KnowItAll Installation Instructions & Quick Start Guide...KnowItAll Installation Instructions &...

KnowItAll™

Installation Instructions

& Quick Start Guide

KnowItAll Installation Instructions & Quick Start Guide

Copyright


Copyright © 2018

Bio-Rad Laboratories, Inc.

All Rights Reserved.

Published by

Bio-Rad Laboratories, Inc., Informatics Division

Philadelphia, Pennsylvania

Bio-Rad Laboratories makes no representations or warranties with respect to the contents of this publication or the accompanying software or databases. Bio-Rad specifically

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Table of Contents

KnowItAll Installation Instructions .................................................................................................................................... 1 Technical Support .............................................................................................................................................................................. 2 Training Resources ............................................................................................................................................................................. 2 The Interface ...................................................................................................................................................................................... 3 The Tools ............................................................................................................................................................................................ 4

KnowItAll® ID Expert™ Tool ............................................................................................................................................... 5

How to Perform a Spectral Identification .......................................................................................................................................... 5 SearchIt™ Tool ................................................................................................................................................................. 7

How to Perform a Spectral Search ..................................................................................................................................................... 7 How to Perform a Search if Processing Is Required (For IR & Raman Spectra) ................................................................................. 9 How to Include or Exclude Ranges from Your Search ...................................................................................................................... 10 How to Perform a Peak Search ........................................................................................................................................................ 11 How to Perform a Property/Name Search ....................................................................................................................................... 12

Mixture Analysis Tool ...................................................................................................................................................... 13 How to Perform a Mixture Analysis ................................................................................................................................................. 13 Mixture Analysis Results .................................................................................................................................................................. 14

MineIt™ Tool ................................................................................................................................................................... 15 How to Open a Database or Hit List ................................................................................................................................................ 15 Spectral Display Options .................................................................................................................................................................. 16 Hit Quality Index (HQI) - Search Result Ranking .............................................................................................................................. 17

ReportIt™ Tool ................................................................................................................................................................ 18 Create a Report for Your Search Results .......................................................................................................................................... 18


AnalyzeIt™ Tools (Spectral Interpretation) ....................................................................................................................... 20 About the AnalyzeIt Knowledgebases ............................................................................................................................................. 20 How to Interpret a Peak .................................................................................................................................................................. 21 Advanced Topic: How to Create a User Knowledgebase ................................................................................................................ 23

Database Building ........................................................................................................................................................... 25 How to Create a User Database ...................................................................................................................................................... 25 How to Import Spectra .................................................................................................................................................................... 27 How to Batch Import Spectra .......................................................................................................................................................... 27 How to Add a Property to a Record ................................................................................................................................................. 28 How to Create Your Own Properties ................................................................................................................................................ 29 Advanced Topic: How to Build a Multi-Technique Database ........................................................................................................... 29

ProcessIt™ Tools – Spectral Processing ............................................................................................................................ 30 How to Perform Spectral Addition or Subtraction ........................................................................................................................... 30


1

KnowItAll Installation Instructions

Before installing the software, review the system recommendations at www.knowitall.com/minimum_system.

1. Plug the KnowItAll Installation USB into your computer. Open the KnowItAll Installation folder on the USB, double-click

KnowItAllInstall.exe and follow the instructions. If you are unable to install from the USB, download the software from

www.knowitall.com/download.

Note: During the installation, if you have purchased the KnowItAll NMR, UV-Vis, or Mass Spectral Library, you will need to select the

appropriate check boxes to install these databases. The KnowItAll IR and Raman Spectral Libraries are automatically installed.

2. Start the KnowItAll software and follow the instructions to activate your license. The License Verification Code can be found on the

back of the KnowItAll packaging or in an email if downloaded.


2

Technical Support

Bio-Rad provides support for entire "Service Life" which terminates on “End of Technical Support Date” for the KnowItAll product

licensed. See www.knowitall.com/supportpolicy for details. For contact information, visit www.knowitall.com/contactus.

Training Resources

KnowItAll Installation Instructions &

Quick Start Guide

This document reviews main features of the software so users can get started quickly.

KnowItAll Training Resources Access the latest training resources, including demo movies at www.knowitall.com/training.

Help System A comprehensive help system is available in KnowItAll’s Help Menu.

Sample Files Find sample files, such as structures and spectra in the Users\Public\Documents\Bio-Rad

Laboratories\KnowItAll\Samples folder on your computer.


3

The Interface

The KnowItAll interface is designed so users can transfer information from one tool to another and move from one task to the next.

• Click on each Toolbox (A) to see the tools

available. Then click on the individual tools

(B) and the Active Tool Area (C) will show

the selected tool.

• A key to using KnowItAll is learning how to

transfer objects from one tool to another

using the Transfer to bar (D). For example,

process a spectrum in ProcessIt and send it

to SearchIt using this bar.

• Use the Back button (E) to return to the

most recently used tool or Back button

drop-down (F) to go back several steps.

Integrated interface for easy transfer of data from tool to tool.


4

The Tools

Below are tools in the KnowItAll software. Tools and file formats supported vary depending on license.

Toolbox Tools What It Does

Data

KnowItAll ID Expert™ Identify spectra

SearchIt™ Search databases

MineIt™/Database Building View & mine data; build databases with spectra, structures, properties

Mixture Analysis Analyze spectra of mixtures

AssignIt™ NMR Add assignments to NMR databases

Deformulation Expert™ Reverse engineer IR spectra of commercial products

QC Expert™ Compare IR or Raman spectra against reference spectra

Spectral Processing

ProcessIt™ IR Process IR spectra

ProcessIt™ Raman Process Raman spectra

ProcessIt™ NMR Process NMR spectra

ProcessIt™ MS Processing MS and hyphenated MS

Spectral Analysis

AnalyzeIt™ IR, Raman, Polymer IR Interpret spectra

AnalyzeIt™ MVP Perform multivariate analysis (chemometrics)

ValidateIt™ Validate statistical models

PredictIt™ NMR Predict NMR chemical shifts

Basics

ChemWindow® Draw 2D structures

ReportIt™ Create reports

BrowseIt™ Access website with links to training resources for KnowItAll users

Other Options Spectral Databases IR, Raman, NIR, NMR, MS, UV-Vis spectral databases


5

KnowItAll® ID Expert™ Tool

Use KnowItAll ID Expert to identify spectra.

How to Perform a Spectral Identification

1. Click the ID Expert tool in the Data toolbox.

(Click the desktop shortcut if you have ID Expert only.)

2. An Open dialog box appears. Navigate to and open a

spectrum file.

3. KnowItAll ID Expert automatically performs single

component searches, multiple component searches,

and functional group analyses and summarizes the

results on a single screen to give a complete view of all

possibilities for the unknown spectrum (A). Click on

results tabs to view results.

4. If there are problems with the query spectrum, ID

Expert has the spectral intelligence to identify the

issues. Click the appropriate checkboxes next to any

items flagged red to fix them. (B).

5. Once the user has identified the unknown spectrum,

generate a PDF report by clicking Create Report. (C).


6

Note: If the Optimized Corrections feature is turned on, ID Expert

automatically applies a series of iterative corrections (e.g., baseline

correction, clipping, horizontal shift, vertical shift, intensity distortion,

etc.) to both query and/or reference spectra to identify the best

matches within reference spectral databases. Any corrections made

are listed (D).

Tip: To change the search algorithm, toggle Optimized Corrections on

and off, select databases to search, and adjust other settings, from the

File menu, choose Settings and make changes in the dialog box.


7

SearchIt™ Tool

Use SearchIt to search Bio-Rad’s reference databases or your own. Results are displayed in the MineIt™ tool.

How to Perform a Spectral Search

1. Click the SearchIt tool in the Data

toolbox.

2. Choose the databases you wish to search

from the Available for Searching pane (A) on

the Databases tab (B).

3. Click Add; databases now appear in the

Selected for Searching pane (C).

4. Choose a technique in the Search By bar’s

Spectral section (D). An Open dialog box

appears.


8

5. Navigate to and open a spectrum file; it is loaded in a

Spectrum tab.

6. Click Search (E).

7. Results appear in the MineIt tool sorted by Hit Quality

Index (HQI) (F).

Tip: Use tools in Spectrum toolbar (G) to change spectral display

(H): e.g., Overlay, Offset, Stack Spectra; Zoom, etc.


9

How to Perform a Search if Processing Is Required (For IR & Raman Spectra)

1. Click the SearchIt tool in the Data toolbox.

2. Choose the databases you wish to search from the

Available for Searching pane on the Databases tab.

3. Click Add; databases now appear in the Selected for

Searching pane.

4. Choose a technique in the Search By bar’s Spectral

section. An Open dialog box appears.

5. Navigate to and open a spectrum file; it is loaded in a

Spectrum tab.

6. Click Edit Spectrum. The spectrum is transferred to

the ProcessIt IR or ProcessIt Raman tool.

7. Click a processing tool (Flatline, Truncation/Padding,

Normalization, etc.) on the Process toolbar (A).

8. Click Return to SearchIt and Save (B). The edited

spectrum appears in SearchIt’s Spectrum tab.

9. Click Search. Results appear in the MineIt tool.


10

How to Include or Exclude Ranges from Your Search

1. In SearchIt, open a spectrum.

2. Specify ranges to include or exclude:

• Click and drag in the Include Range Bar (A) to

specify a limited range of the spectrum to search.

The included range (B) appears on the Include

Range Bar; excluded areas (C) appear on the

spectral display. To exclude ranges, use the Exclude

Range Bar (D).

• Alternately, click the Manually Edit Mask Ranges

button (E) to open the Spectral Include/Exclude

Masks dialog box. Uncheck Use full range (F) and

choose from a list of common ranges to exclude (G)

or manually enter peaks to include (H). Click OK.



11

How to Perform a Peak Search

Use a peak search to compare peak tables from databases to a

peak table you enter or extract from a spectrum.


2. Choose databases you wish to search from the Available for

Searching pane on the Databases tab.

3. Click Add; databases now appear in Selected for Searching

pane.

4. Choose a technique in the Search By bar’s Peak section (A).

The Peaks tab opens. A red X next to the selected technique

means more information is needed to perform search.

5. You can then pick peaks from a spectrum or enter them

manually without loading a spectrum.

a. Peak Picking from a Spectrum:

• Open a spectrum with the Open Spectrum or

Structure File tool (B).

• Drag the Minimum Peak Intensity bar (C) to set the

threshold above which peaks will be picked.

• Click Pick (D) to pick peaks.

b. Manual Peak Picking:

• Click Add to enter a peak (E). The Enter Peak dialog

box opens.

• Type Peak Position and Peak Min. Intensity values in

the text boxes and click OK. The values are added to

the peak table. Add additional peaks if desired.



12

How to Perform a Property/Name Search

Use a property/name search to locate compounds in the

database with specific names or properties. You can perform

this type of search with or without loading a spectrum and can

use Boolean operators to define your search parameters.


2. Choose the databases you wish to search from the

Available for Searching pane on the Databases tab.

3. Click Add; databases now appear in the Selected for

Searching pane.

4. Click Property/Name (A) at the top of the Search By bar.

The Property/Name tab appears.

5. Select a property field to search from the Property drop-

down (B). Enter the information you wish to search.


Note: Select the property Any Field to search for text strings in

all database fields that contain text values.


13

Mixture Analysis Tool

The Mixture Analysis tool aids in the analysis of spectra that are mixtures by finding matching combinations of reference spectra.

How to Perform a Mixture Analysis

1. Click the Mixture Analysis tool in the Data toolbox.

2. Choose the databases to search from the Available for Searching

pane on the Databases tab (A).

3. Click Add; databases now appear in the Selected for Searching pane.

4. Click the Open Spectrum toolbar button ; then navigate to and

open a mixture spectrum.

5. Set Maximum number of components (B) to 2, 3, or 4.

6. Click Search (C).


14

Mixture Analysis Results

Results are automatically displayed along with the

query spectrum in the MineIt tool and are sorted

by the Hit Quality Index, which indicates the

quality of the composite spectrum.

Results include:

• Composite spectra (D)

• Possible components that comprise each

composite spectrum (E)

• A residual spectrum, which is the difference

between the query spectrum of the actual

mixture and the composite spectrum (F)


15

MineIt™ Tool

With MineIt, view results (hit lists) from searches performed with the SearchIt tool; access and view databases; build and manage user

databases. If your license includes database building, the MineIt tool appears in the Data toolbox with text “MineIt/Create Database.”

How to Open a Database or Hit List

1. Click the MineIt tool in the Data toolbox.

2. Choose File > Open Database. The Select a Database

dialog box opens.

3. Click Open by Browsing; then navigate to and select

a database.

4. Use the Navigation toolbar (A) to browse the

database or scroll through the list manually.

5. Use the View menu to change what information is

visible in your display such as:

• Spectrum Pane (B) - displays spectrum for current

record

• Spectrum Toolbar (C) - use to zoom, scale, etc.

• Structure/Properties Pane (D) - displays

structure/properties for current record

• Spectrum Overview Pane (E) - shows small version

of active spectrum indicating areas in which the

spectrum has been zoomed


16

Spectral Display Options

Click the Overlay tool on the Spectrum toolbar to view spectra

overlaid directly on top of one another.

Click the Offset tool on the Spectrum toolbar to view spectra

on top of one another, but vertically offset.

Click the Stack tool on the Spectrum toolbar to stack the

spectra on top of each other.


17

Hit Quality Index (HQI) - Search Result Ranking

The Hit Quality Index (HQI) is a ranking system for search results. The HQI

appears with each record in a hit list. Choose File > Preferences and use

controls on the Hit List tab to select one of three HQI scales:

• Best = 999, worst = 0 (Sadtler scale)

• Best = 0, worst = 1.4

• Best = 100, worst = 0

Note: The HQI does not replace your own critical analysis of the results.

You may find that the highest ranked hit or the first hit in the hit list is not

always the best result.


18

ReportIt™ Tool

The ReportIt tool is a full-featured chemical publishing program.

Create a Report for Your Search Results

1. When the MineIt tool displays a hit list or database, click

ReportIt on the Transfer to bar (A). The Select a Report

Template dialog box opens.

2. Select a template and click OK. The database or hit list

record is transferred to the ReportIt tool.


19

ReportIt allows you to combine spectra, structures, and text in

the same document.

Many tools are available to customize reports, e.g., add

annotations (B), text (C), or align objects (D).

You can also double click on an object in your report to open a

context-sensitive tool palette. For example, double click on a

spectrum to open a spectrum tool palette (E).


20

AnalyzeIt™ Tools (Spectral Interpretation)

KnowItAll’s AnalyzeIt IR, AnalyzeIt Raman, and AnalyzeIt Polymer IR can be used to assist in the basics of spectral interpretation and can

also aid experienced analysts in interpreting complex spectra.

AnalyzeIt is an interactive chart of functional groups. It shows all functional groups from the knowledgebase that absorb in the same area

as a selected peak and lists the type of bond that causes the absorption, as well as other characteristic absorbances for each functional

group. Summary functions enable quick accumulation of matches between the peaks of your spectrum and the functional groups.

About the AnalyzeIt Knowledgebases

• The knowledgebases used by AnalyzeIt IR and AnalyzeIt Raman currently have over 600 band assignments corresponding to over

200 functional groups, subdivided into general chemical classes.

• The knowledgebase used by AnalyzeIt Polymer IR currently has over 1,300 band assignments corresponding to functional groups,

subdivided into over 100 polymer classes.

• In addition, users can build their own knowledgebases and use them to interpret functional groups in a spectrum.


21

How to Interpret a Peak

1. Choose File > Open Spectrum, then navigate to and open a spectral file.

2. Click the Suggest tool to allow the software to select a peak for correlation. A selection line and wavenumber label will appear

in the Spectrum pane for the suggested peak. You can obtain more suggestions by repeating this procedure.

3. With a peak selected, click the Correlate tool . The results for that peak appear in a tab.

4. Scroll through the results to overlay and compare with your spectrum.

5. Tag likely matches by clicking the Summary + tool and those you eliminate with the Summary – tool .

Tip: Look for peaks that are strong and/or unique, and focus on peaks above 1500 cm-1

.

• Weak peaks may be overtones, combination bands of lower frequencies, or impurities. While weak peaks can be used to support

identification of a possible functional group, they should only rarely be used as the basis for proposing a functional group.

• Peaks above 1500 cm-1

are much more characteristic of individual group frequencies; while peaks below 1500 cm-1

constitute

the fingerprint region, useful in the overall identification of individual molecules.


22

(A) Structure Pane - Displays a structure imported from a

file or the ChemWindow tool to compare with the

AnalyzeIt knowledgebase (AnalyzeIt IR and Raman only).

(B) Selected Fragment Structure Pane - Shows the

corresponding fragment for the highlighted entry in (D).

(C) Spectrum Pane - Displays an imported spectrum with an

overlay of peak ranges for functional groups in the

knowledgebase.

(D) Functional Group Data Pane - Displays a list of all

functional groups possible at a peak position, along with

classification, bond, range, intensity, etc.

(E) Bar Chart Pane - Displays color-coded bars that visually

link information in (D) with (C).

(F) Results Tab - Shows results for an individual peak.

(G) Summary Tabs - Compile results the user has tagged as

good or bad matches.

(H) Spectral Handbook - Click the Sadtler Handbook tool

to view additional information on functional groups

(AnalyzeIt IR only).

Notes Pane - Displays detailed information about

functional group currently selected in (D) (AnalyzeIt

Polymer IR only).


23

Advanced Topic: How to Create a User Knowledgebase

1. Choose Knowledgebase > New.

2. Type in a name for the user knowledgebase and save it to a

location on your hard drive.

3. Right-click in the Functional Group Tree (on the left); then

select Add Classification. The Classification dialog box opens.

4. Type in a classification name and click OK.

5. Right click on the new classification name; then select Add

Functional Group. The Functional Group dialog box opens.

Type in a chemical formula in the upper text box.

6. Click Browse, then browse to and select a corresponding

spectral file. The file is displayed in the Reference spectrum

text box.

7. Click OK to close the dialog box; then right-click on the new

functional group in the Functional Group Tree. A pop-up

menu opens.


24

8. Click Add Band. The Band dialog box opens. Add appropriate

band information: Range, Height, Width at Half Height, etc.

Note: Knowledgebase information is saved automatically.

9. Choose File > Preferences to open the Preferences dialog box.

To use the a new knowledgebase, check the Use AnalyzeIt

Knowledgebase checkbox, then use the Add and Remove

buttons to select which user knowledgebases to use.


25

Database Building

KnowItAll’s MineIt tool can be enhanced with the Database Building Option. With this option, build databases

of IR, Raman, NIR, NMR, MS, UV-Vis, and chromatograms. If database building is available in your license, the

MineIt tool is renamed to MineIt/Create Database.

How to Create a User Database

1. Click the MineIt/Create Database tool in the Data

toolbox.

2. Choose Database > New. The New Database Creation dialog

box opens.

3. Click Browse to select a location on your computer where the

database will be saved; then type in a file name and click Save.

4. Type in the Database Name and Database Code.


26

5. Click OK. The new database has been created. The database

code appears on the database tab.


27

How to Import Spectra

1. Choose File > Open Database to open the database to which you want to add entries.

2. Choose File > Import. A standard Windows Open dialog box appears.

3. Browse to and select the file(s) you wish to add to the user database; then click OK to import the spectrum.

Note: Multiple spectra of the same or different type can be stored in a single database record or as separate records as needed.

How to Batch Import Spectra

1. Open the database to which you want to add entries.

2. Choose File > Batch Import. The Select Files dialog box opens. Select

the file type; then browse to and select the files you wish to add to

the user database.

3. Click OK to add the files to the database.


28

How to Add a Property to a Record

1. With a user database open, click Add on the

Structure/Properties pane to open the Property dialog box.

2. Click the Property down arrow to view available properties.

3. Select a property; then enter values.

4. Click OK to add the property to the database record

Note: Use the Attachments tab (A) to add files such as PDF

documents, spreadsheets, or images to a database record.

Tip: Use the Preferred Properties tab (B) to display only selected

properties. Choose File > Preferences; then use the Property

Display tab to specify which properties are displayed on the

Preferred Properties tab. You can also customize the order in

which the preferred properties appear.


29

How to Create Your Own Properties

1. Choose Database > Define User Property Fields to open the User Property Fields dialog box.

2. Click Add to open the Property Field Definition dialog box.

3. Type in a property Name and select Type, Physical Quantity, and Unit from the drop-down lists. Click OK to add the new property

field to the list of properties displayed in the Property dialog box.

Advanced Topic: How to Build a Multi-Technique Database

1. Select a spectrum record in a user database.

2. Choose File > Import, then browse to and select the

spectrum you wish to add to the record.

3. A new tab is added to the spectrum pane if this is a

new technique. If the technique already exists in

the database record, you can choose to Replace in

the current record, Add as a new record, or Add to

this record.


30

ProcessIt™ Tools – Spectral Processing

The ProcessIt™ IR and ProcessIt Raman tools allow you to process spectra. Use the Process menu to access options including: Flatline,

Truncation/Padding, Normalization, Smoothing, Baseline Correction, Add/Subtract Spectrum, etc.

How to Perform Spectral Addition or Subtraction

Use spectral addition or subtraction to accomplish point-by-point addition or subtraction of one spectrum

from another. This technique is especially useful when analyzing mixtures or composite spectra.

1. Open the ProcessIt IR or ProcessIt Raman tool and import your spectra:

a. For the 1st

spectrum, import using File > Open Spectrum

b. To import the 2nd

spectrum, use File > Open Overlay Spectrum

2. Choose Process > Add/Subtract Spectrum; Add/Subtract dialog box opens. Two spectra are involved:

• The Experimental Spectrum (the spectrum being processed)

• The Reference Spectrum

3. Select Replace; the Sum or Difference Spectrum (the result of the addition or subtraction process) is

displayed with the Reference spectrum.

Note: The Factor value determines how much of the Reference Spectrum is added to or subtracted from the

Experimental Spectrum. Mathematically, this is expressed as: Difference = Experimental - (Reference x

Factor) or Sum = Experimental + (Reference x Factor). The default value is 1. Negative values can be entered

if desired.

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