Thermo Fisher Scientific Sizing Analysis Module Peak Scanner Software User guide

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

Sizing Analysis Module Peak Scanner™

Software

USER GUIDE

Publication Number MAN0017576

Revision A.0

Manufacturer: Life Technologies Corporation | 200 Oyster Point Blvd | South San Francisco, CA 94080 | USA

The information in this guide is subject to change without notice.

DISCLAIMER: TO THE EXTENT ALLOWED BY LAW, LIFE TECHNOLOGIES AND/OR ITS AFFILIATE(S) WILL NOT BE LIABLE FOR SPECIAL, INCIDENTAL,

INDIRECT, PUNITIVE, MULTIPLE, OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING FROM THIS DOCUMENT, INCLUDING YOUR

USE OF IT.

Revision history: Pub. No. MAN0017576

Revision Date Description

A.0 05 February 2018 New document. Material represents the Help content in the Sizing

Analysis Module Peak Scanner™ Software.

Important Licensing Information: This product may be covered by one or more Limited Use Label Licenses. By use of this product, you accept the

terms and conditions of all applicable Limited Use Label Licenses.

TRADEMARKS: All trademarks are the property of Thermo Fisher Scientiﬁc and its subsidiaries unless otherwise speciﬁed.

Contents

■CHAPTER 1 About the Sizing Analysis Module Peak

Scanner™ Software ........................................................ 6

Compatible instruments ......................................................... 6

■CHAPTER 2 Workﬂows .................................................. 7

Sizing Analysis Module Peak Scanner™ Software Workﬂow ........................... 7

Data analysis workﬂow .......................................................... 8

■CHAPTER 3 Create a project and import samples .................... 9

Create a demo project ........................................................... 9

Create your own project ......................................................... 10

Other ways to create projects .................................................... 10

Create from the DataConnect window ........................................ 11

Create from My Apps in the Home window .................................... 11

Share an object ................................................................ 12

■CHAPTER 4 Review and analyze samples in the Setup screen ..... 13

Review samples after ﬁrst import ................................................ 13

Analyze samples using default analysis settings ................................... 14

Reanalyze samples using custom settings ......................................... 15

Add/remove samples ........................................................... 15

Search tables and lists .......................................................... 15

Apply a different size standard to the project or a sample ........................... 15

Edit a sample name and type .................................................... 16

Customize the columns in the sample or sizing table ............................... 16

Sizing Analysis Module Peak Scanner

™

Software User Guide

3

■CHAPTER 5 Examine low quality samples ............................ 17

View data collection settings ..................................................... 17

Examine EPT and raw data ...................................................... 17

Modify the default analysis settings .............................................. 17

Adjust Quality Flag ranges ...................................................... 18

Apply a different size standard to the project or a sample ........................... 18

Select a single size standard for a project ..................................... 19

Select a size standard for individual samples .................................. 19

Create a new size standard deﬁnition ......................................... 20

■CHAPTER 6 Review the plot and peak information in the

Results screen ............................................................ 21

Review results ................................................................. 21

Review and edit peaks .......................................................... 21

Sort and ﬁlter peaks in the sizing table ....................................... 21

Edit peaks in the sizing table ................................................ 21

Edit peaks using Peak Editor ................................................ 22

Zoom on the electropherogram .................................................. 23

Modify size matches using the Size Match Editor ................................... 24

Customize plot data and views ................................................... 26

Select dye data to display ................................................... 26

View dyes in combined or separate plots ..................................... 27

View raw and/or analyzed data in the plot ..................................... 28

Customize the Plot View .................................................... 29

Set plot Zooming and Scaling Options ........................................ 31

Customize labels on the plot ................................................ 32

Show/Hide the Sizing Table ................................................. 34

■CHAPTER 7 Export size standard, sample information,

and results ................................................................ 35

Export size standard ............................................................ 35

Export the sample table ......................................................... 35

Export Sizing Table ............................................................. 35

Export Plot .................................................................... 36

Export Summary Report ........................................................ 36

■APPENDIX A Troubleshooting ......................................... 37

Troubleshooting ............................................................... 37

Contents

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Sizing Analysis Module Peak Scanner

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■APPENDIX B Software screen descriptions .......................... 38

Setup ......................................................................... 38

Parts of the Setup screen ....................................................... 39

Sample table ﬁelds ............................................................. 40

Results ....................................................................... 41

Parts of the Results screen ...................................................... 42

Parts of the electropherogram ................................................... 43

Sizing table ﬁelds .............................................................. 44

■APPENDIX C Reference information .................................. 45

Size Standard selected by the software ........................................... 45

Analysis status ................................................................ 46

Analysis settings ............................................................... 46

Peak detection overview ........................................................ 48

Baseline Window size ...................................................... 49

Smoothing ................................................................ 51

Polynomial Degree and Peak Window Size .................................... 51

Slope Thresholds for Peak Start/End parameters .............................. 52

Sizing overview ................................................................ 55

Size matching ............................................................. 55

Size-calling curve generation and size calling ................................. 56

Sizing Quality (SQ) status ................................................... 62

■Documentation and support ............................................. 63

Related documentation ......................................................... 63

Customer and technical support ................................................. 63

Limited product warranty ....................................................... 63

Contents

Sizing Analysis Module Peak Scanner

™

Software User Guide

5

About the Sizing Analysis Module

Peak Scanner™ Software

Sizing Analysis Module Peak Scanner™ Software is a DNA sizing module available on

Thermo Fisher Cloud.

Use this software to perform DNA fragment analysis, separate a mixture of DNA

fragments according to their sizes, provide a prole of the separation, and precisely

calculate the sizes of the fragments.

The software allows you to view, edit, analyze, print, and export fragment analysis

data generated using Applied Biosystems™ genetic analyzers.

Compatible instruments

Capillary Electrophoresis System Supported software

version(s)

File

extension

Applied Biosystems™ SeqStudio™ Genetic

Analyzer (3200)

v1.0 or later FSA

Applied Biosystems™ 3500/3500xL Genetic

Analyzer

Applied Biosystems™ 3130/3130

xl

Genetic

Analyzer

Applied Biosystems™ 3730/3730

xl

DNA

Analyzer

1

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Sizing Analysis Module Peak Scanner

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Software User Guide

Workﬂows

Sizing Analysis Module Peak Scanner™ Software Workﬂow

Chapter 3, “Create a project and import samples“

▼

Chapter 4, “Review and analyze samples in the Setup screen“

▼

Chapter 5, “Examine low quality samples“

▼

Chapter 6, “Review the plot and peak information in the Results

screen“

▼

Chapter 7, “Export size standard, sample information, and

results“

2

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Software User Guide

7

Data analysis workﬂow

The workow shown below is an example approach for data analysis.

Chapter 4, “Review and analyze samples in the Setup screen“

“Review samples after ﬁrst import“ on page 13

(If needed)

“Add/remove samples“ on page 15

“Analyze samples using default analysis settings“ on page 14

▼

(If needed)

“View data collection settings“ on page 17

“Examine EPT and raw data“ on page 17

“Modify the default analysis settings“ on page 17

“Apply a different size standard to the project or a sample“ on

page 15

“Reanalyze samples using custom settings“ on page 15

▼

Chapter 6, “Review the plot and peak information in the

Results screen“

“Customize plot data and views“ on page 26

“Review and edit peaks“ on page 21

(If needed)

“Modify size matches using the Size Match

Editor“ on page 24

▼

Chapter 7, “Export size standard, sample information, and

results“

Chapter 2 Workﬂows

Data analysis workﬂow

2

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Software User Guide

Create a project and import samples

Create a demo project

IMPORTANT! We recommend that new users create a Demo project to quickly learn

how to use the module.

1. In the Thermo Fisher Cloud Dashboard, go to the Home page, click Tutorials,

then click Create a Demo project.

2. At the boom of the Tutorials screen, click , then click OK.

3. Click Recent projects and les, then click PeakScanner_DEMO_Project.

Note: It may take several minutes for the Demo project to appear in the Recent

projects and les screen.

4. (If needed) Review the Geing Started pop-up window, then click OK.

5. Proceed to Chapter 4, “Review and analyze samples in the Setup screen“.

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Create your own project

You must have saved FSA les from an instrument run before you can create a project

in the module. The FSA les can be analyzed or unanalyzed.

1. In the Thermo Fisher Cloud Dashboard, click Create project.

2. Enter a project name, select a save location, then click Create.

3. (If needed) Review the Geing Started pop-up window, then click OK.

4. In the Manage Data Files window, select an option to import FSA les:

1. Import From My Computer—Imports FSA les from your computer.

2. Import from Thermo Fisher Cloud—Imports FSA les from the Thermo

Fisher Cloud. The Cloud contains Demo les from Thermo Fisher Scientic

and any les that you have previously uploaded in Data Manager.

3. Import From Dropbox—Imports FSA les from Dropbox.

5. The imported les are displayed in the table. In the navigation bar, click the

Sizing Analysis Module Peak Scanner™ Software icon

Common Callouts and Arrows

1. Copy-paste a callout or arrow to use in this SVG.

Note: If you need more advanced callouts or arrows

use the TechComm_Inkscape_Callout&Arrow_Libary.

3. Delete this text, this rectangle, and unused

callouts, arrows, or other SVG elements

before adding this SVG to the repository.

2. Edit number and/or line-length, as needed.

1 1

1

.

6. In the Import Project Seings dialog box, select an option:

•Yes—Imports size standard, analysis seings, table seings and plot seings

from an existing project. Use this option to import a custom size standard

from a previous project.

No—Uses the default system seings.

Other ways to create projects

You must have saved FSA les from an instrument run before you can create a project

in the module. The FSA les can be analyzed or unanalyzed.

Chapter 3 Create a project and import samples

Create your own project

3

10

Sizing Analysis Module Peak Scanner

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Software User Guide

1. In the Thermo Fisher Cloud Dashboard, click in the navigation bar to open

the DataConnect screen.

2. Browse to and select the trace les of interest, then click

Common Callouts and Arrows

1. Copy-paste a callout or arrow to use in this SVG.

Note: If you need more advanced callouts or arrows

use the TechComm_Inkscape_Callout&Arrow_Libary.

3. Delete this text, this rectangle, and unused

callouts, arrows, or other SVG elements

before adding this SVG to the repository.

2. Edit number and/or line-length, as needed.

1 1

1

.

3. In the Create Project dialog box, enter a project name, select a save location, then

click Create.

4. Proceed with step 3 in “Create your own project“ on page 10.

You can import additional trace les, or skip “Create your own project“ on

page 10.

Common Callouts and Arrows

1. Copy-paste a callout or arrow to use in this SVG.

Note: If you need more advanced callouts or arrows

use the TechComm_Inkscape_Callout&Arrow_Libary.

3. Delete this text, this rectangle, and unused

callouts, arrows, or other SVG elements

before adding this SVG to the repository.

2. Edit number and/or line-length, as needed.

1 1

1

2

3

1Files icon—Click to open the DataConnect window

2Project folders and trace ﬁles

3Create project link—Click to open the Create Project dialog box

1. In the Thermo Fisher Cloud Dashboard, click in the navigation bar to open

the Home screen.

2. In the My Apps pane, click

Common Callouts and Arrows

1. Copy-paste a callout or arrow to use in this SVG.

Note: If you need more advanced callouts or arrows

use the TechComm_Inkscape_Callout&Arrow_Libary.

3. Delete this text, this rectangle, and unused

callouts, arrows, or other SVG elements

before adding this SVG to the repository.

2. Edit number and/or line-length, as needed.

1 1

1

.

3. In the Open Project dialog box, select Create New Project, enter a project name,

select a save location, then click OK.

4. Proceed with step 3 in “Create your own project“ on page 10.

Common Callouts and Arrows

1. Copy-paste a callout or arrow to use in this SVG.

Note: If you need more advanced callouts or arrows

use the TechComm_Inkscape_Callout&Arrow_Libary.

3. Delete this text, this rectangle, and unused

callouts, arrows, or other SVG elements

before adding this SVG to the repository.

2. Edit number and/or line-length, as needed.

1 1

1

2

1Home icon—Click to open the Home window

2Module icon in the My Apps pane—Click to open the Peak Scanner™ module

Create from the

DataConnect

window

Create from My

Apps in the Home

window

Chapter 3 Create a project and import samples

Other ways to create projects

3

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Software User Guide

11

Share an object

• To Share a single le, folder, or project with another Thermo Fisher Cloud user:

1. Click (Home) if necessary to return to the platform, then click (Files).

2. In Files, select the object to be shared, then click Share with people.

3. Enter the email address of the user(s) with whom you want to share the

selected object, separating each email address by a comma. Click Add.

4. Click Conrm.

The user(s) will receive a notication and email that you have shared an

object with them and the shared object will appear in their Home Folder.

Chapter 3 Create a project and import samples

Share an object

3

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Sizing Analysis Module Peak Scanner

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Software User Guide

Review and analyze samples in the

Setup screen

Review samples after ﬁrst import

When you import samples, the Setup screen is displayed (see “Parts of the Setup

screen“ on page 39) and shows data collection results with an analysis status of

Unanalyzed or Reanalyze.

1. Review information that is imported for the project.

• The total number of samples in the project is color-coded red to indicate that

samples have not been analyzed.

• A size standard is selected for the project (see “Size Standard selected by the

software“ on page 45).

• Analysis status for the project (see “Analysis status“ on page 46).

• The analysis and sizing ranges from the data collection analysis seings are

shown.

•Size Quality and Oscale overviews are shown. Color-coding is based on

the imported data collection analysis seings.

Note: The Quality Flags Size Quality and Oscale bar shows a gray portion

for any imported samples that are unsized.

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Software User Guide

13

2. Review the following information for the samples in the sample table.

Parameter Description

Status • for SeqStudio™ (3200) and 3500 FSA ﬁles

• for ﬁles analyzed using the current analysis

settings. Analyze samples after the ﬁrst import to

apply current settings.

• for 31xx FSA ﬁles[1]

SQ • , , or for SeqStudio™ and 3500 FSA ﬁles, based

on the Quality Flags setting from the data collection

analysis settings.

• Blank for 31xx FSA ﬁles[1]

OS • or for SeqStudio™ and 3500 FSA ﬁles, based on

the Quality Flags setting from the data collection

analysis settings.

• Blank for 31xx FSA ﬁles[1]

Size Standard See “Size Standard selected by the software“ on page 45

[1] If 31xx FSA files were previously analyzed using the Peak Scanner™ desktop software, the imported

Status, SQ and OS parameters will be the same as those for SeqStudio™ (3200) and 3500 FSA files.

Note: This table describes the parameter elds following initial import. These

parameters will update as the user applies modied analysis seings to the

project.

3. As needed:

•Click the Sample Type column header to sort and view control samples as

needed.

• “Customize the columns in the sample or sizing table“ on page 16.

• “Search tables and lists“ on page 15.

Analyze samples using default analysis settings

1. In the Setup screen, select one or more samples to analyze.

2. Click Analyze.

3. Review results in the Setup screen, then:

• If the sample quality is , proceed to Chapter 7, “Export size standard,

sample information, and results“.

•If the sample quality is or , or analysis fails, proceed to:

–“Reanalyze samples using custom seings“ on page 15

– Chapter 6, “Review the plot and peak information in the Results screen“

Chapter 4 Review and analyze samples in the Setup screen

Analyze samples using default analysis settings

4

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Sizing Analysis Module Peak Scanner

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Software User Guide

Reanalyze samples using custom settings

1. Perform any of the following tasks as needed:

• “Modify the default analysis seings“ on page 17

• “Edit a sample name and type“ on page 16

• “Apply a dierent size standard to the project or a sample“ on page 15

• “Modify size matches using the Size Match Editor“ on page 24

• “Adjust Quality Flag ranges“ on page 18

2. Click Reanalyze.

Add/remove samples

In the Setup screen, select the appropriate option:.

Option Description

Add more ﬁles 1. Click Actions

2. Click Add More Files

3. Select the appropriate import option.

Remove ﬁles 1. Select the samples to remove in the sample table.

2. Click Actions.

3. Click Remove Files.

Search tables and lists

Click in the upper-right corner of a table or list to search the contents of that table

or list.

Click Clear All to clear previous search results.

Apply a different size standard to the project or a sample

You can do any of the following:

• “Select a single size standard for a project“ on page 19

• “Select a size standard for individual samples“ on page 19

• “Create a new size standard denition“ on page 20

Chapter 4 Review and analyze samples in the Setup screen

Reanalyze samples using custom settings

4

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Software User Guide

15

Edit a sample name and type

Edit a sample name and type in the sample table.

•Edit the sample name—Click the sample name.

•Edit the sample type—Click the sample type, then select an option from the

dropdown list.

–Sample

–Positive Control

–Allelic Ladder

–Primer Focus

–Negative Control

Note: The software designates Positive Control, Allelic Ladder, Primer Focus,

Negative Control sample types as controls, and does not apply additional

processing to these samples. The user has the option to arrange control plots on

top during review of sample plots in the Results screen. See Chapter 6, “Review

the plot and peak information in the Results screen“.

Customize the columns in the sample or sizing table

Customize the columns displayed in the sample table.

•Sort the columns in the table—Double-click a column header.

•Edit the order of columns in the table—Click a header, then drag and drop in

the desired order.

•Show/Hide columns in the table—Click at the top right corner of the table,

click Show/Hide Columns, then select the columns to show or hide.

Click Restore to default to undo previous Show/Hide selections.

Chapter 4 Review and analyze samples in the Setup screen

Edit a sample name and type

4

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Software User Guide

Examine low quality samples

View data collection settings

1. In the Setup screen, open the Sample Details window using one of the following

methods:

• Double-click, or right-click on the sample le.

• Click Actions, then click View Sample Details.

2. Click Information to review the following data collection seings for a sample.

3. Click Close.

Examine EPT and raw data

Review the EPT (ElectroPherogram Telemetry) plot to identify instrument

performance issues that can aect size quality.

Review the raw data to evaluate anomalies, the causes of poor size-calling, and to

determine the start and stop points for analysis. The start point for data analysis

occurs after the primer peak and before the rst sizing peak. The stop point for

analysis occurs after the last sizing peak.

1. Open the sample details window using one of the following methods:

• Double-click, or right-click on the sample le.

• Click Actions, then click View Sample Details.

2. Click EPT Data to view the EPT plot.

3. Click Raw Data to view the raw data plot.

4. Click Close.

Modify the default analysis settings

1. In the Setup screen, click Seings.

2. Modify the seings as needed (see “Analysis seings“ on page 46 ).

3. Click Reanalyze all les with seings.

4. Click Done.

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17

To restore project analysis seings to the default seings, click Seings4Restore to

default.

Adjust Quality Flag ranges

1. In the Setup screen, click Seings.

2. Click Quality Flags.

3. Adjust the low, medium and high Quality Flag ranges as appropriate. See “Sizing

Quality (SQ) status“ on page 62.

Common Callouts and Arrows

1. Copy-paste a callout or arrow to use in this SVG.

Note: If you need more advanced callouts or arrows

use the TechComm_Inkscape_Callout&Arrow_Libary.

3. Delete this text, this rectangle, and unused

callouts, arrows, or other SVG elements

before adding this SVG to the repository.

2. Edit number and/or line-length, as needed.

1 1

1

Figure 1 Quality Flag ranges

1Drag to adjust to quality ﬂag ranges.

Apply a different size standard to the project or a sample

You can do any of the following:

• “Select a single size standard for a project“ on page 19

• “Select a size standard for individual samples“ on page 19

• “Create a new size standard denition“ on page 20

Chapter 5 Examine low quality samples

Adjust Quality Flag ranges

5

18

Sizing Analysis Module Peak Scanner

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Software User Guide

See “Create a new size standard denition“ on page 20 to create a custom size

standard for your project.

1. In the Setup screen, click Size Standard.

2. Select an option to apply a size standard:

Option Action

Factory default Size

Standard 1. Select a factory default Size Standard from the

dropdown list.

Import Size Standard

(.xml)—Import a size

standard ﬁle from your

computer.

1. Scroll to the bottom of the dropdown list, then

select Import Size Standard (.xml).

2. Browse to and select a size standard, then click

Open.

Note: Imported size standards only appear in the

project in which they were imported.

3. Click Reanalyze all les with this size standard.

4. Click Apply.

The software allows you to apply dierent size standards to, then analyze individual

samples in a project. When you analyze the project, only the size standard that is

selected for the project is used, and size standards that are selected for individual

samples are overwrien.

1. From the Setup screen, select the samples to which you want to apply a specic

size standard.

2. Click Size Standard, then select the appropriate option to apply a size standard.

See “

Apply a dierent size standard to the project or a sample“ on page 15.

3. Deselect Reanalyze all les with this size standard.

4. Click Apply.

Note: The new size standard is not displayed in the Size Standard column of the

sample list until the samples are analyzed.

5. In the Setup screen, click Reanalyze.

Select a single

size standard for a

project

Select a size

standard for

individual samples

Chapter 5 Examine low quality samples

Apply a different size standard to the project or a sample

5

Sizing Analysis Module Peak Scanner

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Software User Guide

19

Customized size standards only appear in the project in which they were created. See

“Export size standard“ on page 35 and “Create your own project“ on page 10 for

information about exporting and importing a previously dened custom size

standard when creating your project.

1. In the Setup screen, click Size Standard.

2. Create a new size standard using one of the following options:

Option Action

Customize a factory default

Size Standard 1. Select a Size Standard from the dropdown list.

2. Select Clone size standard to make changes.

3. Edit the numeric values for the size standard

deﬁnition. Separate size peak values with

commas.

Manually create a

customized Size Standard 1. Select Enter new Size Standard from the

dropdown list.

2. Enter the following information:

• Name

• Color

• Description

• Numeric values for the size standard

deﬁnition. Separate size peak values with

commas.

3. (Optional) Select Reanalyze all les with this size standard.

4. Click Apply.

Create a new size

standard

deﬁnition

Chapter 5 Examine low quality samples

Apply a different size standard to the project or a sample

5

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Software User Guide

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Thermo Fisher Scientific Sizing Analysis Module Peak Scanner Software User guide

Thermo Fisher Scientific Sizing Analysis Module Peak Scanner Software User guide

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