal change from the baseline value is calculated as an absolute or relative (%) value. Set
the value or percentage. This change is added to the baseline value to create a required change value.
The result is the exact interpolated time at which the given change occurs.
Absolute: Set the absolute value.
Relative[%]: Set the relative value in percentages.

Window
Specify the number of consecutive readings to use for evaluation. The first point of the window must
be less than the required change value, and the other points of the windows must be above it to
confirm the calculated change to be real. The opposite is true if looking for a negative change.

Advanced
Define the Ignore readings settings.
From beginning: Ignores a defined number of points (readings), counted from the first reading.
From end: Ignores a defined number of points (readings), counted from the last reading.

Spectral
Use spectral analysis to handle spectral scanning measurement data.

Sample Groups
Select the sample group for the calculation. You can choose all, or selected groups. Click OK to take
the selection into use.

Calculation Type
Select the calculation type from the list.

Spectral Peak Search

Locates the wavelengths with peak values above the threshold value.

A peak is defined by comparing the window count of adjacent measurement values to a possible peak
value. A true peak value is declared if the measurement values of the window count before and after the
possible peak are smaller.
Wavelength (start) / (end): The start and end wavelengths for the peak search.
Window (1...3): The number of adjacent measurements considered when determining a peak
value.
Threshold: The intensity threshold for the peak search. Only values above the threshold are
considered.

Spectral Maximum
Returns the maximum measured value and the respective wavelength in each well.

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Multipoint

Wavelength (start) / (end): The start and end wavelengths for the maximum value search.
Threshold: The intensity threshold for the maximum value search. Only values above the
threshold are considered.

Spectral Normalization
Spectral normalization first searches for the spectral maximum of each sample and sets a value of that
wavelength to 1. After that the data of all the other wavelengths is normalized vs. the maximum.

Ratio Within Spectrum

Calculates the ratio between measurement values of two wavelengths in the same spectrum.

Enter the wavelength values used for ratio calculation:

Ratio = ValueWl1 / ValueWl2

Wavelength 1: wavelength of ValueWl1 .
Wavelength 2: wavelength of ValueWl2 .

Ratio Between Spectra

Calculates a ratio curve over a wavelength range. All the sample values are divided by the reference
sample values of the same wavelengths. You can use it, e.g., to calculate the signal to blank spectra.

The calculation uses the following formulas:

Ratio = SpectrumSample / SpectrumReference

Wavelengths (start) / (end): set the start and end wavelengths for the ratio calculation.
Reference: Select the reference sample that will be used as the base of the ratio calculation. The
spectra of all samples are divided with the spectrum of this sample.

Select Wavelength Range

Select part of the measured spectrum for viewing.
Wavelengths (start) / (end): set the start and end wavelengths for the range.

Select Single Wavelength

Select a measurement value of a single wavelength for viewing.
Wavelengths (start) / (end): set the start and end wavelengths for the range.

Multipoint
Multipoint calculation is used to reduce multiple measurement points in each well to just one result
per well. Multipoint calculation is available only for measurement data originating from a multipoint
measurement Fluorescence measurement and bottom reading. See Fluorescence: Advanced Parameters.

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Classification

Note Multipoint calculation must be performed before any other data reduction, except Blank
subtraction or Basic calculation, is attempted.

Multipoint calculation reduces multiple measurement points in each well to one point per well.
Multipoint calculation is available for 6- to 96-well plates in fluorometric bottom reading
measurements.

Multipoint Calculation Types

Average: The average value of all the measurement points in each well.

Minimum: The minimum value of all the measurement points in each well.

Maximum: - The maximum value of all the measurement points in each well.

Maximum - Minimum: The minimum value of all the measurement points in each well is subtracted
from the maximum value of all measurement points in the same well.

Standard deviation: The standard deviation of all measurement points in each well.

Sum: The sum of all the measurement points in each well.

Classification
Classification categorizes the source data based on user-defined limit values. The limit values can be
defined as a number, a specific sample, or a formula that can contain both samples and numbers.

These formulas can contain mathematical operators, such as +, -, / and *. Sample values that are less
than the defined limit are placed into the lower category, and samples that are equal to, or higher, than
the limit are placed into the higher category.

To categorize samples into two sets (e.g. positive and negative), you must define one limit value.
Figure 76. Classification parameters.

Number of categories: Select how many categories the samples are classified to.
Define category name: Name the category. The name is shown in the results.
Color: Select a color for each category. The color is used together with the category name to
differentiate samples belonging to different categories.

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Quality Control

Limit value text box. Enter the limit value. Click the text box, or the + icon to open the pop-up
window.
Sample: Select a sample average or replicate.
Values. Enter the formula by clicking the numbers and characters.

Quality Control
Use the Quality Control calculation to check the validity of the assay with known control samples. You
can create several quality control rules from the same source data using one Quality Control step. To
do a Quality Control calculation from different step results, you need to add a Quality Control step
under each source step.
Figure 77. In this example, the Quality Control rules of the assay state that the average absorbance value of
blanks must be less than 0.15 and the absorbance of all control sample replicates must be
greater than 1.2.

Quality Control Use Overview

1. Create the rule.
2. Add the samples or value.
3. View the results.

Note If you want to use the Average, SD or CV% options in the quality control rule, the Quality
Control step goes under the step in which each replicate is situated, and not under the Average,
SD, CV% step.

Add rule button: Create a rule by clicking the options listed in the menu and submenu.

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Quality Control

Figure 78. Quality Control parameter Add rule menu and submenu.

?????? : Add the sample or value for the rule. Click to open the sample pop-up menu and formula
menu.
Figure 79. The sample selection pop-up window.

Advanced Parameters: Add text that is shown in the results after the Quality Control check.
Passed Text: Write the text that is shown in the results if the Quality Control check passed.
Failed Text: Write the text that is shown in the results if the Quality Control check failed.
Color label: Select a color for the Passed Text and Failed Text result texts.

The results are listed in a table under the Add rule button. The text for the passed and failed samples
are shown in the colors you defined.

The result is interpreted as passed only if the results of all the individual samples passed. If even one of
the samples fails, the result of the quality control rule is interpreted as failed. By clicking the arrow icon
beside the result, you can view the value and interpretation of each sample individually.

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Custom Formula

Figure 80. Quality Control Passed and Failed results.

Custom Formula
You can manually define your own custom calculations for measurement or calculation data. The
custom formula step is added to the root level of the result tree. That way you can use almost any
measurement or calculation step as source data in the custom formula.

Define the custom formula by first defining variables from measurement or calculation data, and then
entering the desired formula using the defined variables, mathematical operators and numbers.

Figure 81. Custom Formula parameters.

1. Click Define variables to define the variables to use in the formula.

Variable name: Give a name to the variable. Do not use only numbers for the name.
Source step: Select the result step which includes the source data for the calculation
Wavelength: If the source data includes multiwavelength data, select which wavelengths data to
use in the calculation

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Graph

2. Select which samples the variable will represent.

All samples: Variable represents all samples of the selected result step.
Sample average: Variable represents the average of sample replicates of a specific sample. Select the
sample from the list.
Sample replicate: Variable represents a single replicate of a specific sample. Select the replicate
from the list.
3. Click Add to add the defined variable to the list of variables.
4. When all needed variables have been added to the variables list, click OK to close the dialog.
The defined variables are shown as buttons above the calculator.
5. Define the formula to the text field by entering numbers, mathematical operators and adding the
defined variables by clicking the variable buttons.
Click Advanced parameters to access additional mathematical functions to use in the calculation.

Table 8. Custom Formula Advanced parameters.

AVG Calculates the average of the selected values.
SUM Calculates the sum of the selected values.
SQRT Calculates the square root of the selected values.
LOG Calculates the base -10 logarithm of the selected values.
LN Calculates the natural logarithm of the selected values.
EXP Raises e to the selected power.
MAX Determines the maximum of the selected values.
MIN Determines the minimum of the selected values.

Graph
You can create graphs from kinetic curves and spectra.
Graph title, X axis title and Y axis title: Write titles for the graph, and the X and Y axes.
Select wells: Select which wells and readings to display on the graph by selecting the check boxes
in question.

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Graph

Figure 82. Graph

View Results as a Graph

Select a result step under Results in the Session tree, and click Graph in the Results ribbon. The
results are shown as a graph.

View Spectral or Kinetic Data as Graph

1. Add the Graph step under the step including spectral data.
2. Write the Graph, X axis and Y axis titles.
3. To alter the number of wells in the graph, click Select wells.
Select the wells you want to exclude from, or include in the graph and click OK. The graph is
automatically updated.

View Kinetic Curves or Spectral

Results of kinetic or kinetic spectral measurements are shown as curves in the plate view. You can
enlarge a single curve or several curves and view them in a separate window.
1. Click Results in the Session tree.
2. Select Kinetic or Spectral from the Results ribbon.
Kinetic or spectral calculations that produce data as curves can be viewed as curves.
3. Click the Plate tab to see the results in a plate format.
4. Drag the mouse over the well(s) you want to select.
5. Right-click and select Show Graph. The Curve dialog opens showing, for example, curves for
several wells.

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Graph

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Result Report
You can create a result report that includes both measurement and calculation data. You can export the
result report to Excel, PDF, TXT, and XML formats.
Figure 83. Report ribbon.

Create a Data Report

1. Click Report in the Session tree.
2. Check the sections you want to include in the report from the Report sections list.
Figure 84. Report pane.

Tip You can drag-n-drop a report section in the list: click the section you want to move and drag it
up or down. The report order you select here is the same order used to show the results in the
export file.

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Export a Result Report Manually

Export a Result Report Manually

Export a result report by clicking on the PDF, Excel, TXT, or XML format on the Results ribbon.

Export to Excel
1. Click Report in the Session tree.
2. Click to Excel in the Report ribbon.
3. Write the file name and select the folder.
4. Click Save.
The report opens in Excel format.

Export to PDF
1. Click Report in the Session tree.
2. Click to PDF in the Report ribbon.
The report opens in PDF format.

Export to XML
1. Click Report in the Session tree.
2. Click to XML in the Report ribbon.
3. Save the report.
The report opens in XML format.

Export to TXT
1. Click Report in the Session tree.
2. Click to TXT in the Report ribbon.
3. Save the report.
The report opens in TXT format.

Export a Result Report Automatically

Set the software to export the report automatically after the run to a specific destination.
1. Click Report in the Session tree.
2. Select Save to file in the Automatic export after execution pane.
3. Name the file and click Browse to select the destination folder and the file format.
4. Save the session.
The next time you start the session, a report is automatically saved in the destination folder you
selected.

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Email Report Automatically

Figure 85. Automatic export after execution with Save to file selected.

Save to file: Select to save the result report automatically to a specific destination after run.

Browse: Click to define where you want to save the file, in which file format and with what file name.
Append: Add the data to the end of the existing file.
Overwrite: Overwrite the data in the existing file.
Unique name: Extend the file name with a unique date and time. A new file is created each time.
Browse: Select a file name and folder.
{abc}: Add a placeholder to the file name of the file path. Click to select a placeholder from the list.
Place your cursor in the File name field at the position where you want to add the placeholder. The
placeholder is replaced with a current value when the file is created.
The format of the timestamp placeholder is yyyymmdd - hhmmss. For example, to create a folder for
each year: add the year placeholder to the file path and separate it with the backslash (\) character.

Email Report Automatically

Set the software to automatically email reports in Excel format after the run.
1. Click Report in the Session tree.
2. Select the report sections from Select included report sections.
3. Select Send Excel report via email to under Automatic export after execution.
The next time you complete the session, a report in Excel format is automatically emailed.

Email Address Settings

Define the email reporting settings.
1. Click General under Settings.
2. Write the email server name and sender address under Email reporting.
3. Click Test connection.

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Print Report Automatically

Print Report Automatically

Set the software to print the report automatically after the run.
1. Click Report in the Session tree.
2. Select Print to default printer in the Automatic export after execution pane.
The next time you complete the session, a report is automatically printed.

Result Summary
The result summary is a combined table of the measurement and calculated data. It is automatically
created after the run in the report view. The summary table does not include kinetic, spectral or
multipoint format data.
1. Click Summary under Report
The General tab is for each sample group, and the Special tab is for Standard curve, Dose response
and Quality control step summaries.
Figure 86. Report Summary.

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Settings
You can define certain software and instrument parameters in Settings.

Open Settings from the Application Menu.

Figure 87. General settings window.

General
You can change the general settings and email reporting address. You can also enter your laboratory
information, and change the color theme for the software.

General Settings

Change the Software Language

The default language is English. You can change the language to French, German, Italian, Japanese,
Portuguese, Russian, Simplified Chinese or Spanish.

To change the language:

1. Click Settings in the Application menu.
The Settings window opens.
2. Select the language from the drop-down list under General settings.
3. Restart the software to set the new language.

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General

Check Plate and Tip Prime Vessel Before Session Execution (Default)
The instrument checks that a plate and tip prime vessel are inserted to the plate tray before running the
session. We recommend you keep this check enabled.

Leave Plate in after Session Execution

The instrument leaves the plate inside after the run. If you do not select this, the plate is always run out
of the instrument after session executions.

Optical Response Compensation (Default)

Varioskan LUX compensates for the different wavelength dependent response characteristics of the
optical system in emission and excitation. The RFU values between different wavelengths are
comparable with each other and the spectral peaks correspond to the real light emitted from the
sample.

If you do not select this, the optical component wavelength dependent effects influence the results. In
fluorometry instrumentation, the emission reading ability is not necessarily comparable between
wavelengths. The components of the optical system do not have constant responses over the emission
wavelength range. This causes results which are dependent on the emission wavelength even with the
same excitation conditions. This uneven emission response can cause difficulties in interpreting the
spectral results. The emission peaks can shift even more that 10 nm.

Generate Instrument Communication Log

You may be asked for the instrument communication log when contacting service in troubleshooting
cases. In normal use you do not need to generate an instrument communication log.

If you generate an instrument communication log, you need to restart the software for the selection to
take effect.
Note The instrument communication log files grow quickly; do not leave this feature selected for
very long.

Email Reporting
You can set the software to automatically send result reports to an email address after executing a
session.

The software needs to know your email server address to send the reports through. Contact your local
administrator for the email server address.
1. Click Settings to open the General Settings window.
2. Write the email server name and the sender address in their relevant boxes.
3. Click Test connection to test the connection to the email server

Laboratory Information
Add your laboratory contact details.The information that you add here is shown in the results reports.

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Database

Colors
You can change the software background color theme from the drop-down list.

Database
In SkantIt Software all data is stored inside a database. You can change the database file and create a
new database. If your current database is getting full, first create a new database, then change to the
new one.

The software informs before a database is full.

The location of the database is defined when the software is installed.

Figure 88. The Database settings window.

Change the Database

Change the database e.g., when you have created a new database and want to take it into use. You can
only change to a database that has your user name defined.
1. Click Database under Settings.
2. Click Change.
3. Select the database from the list.
4. Click Yes.
You may need to restart your computer.

Create a New Database

You can create a new database to use with the software. The user groups (and the users in the groups)
are copied from the existing database to the new database. You can add new users from Security -> Add
new member.
1. Click Database under Settings.
2. Click Create new.
3. Write the name of the new database.
4. Click OK.
The new database is added to the list under the Change button. To take the new database into use,
select the database from the list and click Yes.

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Results

Note When creating a new database, do not use keywords reserved for Microsoft SQL Server (e.g.
database or backup) separately in the name of the backup database. The reserved words can be used
only if something is attached to them without space (e.g. database1 or backup_2015).

Database Backup
To take a backup of the database, type:

%programdata% in the address bar then click enter

go to /Thermo -> MIP -> Readers -> Databases -> copy all *.mdf and *.ldf files to a backup location.

You can also automate backup.

Results
Number Formats
Select the number of decimals or significant digits that will be shown for measurement raw data and
calculated data in the Results view and export files. The original accuracy of the data is retained in the
memory and used in the calculations.
1. Click Settings in the Application menu.
2. Click Results.
3. Set the decimals or significant digits.

Table 9. Examples of the way selected number formats are displayed.

Selected number Original number Decimals Significant digits
5 0.0012345 0.00123 0.0012345
3 123.45678 123.457 123

Saved Curves
You can view and delete standard curves that you have saved from standard curve calculations in the
software database.

You can save the standard curve of a session and use it in another session.

View the Standards of a Saved Standard Curve

1. Click Saved curves under Settings.
2. Select the curve under Saved standard curves.
The curve properties are listed under Standards.

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K-Factors

Delete a Saved Standard Curve

You can only delete curves that are not in use in any session.
1. Click Saved curves under Settings.
2. Select the curve to delete.
3. Click Delete.

K-Factors
K-factors are values used in pathlength correction calculations. The software has pre-defined K-factors
for commonly used assay solutions and microplate materials. The same K-factors which are listed in
the settings are also available in the pathlength correction calculation step (Results view).
Figure 89. K-factors settings window.

Add New K-Factor to Software Database

1. Click K-factors under Settings.
2. Click Add new.
3. Write the Name and Description.
4. Select the Value.
5. Click OK.

Edit K-Factor
See Pathlength Correction for more information.
1. Click K-factors under Settings.
2. Select the K-factor to edit.
3. Click Edit.
4. Click OK.

Delete K-Factor
1. Click K-factors under Settings.

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Instruments

2. Select the K-factor to delete.

3. Click Delete.
4. Click Yes.

Instruments
You can edit the instrument parameters from the Instrument settings. You can also poll for
instruments to update the instruments list.

The default instrument defines the types of sessions that are created by default. When you click

the New session split button on the Home ribbon, the session is created for the default instrument.
The default instrument is also the main button instrument under New & Recent > Create new
session.
Figure 90. New session split button on the Home tab.

If the instrument and software have lost their connection, click the reconnect icon under Settings >
Instruments.
Figure 91. Reconnect icon under Settings > Instruments

Instrument Module Information

1. Click Instruments under Settings.
2. Click the instrument in the instruments list.
The instrument module information is visible under the instruments table.

Wash Dispensers
See Instruments: Wash Dispensers on page 115.

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Instruments

Edit Instrument Parameters

To edit instrument parameters:

1. Click Instruments under

Settings.
2. Click the icon next to the
instrument.
3. Click the tab to open the
relevant parameters.

Instrument Parameters: General

In Varioskan LUX you can set the instrument temperature, regulate the oxygen level (O2), and carbon
dioxide (CO2)levels.
1. Click Instruments under Settings.
2. Click the icon (on the right side) next to the instrument.
Select Use instrument temperature to set the instrument temperature.
Select Regulate oxygen (O2) level [%] to set the oxygen level.
Select Regulate carbon dioxide (CO2) level [%] to set the carbon dioxide level.
3. Click Close.
Note When you have a session open, you can set the instrument temperature, O2 level and CO2
level from the related buttons above the Start button in SkanIt software.

Multiskan GO has a Power Save feature, which decreases power consumption when the instrument is
idle.

Check Power Save On to activate the feature.

Use the time control to set the delay before activating Power Save.
Note When the instrument enters the Power Save mode, the instrument incubator is switched off.

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Instruments

Instrument Parameters: Dispensers

You can set the dispensers syringe size, tip size, and pull-back volume. You can also set the prime tip
volume.

Set the Dispenser Syringe Size

If you change the dispenser syringe size in the instrument, set the correct syringe size also in SkanIt
Software. The syringe sizes are available in 1ml and 5ml.
1. Click Instruments under Settings.
2. Click the icon (on the right side) next to the instrument.
3. Click the Dispensers tab in the Edit instrument parameters window.
4. Click on the dispensers syringe size to open the drop-down menu.
5. Select the syringe size.
6. Click Apply.
Figure 92. Dispenser instrument parameters with syringe size selection open.

Set the Dispenser Tip Size

If you change the dispenser tip size in the instrument, set the correct tip size also in SkanIt Software.
The tip sizes are available in 0.4 mm and 0.25 mm.
1. Click Instruments under Settings.
2. Click the icon (on the right side) next to the instrument.
3. Click the Dispensers tab in the Edit instrument parameters window.
4. Click on the dispensers tip size to open the drop-down menu.
5. Select the tip size.
6. Click Apply.

Set the Dispenser Pull-Back Volume

The pull-back feature prevents liquid droplets from forming onto the dispensing tip between
dispensing. When set, the dispenser automatically pulls back the selected amount of liquid into the
syringe each time the instrument dispenses.

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Instruments

1. Click Instruments under Settings.

2. Click the icon (on the right side) next to the instrument.
3. Click the Dispensers tab in the Edit instrument parameters window.
4. Click on the dispensers pull-back volume to open the drop-down menu.
5. Select the pull-back volume.
6. Click Apply.

Set the Prime Tip Volume

The dispenser dispenses the selected amount of reagent into the tip priming vessel every time the
instrument fills the dispenser syringe. This makes the volume of the first equal well to that of the
others, and compensates for drawback phenomenon.

Use tip priming to achieve greater accuracy when the dispensing volumes are small.
1. Click Instruments under Settings.
2. Click the icon (on the right side) next to the instrument.
3. Click the Dispensers tab in the Edit instrument parameters window.
4. Select the prime tip volume from the drop-down menu.
5. Click Apply.
Figure 93. Dispenser instrument parameters with Dispenser options open.

Instruments: Wash Dispensers

This is an automatic program for washing the dispensers with a defined number of wash cycles and
soaking time.
1. Check that the dispensers are not in dispensing position in the instrument.
2. Place the dispensing head into a waste vessel and place the aspirate tubing into washing liquid
bottle.
3. Insert a plate into the instrument.
4. Click Instruments under Settings.

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Instruments

5. Click the instrument in the instruments list.

6. Click the Wash dispensers button below the instruments list.
7. Select the dispenser to wash in the Wash pop-up window.
8. Select the number of wash cycles.
Each cycle flushes the full volume of a syringe (1 t1 or 5 ml of liquid) through the tubing.
9. Select how long the dispenser tubing is soaked with the washing liquid.
10. Click Wash.
Figure 94. Dispenser Wash pop-up window.

Instrument Parameters: LAT Module

The LAT module parameters of Varioskan LUX include the serial numbers of the measurement
sub-modules. You can also see the last calibration and alignement date of the LAT module.

When you calibrate the LAT module, you need to add the Luminescence module serial number, TRF
module serial number, and AlphaScreen module serial number to SkanIt Software.

After calibration, the software shows the calibration run date in Last calibration date. When you run
the LAT measurement alignment, the software adds the alignment run date in Last alignment date.

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 13 Settings
Instruments

Figure 95. LAT module parameters.

Calibrate LAT Module

You must run the calibration if you install a completely new LAT module to Varioskan LUX.

The last calibration date informs you when the LAT module was last calibrated.
Note Verify that you have the new module serial number; you will need to add it in SkanIt
Software.

To calibrate the LAT module:

1. Plug the dispensing positions in the instrument.
2. Click Instruments under Settings.
3. Click the icon (on the right side) next to the instrument.
4. Click the LAT module tab in the Edit instrument parameters window.
5. Click Calibrate.
6. Enter the module serial numbers.
7. Click Next to start the calibration.
8. Read the report and click Finish.
The Last calibration date and module serial number information are updated.

Align LAT Measurement Position

Aligns the LAT module measurement position to minimize crosstalk from adjacent wells. It is
recommended to align the measurement position after installing a new LAT module and when an
existing LAT module has been reinstalled after cleaning or service. For more information, see the
Varioskan LUX Technical Manual.

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Instruments

The last alignment date informs you when the LAT measurement position was last aligned. To align
the LAT measurement position:
1. Select a white 384-well plate.
2. Pipette 30% of the well volume with luminous reagent into well H12.
3. Place the plate on the plate tray and click Next.
4. Select the relevant 384-well plate and click Next.
5. Verify the alignment result and click Finish.
The Last alignment date information is updated.

Instrument Parameters: Report

Instrument reports give you information on the status of the instrument. These reports are useful in
problem situations where the instrument does not seem to function properly. Reports are used by
service personnel.

Run Instrument Reports

1. Click Instruments under Settings.
2. Click the icon next to the instrument to open the Edit instrument parameters window.
3. Click Report.
4. Select the reports to run.
5. Click Run report(s).
You can save the report as a PDF or text file.
Figure 96. To run Report(s), go to: 1. Instruments, 2. Edit instrument parameters, 3. Run reports.

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 13 Settings
Instruments

Instrument Parameters: Filter Definition

In Filter definition you can see the filters installed in the instrument's filter wheel. If you install new
filters, you have to define the filter information also to SkanIt Software. You can also edit and remove
filter information.

The filter name allows any ASCII characters, with the exception of &.

Varioskan LUX: Add a New Filter

1. Click Instruments under Settings.
2. Click the icon (on the right side) to open the Edit instrument parameters window.
3. Click the Filter definition tab.
4. Click Add to open the Define filter pop-up window.
5. Add the new filter information and click Next.
6. Open the filter nest lid.
7. Loosen the filter holding mechanism on the selected position.
8. Place the filter on a clean, dust-free surface with the arrow on the side of the filter pointing
upwards.
9. Use the filter pick-up tool to place the filter into the bottom of the filter nest.
10. Tighten the filter holding mechanism.
11. Close and fasten the filter nest lid.
12. Click Finish and Close.

Multiskan FC: Add a New Filter

Install the filter manually to the filter wheel of Multiskan FC. Then add the filter information to
SkanIt Software.
1. Click Instruments under Settings.
2. Click the icon (on the right side) to open the Edit instrument parameters window.
3. Click the Filter definition tab.
4. Click Add to open the Add new filter pop-up window.
5. Add the new filter information to the filter position where you installed the filter.
6. Click OK.
7. Click Apply and Close.

Varioskan LUX: Remove a Filter

1. Click Instruments under Settings.
2. Click the icon (on the right side) to open the Edit instrument parameters window.

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13 Settings
Plate Adapters

3. Click the Filter definition tab.

4. Select the filter you want to remove.
5. Click the red Remove filter x-mark.
6. Open the filter nest lid.
7. Loosen the filter holding mechanism.
8. Use the filter pick-up tool to remove the filter.
9. Tighten the filter holding mechanism.
10. Close and fasten the filter nest lid.
11. Click Finish.

Multiskan FC: Remove a Filter

First remove the filter manually from the filter wheel of Multiskan FC, then remove the filter
information from SkanIt Software.
1. Click Instruments under Settings.
2. Click the icon (on the right side) to open the Edit instrument parameters window.
3. Click the Filter definition tab.
4. Select the filter you want to remove.
5. Click Remove.
6. Click Apply.

Figure 97. Filter definition parameters.

Plate Adapters
You can view the current list of Varioskan LUX plate adapters and their associated plate templates. You
can also associate new plate templates to the plate adapters.

Associate a New Plate Template

You can associate plate templates that you have defined.

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Plate Templates

1. Click Plate Adapters under Settings.

2. Select the plate adapter from the Plate adapter window.
3. Click Associate new below Associated plate templates.
4. Add the new plate template.
Note The Associate new button is disabled when all possible templates have been associated. The
button is also disabled for factory defined plate templates (they cannot be associated).

Plate Templates
You can see what the current default plate template is in the Plate Layout, and select a new default
template. You can also add and edit plate templates, and delete some plate templates.

The plate template you select as the default plate template is used for new sessions.

Select a New Default Template

1. Click Plate Templates under Settings.
2. Click to select the new default template from Plate templates.
3. Click Set as default.
The new default template is now visible under Default plate template.

Add a New Plate Template

1. Click Plate Templates under Settings.
2. Click Add new.
3. Add the new plate template and plate template well properties in the Add Plate Template window.
4. Select the supported instruments.
5. Click OK.
Figure 98. Add Plate Template window.

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13 Settings
Security

Edit a Plate Template

Note You can only edit plate templates that users created.

1. Click Plate Templates under Settings.

2. Click to select the template to edit.
3. Click Edit.
4. Edit the plate template and plate template well properties in the Add Plate Template window.
5. Click OK.

Delete a Plate Template

You can delete some of the plate templates.
1. Click Plate Templates under Settings.
2. Click to select the template to delete.
3. Click Delete.

Security
You can activate user accounts for controlling access to the software.

The person who has SkanIt software administrator rights can control who uses the software by
activating the user accounts for logging in.

The administrator creates user groups, adds users to groups and adds group privileges. The
administrator can set the automatic lock time for all of the user groups. User control is always required
when using the Drug Discovery Edition of the software (see Drug Discover Edition).

Windows Authentication
You need to use Windows Authentication to log in to SkanIt Software. Windows Authentication
requires a user name and password.

When the automatic lock feature is enabled, or when using the DDE version, SkanIt Software will lock
up after a set time of inactivity. You can unlock the software by logging in using Windows
Authentication.

Add a User Group

1. Click Security under Settings.
2. Click Add new user group.
3. Write the group name and description in the Add User Group pop-up window.
4. Select the privileges.
5. Click Ok.

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 13 Settings
Security

Add Group Members

1. Click Security under Settings.
2. Click the user group under User Groups.
3. Click Add new member under User group members.
4. Enter the user information in the Windows pop-up window.
5. Click OK.

Add or Remove User Group Privileges

1. Click Security under Settings.
2. Click the pencil icon next to the user group name.
3. Add or remove privileges from the Privileges list.
4. Click OK.

Remove a User Group

1. Click Security under Settings.
2. Click the red x-mark next to the group name.

Set the Auto Lock Time

You can set the software to lock up after a set time of non-activity. The set time is in minutes. The auto
lock setting applies to all user groups.
1. Click Security under Settings.
2. Select Require user to log in under Settings.
3. Set the Auto lock time.

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13 Settings
Security

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 14

Drug Discover Edition

The Drug Discovery Edition of SkanIt Software offers special features for compliancy with FDA 21
CFR Part 11.

The main features are:

Electronic signature.
Audit trail for viewing the log of operations made by the users.
Prompting to provide a reason for any changes made that affect the information content of the
database.
Access control to software via user accounts.

Windows Authentication
You need to use Windows Authentication to log in to SkanIt Software. Windows Authentication
requires a user name and password.

The name given by Windows Authentication is used to identify users within the SkanIt DDE features,
such as audit trail, and it is required that the end user organization ensures that sufficient information
is available from the Windows user information, and that relevant security policies are enforced already
with the Windows user management.

SkanIt Software will lock up after a set time of inactivity. You can unlock the software by logging in
using Windows Authentication. The software administrator sets the auto lock time for all user groups.

To add users and user groups, go to Add a User Group.

Export Session History

To export a session audit trail in *.xml format:
1. Click History in the Session tree.
2. Click the Details button to open the Audit Trail window.
3. Click the Export to XML-file button.

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14 Drug Discover Edition
Digital Signatures

Figure 99. Audit Trail session record details window.

Digital Signatures
You can sign sessions using a digital signature. You must authenticate your signature using Windows
Authentication.

A signed session contains the printed name of the signer, the date and time of the signing, and the
meaning and comments of the signing. Signatures cannot be removed, copied or transferred to any
other session in the software database.

Add your digital signature

1. Click History in the Session tree.
2. Click the Sign the session button to open the pop-up window.
Figure 100. Sign session pop-up window.

3. Select Reviewed or Approved under Type.

4. Write your name in the Print name box.

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Software Audit Trail

5. Add a comment, if needed.

6. Click OK.
7. Write your Windows Authentication password.
8. Click OK.

Add a digital signature on behalf of someone else

1. Click History in the Session tree.
2. Click the Sign the session button.
3. Select Reviewed or Approved under Type.
4. Select Signed behalf of.
5. Write who you are signing on behalf of.
6. Add a comment, if needed.
7. Click OK.
8. Write your Windows Authentication password.
9. Click OK.

Software Audit Trail

The audit trail shows who did what and when and what kind of operation was carried out in the
system. To print or export the software audit trail in *.xml format:
1. Click Audit Trail under Settings.
1. Select the search criteria under Search filters.
2. Click Search.
3. Click Print to print the results, or Export to export the results.

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14 Drug Discover Edition
FDA 21 CFR Part 11

FDA 21 CFR Part 11

Table 10. Subpart B - Electronic Records. Section 11.10 Controls for closed systems. (Sheet 1 of 3)
End user
Regulation Implementation in SkanIt Software
requirement
11.10.a. x The software has been developed and documented according
Validation of systems to ensure to approved Thermo Fisher Scientific Oy LHC Product
accuracy, reliability, consistent Development Process SOPs. The software is verified to
intended performance, and the ability function according to specifications and validated to function
to discern invalid or altered records. properly in certain selected end user applications.

The testing related to electronic record handling, within the

software, is documented according to the Product
Development Process. The development documents can be
audited at Thermo Fisher Scientific Oys facilities in Vantaa,
Finland.

However, it should be noted that the end user organization is

always responsible for validating the software for his/her
intended use.

All electronic records in the software are stored in a database

and the validity of the database is checked at software startup.
Validity of individual records is checked when importing or
opening said records.
11.10.b. The report and the audit trail in the software can be printed or
The ability to generate accurate and saved in electronic format (electronic copies). The report from
complete copies of records in both a signed session will include the printed name of the signer,
human readable and electronic form date, and time of the signing, and comments related to the
suitable for inspection, review, and signing. It is possible to sign on behalf of someone else, and
copying by the agency. that information is included with the electronic record.

Sessions can be imported and exported to, and from, the

software in electronic form and the audit trails regarding the
said electronic records are included with the export or import.
11.10.c. The software allows backup of the database containing all
Protection of records to enable their information. The backup is instructed in the Technical User
accurate and ready retrieval Manual. The database backup can also be retrieved and
throughout the records retention connected to a new instance of SkanIt Software after a possible
period. system failure.
11.10.d. x The software login control is implemented using Windows
Limiting system access to authorized Authentication. Implementing proper user identification is the
individuals. responsibility of the end user organization. A user who has not
been defined in the database cannot access and use SkanIt
Software.

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Table 10. Subpart B - Electronic Records. Section 11.10 Controls for closed systems. (Sheet 2 of 3)
End user
Regulation Implementation in SkanIt Software
requirement
11.10.e. The software contains a computer generated, time-stamped
Use of secure, computer-generated, audit trail that automatically records any creation,
time-stamped audit trails to modification or deletion of a user account, user group,
independently record the date and software setting or session.
time of operator entries and actions
that create, modify, or delete Additionally, each time a user creates, modifies, or deletes one
electronic records. of the above mentioned electronic records, the user can be
required to enter a reason for change based on the software
Record changes shall not obscure settings.
previously recorded information. Such
audit trail documentation shall be The time stamp is formatted according to ISO 8610.
retained for a period at least as long as
The user cannot change the audit trail in any manner, and it is
that required for the subject electronic
retained as a part of the electronic record for as long as the
records and shall be available for
electronic record exists. The audit trail can be printed and
agency review and copying.
exported in *.xml format.
11.10.f. System steps that happen within the closed system of the
Use of operational system checks to software are forced into the correct order.
enforce permitted sequencing of steps
and events, as appropriate.
11.10.g. The software login control is implemented using Windows
Use of authority checks to ensure that Authentication. Implementing proper user identification, and
only authorized individuals can use therefore limiting access to the software to authorized users
the system, electronically sign a only, is the responsibility of the end user organization. A user,
record, access the operation or who has not been defined in the database, cannot access and
computer system input or output use SkanIt Software.
device, alter a record, or perform the
operation at hand. Additionally, the software supports user groups with different
rights to the features in the software. The users are assigned to
a specific user group by the software administrator. The
administrator can modify the user groups and user accounts,
and thereby control which features a user can access.
11.10.h. Before the software can control a new instrument, the
Use of device (e.g., terminal) checks to instrument must be defined in the software database.
determine the validity of the source of
data input or operational instruction, The software automatically attempts to establish a connection
as appropriate. between the software and an instrument, and if the instrument
is not in the database, the software verifies that the instrument
has compatible USB identifications, serial number, and
embedded software version. If this information does not
match, the connection is denied.

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FDA 21 CFR Part 11

Table 10. Subpart B - Electronic Records. Section 11.10 Controls for closed systems. (Sheet 3 of 3)
End user
Regulation Implementation in SkanIt Software
requirement
11.10.i. x The designers of the software are skilled software designers and
Determination that persons who have been trained on 21 CFR Part 11.
develop, maintain, or use electronic
record/electronic signature systems Training records and job descriptions exist at Thermo Fisher
have the education, training, and Scientific Oy's premises in Vantaa, Finland.
experience to perform their assigned
The training of the users of the software is the responsibility of
tasks.
the end user organization.
11.10.j. x A technical feature is implemented in the software so that it is
The establishment of, and adherence possible for a user who is electronically signing a record on
to, written policies that hold behalf of someone else to indicate, within the signature, that
individuals accountable and he or she is signing the record for someone else. However, this
responsible for actions initiated under is also an end user organization policy (SOP).
their electronic signatures, in order to
deter record and signature When electronically signing a record in the software, it is
falsification. possible to select the sign status On Behalf of . When later
verifying the signature, the comment can be viewed as well.
11.10.k. x All software documentation as well as all SOPs regarding
Use of appropriate controls over software documentation and development are under
systems documentation including: documentation change control.

(1) Adequate controls over the System documentation on all other parts of the system are the
distribution of, access to, and use of responsibility of the end user organization.
documentation for system operation
and maintenance.

(2) Revision and change control

procedures to maintain an audit trail
that documents time-sequenced
development and modification of
systems documentation.

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FDA 21 CFR Part 11

Table 11. Subpart B Electronic Records 11.30 Controls for open systems.
End user Implementation in SkanIt Software
Regulation
requirement
11.30 SkanIt Software is considered a closed system and must be
Procedures and controls to ensure used as a closed system to fulfill the requirements of 21 CFR
authenticity, integrity, and as Part 11.
appropriate, confidentiality.

Include additional measures beyond

11.10 requirements such as document
encryption and use of digital signature
standards.

Table 12. Subpart B - Electronic Records 11.50 Signature manifestations.

End user
Regulation Implementation in SkanIt Software
requirement
11.50.a. When opening a session a "History"-node, showing the
Signed electronic records contain the session audit trail and digital signatures, is available in the
following information associated with Session tree. This node contains a section for digital
the signing: signatures, which contains the printed name of the signer, the
date and time of the signing, as well as the meaning and
(1) Name comments of the signing.
(2) Date and time Any session that has been signed will contain the printed name
of the signer, the date and time of the signing, as well as the
(3) Meaning (author, review, approval,
meaning and comments of the signing.
responsibility, or authorship)
associated with the signature.)
11.50.b. The signature manifestation, i.e. the printed name of the
Readable forms of electronic records signer, the meaning and comments of the signing and the date
are to include the information as and time when the signing occurred, of a signed record can be
defined in item 11.50.a concerning viewed and exported to a printable and human readable
signers. format.

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Table 13. Subpart B - Electronic Records 11.70 Signature/record linking.

End user
Regulation Implementation in SkanIt Software
requirement
11.70.a. The electronic signature in the software is in the form of a
Electronic signatures and handwritten digital signature. Sessions in the software can be signed using
signatures executed to electronic the digital signature. Signatures cannot be removed, and
records shall be linked to their cannot be copied or transferred to any other session in the
respective electronic records to ensure software database.
that the signatures cannot be excised,
copied, or otherwise transferred to
falsify an electronic record by ordinary
means.

Table 14. Subpart C Electronic Signatures. 11.100 General requirements.

End user
Regulation Implementation in SkanIt Software
requirement
11.100.a. x When signing a session or login into the software, the user
Each electronic signature shall be must authenticate by Windows Authentication. Enforcing
unique to one individual and shall not group policies in the authentication process that fulfill these
be reused by, or reassigned to, anyone requirements are the responsibility of the end user
else. organization.

For every Windows user given access to SkanIt Software, a

unique signature key is generated, and this key is never reused
or reassigned.
11.100.b. x End user organization policy (SOP).
Before an organization establishes,
assigns, certifies, or otherwise
sanctions an individual's electronic
signature, or any element of such
electronic signature, the organization
shall verify the identity of the
individual.
11.100.c. x Additional submission to FDA by the end user organization.
Certify in writing to the agency that
the electronic signatures are intended
to be the legally binding equivalent of
handwritten signatures.

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Table 15. Subpart C - Electronic Signatures 11.200 Electronic signature components and controls.
End user
Regulation Implementation in SkanIt Software
requirement
11.200.a. x A user logs on to SkanIt Software using Windows
Electronic signatures not based on Authentication. The Windows Authentication always consists
biometric links: of two components, a user name and a password. A user
logged on to SkanIt Software can sign a session or run by
(1) Employ two distinct identification providing the credentials again.
components.
If the user leaves SkanIt Software unattended, SkanIt Software
(i) First electronic signature executes will lock up after a user defined period of no action. The
all components of the electronic software will remain locked until the original user or the
signature, subsequent signings use at software administrator unlocks the software by logging in
least one component. using Windows Authentication.
(ii) When electronic signature not Enforcing group policies in the authentication process that
executed during continuous period, all fulfill these requirements are the responsibility of the end user
components of the electronic organization.
signature shall be used.

(2) Used only by their genuine owner.

(3) Collaboration of two or more

individuals required to prevent use by
other than the genuine owner.
11.200.b. SkanIt Software does not directly support the use of
Electronic signatures based on biometrics.
biometrics shall be designed to ensure
that they cannot be used by other than
the genuine owner.

Table 16. Subpart C - Electronic Signatures 11.300 Controls for identification codes / passwords. (Sheet 1 of 2)
End user
Regulation Implementation in SkanIt Software
requirement
11.300.a. Maintaining the uniqueness x SkanIt Software uses Windows Authentication. Enforcing
of each combined identification code group policies in the authentication process that fulfill these
and password, such that no two requirements are the responsibility of the end user
individuals have the same organization.
combination of identification code
and password.
11.300.b. Ensuring that identification x SkanIt Software uses Windows Authentication. Enforcing
code and password issuances are group policies in the authentication process that fulfill these
periodically checked, recalled, or requirements are the responsibility of the end user
revised (e.g., to cover such events as organization.
password aging).

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FDA 21 CFR Part 11

Table 16. Subpart C - Electronic Signatures 11.300 Controls for identification codes / passwords. (Sheet 2 of 2)
End user
Regulation Implementation in SkanIt Software
requirement
11.300.c. x SkanIt Software uses Windows Authentication. Enforcing
Following loss management group policies in the authentication process that fulfill these
procedures to electronically requirements are the responsibility of the end user
deauthorize lost, stolen, missing, or organization.
otherwise potentially compromised
tokens, cards, and other devices that
bear or generate identification code or
password information, and to issue
temporary or permanent replacements
using suitable, rigorous controls.
11.300.d. x SkanIt Software uses Windows Authentication. Enforcing
Use of transaction safeguards to group policies in the authentication process that fulfill these
prevent unauthorized use of passwords requirements are the responsibility of the end user
and/or identification codes, and to organization.
detect and report in an immediate and
urgent manner any attempts at their
unauthorized use to the system
security unit, and, as appropriate, to
organizational management.
11.300.e. End user organization policy (SOP).
Initial and periodic testing of devices,
such as tokens or cards, that bear or
generate identification code or
password information to ensure that
they function properly and have not
been altered in an unauthorized
manner.

134 Thermo Scientific SkanIt Software Technical Manual Thermo Fisher Scientific