Analyze Spectra | Thermo Fisher Scientific

Select an article below or watch a video to learn how to view, select and create libraries of FTIR data and how to use libraries to identify unknown sample materials.

Finding Measurements and Reports

When looking for saved measurements and reports, use tags and search keywords to filter the measurements and reports lists.

Searching

When you search for a measurement, the search term is checked against information such as the spectrum tags, title, last modified date, identified compounds, custom strings, serial numbers, etc. If you search for a report, fields used for the search include report name, date created, and the template type.

Tip: Click a column header, such as Measurement Name or Type, to sort the measurements. By default, measurements are sorted to show the most recently modified item first.

To search for measurements and reports

Select either Reports or Measurements from the list.
Select a time to limit the search results.
Enter your search terms and click Search.

Use the following search techniques to refine your results:

Search Technique	Description	Example
Quotation Marks ("")	Use quotation marks to return only exact matches from the tags. This is useful if you are searching for a two-word tag and do not want to see spectra tagged with only one of the words.	“red blue” Returns: only spectra with the tag “red blue”. Does not return spectra with tags “red” or “blue” separately.
* (asterisk)	Add an asterisk () to the end of your search terms to return all results that include the text preceding the asterisk Note: The can be appended to the end of the search terms but cannot come before other terms.	Poly* Returns: Any measurement with a term beginning with poly, such as polystyrene.
AND, OR, NOT operators	These keywords must be in all capital letters, as shown. AND: Returns only results that contain both terms. OR: Returns results that contain either keyword. NOT: Returns only results that contain the first term but do not include the term after NOT.	Sample AND Background Returns: Only measurements that have both Sample and Background in the searched fields. Sample OR Background Returns: Measurements with either sample or background in the data are returned. Sample NOT background Returns: Measurements or reports that have sample in the data and do not have back-ground in the terms.
title:<keyword>	Use to specify that the keyword must be in the measurement or report title.	title:poly Returns: measurements with poly in their name, but those with poly elsewhere (such as identified compounds) are ignored.
tags:<keyword>	Use to specify that the keyword must be a tag. If the tag is two words, use an underscore instead of a space.	tags:blue tags:blue_powder Returns: measurements with blue as a tag, but those with blue elsewhere (such as the measurement name) are ignored. “blue_powder” searches for the two word tag “blue powder”.

Tagging

Tags give you another convenient way to locate measurements and reports in your database. For example, if you are collecting many measurements related to a single project, you might tag each of those measurements with the same “Project A” tag. Later, you can use this tag to filter your measurements to show you only measurements with the “Project A” tag.

To add or delete a tag in the desktop interface

1. Right-click a measurement in the Measurements list and select Manage Tags.

Tags currently assigned to the measurement are listed under Current Tags.

To add a new tag, enter text in the New Tag field and click Add. The new tag is added to the current tags.
To delete a current tag, click the delete icon in the upper right corner of the tag. The tag is removed immediately.

2. To save your changes, click OK. Click Cancel to exit the Manage Tags dialog without saving the changes.

To add or delete a tag in the touchscreen interface

1. From the Home screen, navigate to the Measurements tab.

2. Select a measurement and touch the more options icon.

3. Touch Manage Tags.

To add a tag, enter text in the New Tag field and touch Add. The new tag is added to the current tags list.
To delete a tag, touch the delete icon in the upper right corner of the tag.

4. To save your changes, touch OK. Touch Cancel to exit the Manage Tags dialog without saving the changes.

Set OMNIC Paradigm Software Options

Use the Options dialog to customize the spectral display, to set the number of digits used for peak area, height, and location, and to configure automatic baseline correction.]

To set and save OMNIC Paradigm options

Open the Options dialog.
- Desktop interface: open the Configure menu and select Options.
- Touchscreen interface: Open the settings and navigate to the Options tab.
Select New.
Enter a name for the new options and click Save.
Edit your settings.
When you are finished editing settings, select Save to save your changes.
Select Close to return to your previous screen.

Customize Spectral Display Settings

The Spectral Display group is used to set the color and line weight of spectra in the Spectra view.

Line Weight: Determines the thickness of the line used to draw the spectrum. Applies to all spectra shown in the Spectra view.
Selected Spectrum Color: Determines the color used to highlight the currently selected spectrum.

The additional colors set the colors of spectra that are not selected.

Set Number of Digits

Use the Number of Digits group to set the limit for the number of digits after the decimal separator. The limit is applied to the following:

Peak area
Peak height
Peak location - X value
Peak location - Y value

Note that this setting only applies to operations carried out after the setting is adjusted. Numbers in the spectrum information maintain the settings used at the time they were recorded and are not updated to reflect new settings. For example, if you carry out a find peaks operation with settings specifying 3 digits, the spectrum information shows 3 digits. If you then change your settings to use only 1 digit after the decimal, the spectrum information from the earlier find peaks operation will still show the 3 digits.

Configure Automatic Baseline Correction

Use Automatic Baseline Correct in the Process menu to automatically correct tilted or curving baselines.

Set the polynomial order and number of iterations to specify the order of the equation and number of iterations to use for correcting baselines automatically.

Add a custom logo to reports

Use your own logo on reports and template reports. The image is shown on standard reports and reports you create using the Template Report tile in workflows.

Report images must be a PNG file and are automatically resized to be 120 px by 75 px.

Manage Libraries

Libraries contain lists of compounds and related information and can be purchased or created from your own data. When you perform a correlation or multi-component search, the analysis compares your sample spectrum to compounds stored in the libraries you specify in your search settings.

Use the library manager to view information about your libraries and stored compounds and to create or delete libraries.

Create a new library

Create a new library to manage your spectral data and to search against your own measured data.

Touchscreen
Desktop

To create a new library

From the home screen, open the menu [ ] and select Library Manager.
Open the menu and select New Library.
In the New Library view, enter a name for the library and add any optional fields.
Optional fields are used when you add spectra to a library. For example, Figure 2 shows a library with two optional fields. When adding spectra to My New Library, users can provide a batch number and compound class.

Figure 2. Name your library and customize optional fields in the New Library view.

Touch Save to save your new library.

To create a new library

From the menu bar, select Identify > New Library.
In the New Manager, select New Library.
Enter a name for the library and add any optional fields.
Optional fields are used when you add spectra to a library.

Figure 1. Name your library and customize optional fields in the New Library view.

Click Save to create the new library.
Your new library is listed in the Libraries column of the library manager.

Touchscreen

To create a new library

From the home screen, open the menu [ ] and select Library Manager.
Open the menu and select New Library.
In the New Library view, enter a name for the library and add any optional fields.
Optional fields are used when you add spectra to a library. For example, Figure 2 shows a library with two optional fields. When adding spectra to My New Library, users can provide a batch number and compound class.

Figure 2. Name your library and customize optional fields in the New Library view.

Touch Save to save your new library.

Desktop

To create a new library

From the menu bar, select Identify > New Library.
In the New Manager, select New Library.
Enter a name for the library and add any optional fields.
Optional fields are used when you add spectra to a library.

Figure 1. Name your library and customize optional fields in the New Library view.

Click Save to create the new library.
Your new library is listed in the Libraries column of the library manager.

Add spectra to a library

Add spectra to a library to use your own sample data in other Search analyses.

Touchscreen
Desktop

To add spectra to a library

In the spectral view, select the spectrum to add to a library.
Select Add to Library from the menu.
In the Add to Library view, select a library from the Libraries column.
Name the compound, specify any optional fields and touch Save. The spectrum will now be available in your selected library.

To add spectra to a library

In the spectral view, select the spectrum you want to add to a library.
From the menu bar, select Identify > Add to Library to open the Add to Library view.
Select the library you want to add the spectrum to from the list of libraries.
Make any adjustments to the spectrum information and set a name for the compound. The default name will be the measurement name used when the sample was measured.
Click Save. Your spectrum is now available in the library, and you can view it in the library manager.

Extract spectra from libraries

Extract spectra from libraries to use them as references in your analyses or workflows. Extracted spectra are stored with your measurements in the database but cannot be renamed, tagged, or exported.

To extract a spectrum from a library

Navigate to Library Manager.
Select a compound to extract.
In the toolbar, select Extract. A message confirms that the spectrum has been extracted successfully. View your measurements to find the extracted spectrum.

Delete libraries and compounds

When you delete a compound, that compound is no longer used in search analyses and is crossed out in the list of compounds. The index position of other compounds in the library is maintained.

You can delete or edit only the libraries that you have created. Commercial libraries and their compounds cannot be deleted.

CAUTION Deleted libraries and compounds cannot be recovered.

To delete a compound from a library

Using the desktop interface

In the Library Manager, navigate to the compound you want to delete.
Right-click the compound and select Delete. In the dialog box, click Yes to confirm.

Using the touchscreen interface

In the library Manager, select the compound you want to delete.
Touch Delete in the Spectrum pane.

To delete a library

Using the desktop interface

In the Library Manager, select the library to be deleted.
Click Delete in the toolbar, then click Yes to confirm.

Using the touchscreen interface

In the Library Manager, select the library to be deleted.
Touch Delete in the main toolbar.

Add library locations

Use the Library Locations tab in Search Setup to specify additional library locations. This is useful if your libraries are stored in a shared location such as a network drive. After you add a location, you can use libraries in that location for Search, QCheck, and other analyses.

To add a library location

Using the desktop interface, open the Identify menu and select Search Setup.
Navigate to the Library Locations tab.
Click Add Location.
Browse to the location of the additional libraries and click Open.
Click Save.

Touchscreen

To add spectra to a library

In the spectral view, select the spectrum to add to a library.
Select Add to Library from the menu.
In the Add to Library view, select a library from the Libraries column.
Name the compound, specify any optional fields and touch Save. The spectrum will now be available in your selected library.

Desktop

To add spectra to a library

In the spectral view, select the spectrum you want to add to a library.
From the menu bar, select Identify > Add to Library to open the Add to Library view.
Select the library you want to add the spectrum to from the list of libraries.
Make any adjustments to the spectrum information and set a name for the compound. The default name will be the measurement name used when the sample was measured.
Click Save. Your spectrum is now available in the library, and you can view it in the library manager.

Extract spectra from libraries

Extract spectra from libraries to use them as references in your analyses or workflows. Extracted spectra are stored with your measurements in the database but cannot be renamed, tagged, or exported.

To extract a spectrum from a library

Navigate to Library Manager.
Select a compound to extract.
In the toolbar, select Extract. A message confirms that the spectrum has been extracted successfully. View your measurements to find the extracted spectrum.

Delete libraries and compounds

When you delete a compound, that compound is no longer used in search analyses and is crossed out in the list of compounds. The index position of other compounds in the library is maintained.

You can delete or edit only the libraries that you have created. Commercial libraries and their compounds cannot be deleted.

CAUTION Deleted libraries and compounds cannot be recovered.

To delete a compound from a library

Using the desktop interface

In the Library Manager, navigate to the compound you want to delete.
Right-click the compound and select Delete. In the dialog box, click Yes to confirm.

Using the touchscreen interface

In the library Manager, select the compound you want to delete.
Touch Delete in the Spectrum pane.

To delete a library

Using the desktop interface

In the Library Manager, select the library to be deleted.
Click Delete in the toolbar, then click Yes to confirm.

Using the touchscreen interface

In the Library Manager, select the library to be deleted.
Touch Delete in the main toolbar.

Add library locations

To add a library location

Using the desktop interface, open the Identify menu and select Search Setup.
Navigate to the Library Locations tab.
Click Add Location.
Browse to the location of the additional libraries and click Open.
Click Save.

Identify an Unknown Sample with Transmission

Your FTIR spectrometer and Thermo Scientific™ OMNIC Paradigm software can help you identify the chemical composition of an unknown sample. This article demonstrates how to measure and analyze a sample using infrared transmission. By “transmission” we mean that the infrared beam passes directly through the sample. Transmission is a common technique for acquiring FTIR data. This article includes a number of examples to help you build confidence in interpreting your analysis results.

You will learn how to:

Prepare the transmission accessory
Set up and run the analysis, and
Evaluate and confirm the results

Prepare the Transmission Accessory

To begin, make sure your transmission accessory or sample holder is inserted in the spectrometer sample compartment. Here is the Thermo Scientific™ iD1 Transmission Accessory in our Nicolet™ Summit FTIR Spectrometer.

Remove any sample from your accessory or sample holder so the spectrometer can take an accurate background measurement when it’s ready. The iD1 accessory cover can be open or closed. (If your transmission accessory is purged with dry air or nitrogen, keep the cover closed unless you are adding or removing a sample.)

Set Up the Analysis

The next step is to set up the OMNIC Paradigm software. After you open the software, you see the dashboard in the main window. The important measurement settings are at the top.

First, make sure the Sampling Accessory readout shows the installed accessory. If it doesn’t, reseat the accessory. Notice that the factory presets for that accessory appear under “Settings.”

Then enter a measurement name, or you can leave the suggested name, which is the exact date and time of the measurement.

Next make sure the Analysis Type is set to Search.

This performs a point-by-point comparison of the sample spectrum against FTIR library spectra. The quality of the output depends on the source and quality of the spectra in the selected libraries.

Finally, check the acquisition settings (sample scans, resolution and final format). The settings shown above are all good starting values for this analysis.

It’s important to note that the quality of the sample data you acquire will affect the analysis results. For example, speeding up the analysis by measuring fewer scans, or decreasing the resolution could lead to a less certain analysis result.

Consider Your Spectral Libraries

All existing spectral libraries are selected automatically by default. Choose Search Setup in the Identify menu to view or change your library selections. For this demonstration, we are using the free libraries provided with OMNIC Paradigm software and the Nicolet Summit Pro spectrometer.

Choose Cancel to close the Search Setup window.

You can also use the Library Manager in the same menu to easily create a spectral library. Any libraries you create should be from pure materials that represent what you expect to find in your unknown samples.

The library spectra are normally the same quality or higher quality than the sample spectrum. It is also helpful if they are acquired using the same sampling technique (transmission in this case). There is no need to perform conversions such as final format, resolution or spectral range on the sample data before performing a search—the software does that for you.

Measure and Analyze the Sample

To start the analysis, click Preview and Measure Sample.

The analysis starts with a background measurement. The only requirement for a transmission background is to remove any sample from the path of the infrared beam. The background spectrum is used to eliminate any signals in the sample data that are due to the spectrometer, your transmission accessory or sample holder, or the background environment.

The software shows a preview of the current background spectrum in the spectral pane. The examples below show typical background spectra for transmission analysis using a transmission accessory that has not been purged with dry air or nitrogen, and one that has been purged.

Figure 1. Background spectrum from a transmission accessory that has not been purged

Figure 2. Background spectrum from a transmission accessory that has been purged

Click Start Background Measurement.

When the background measurement is completed, its image appears in the results panel and in the spectral pane.

To install a mounted film sample, open the cover for the transmission accessory and slide your sample or sample holder into a slot that best fits the sample or sample holder width. If your sample or holder allows it, choose a slot that is close to the beam’s focal point (for the iD1 accessory, this is roughly in the center of the sample compartment). For this demonstration, we are measuring a plastic film mounted on a sample card.

Figure 3. iD1 Transmission Accessory beam focal point

Once a sample is in place, click Preview Sample to preview the sample data in the spectral pane.

If the peaks in the preview spectrum are very small, try using a thicker sample. If the spectrum has no sample peaks, check that the sample material transmits energy in the infrared spectrum.

When you are ready to continue, choose Start Sample Measurement (see the previous image) and wait for the progress bar to complete. The software quickly compares the sample spectrum to the selected library spectra and shows you the results.

What’s in My Sample?

The spectral pane shows the sample spectrum along with the best matched spectrum from the selected libraries. The two spectra are overlaid with the same Y-axis scale so you can compare the results visually. (If the spectra are very similar, as in this case, there are other views that will highlight the differences. We’ll talk more about that later.) The results panel shows a list of the 5 best matched spectra, along with their match values.

Figure 4. Sample and top search result displayed together using the same Y-axis scale

Sample spectrum (red)
Best match (blue)
Results panel

The match values tell you how well each library spectrum matches the unknown sample. The closer this value is to 100, the better the match.

In this example, the top match has a match value that is above 85, which indicates a good match. The match value for the next spectrum in the list is well below that.

Figure 5. Match values showing a clear match

If we look at the overlaid spectra in the spectral pane, the positions of the main peaks line up along the X-axis, and they differ only in their peak heights.

Figure 6. Overlaid spectra showing a clear match

Click the Stack button to see the two spectra scaled to fill each Y-axis. Again, the spectra are well matched except for the slightly raised baseline in the sample spectrum’s low frequency region. As a result, we can conclude that the sample is polyethylene and the analysis is complete.

Figure 7. Stacked spectra showing a clear match

To get more information about a spectrum in the match list, including the library it came from and its identification number, hover over the spectrum’s grey arrow in the results panel.

Figure 8. Information button for a library spectrum

What if there isn’t a clear (single) match?

If the analysis results show several matches that all have similar match values, as in this example, Shift + click the three matches in the results panel to add all three spectra to the spectral pane for a detailed comparison.

Figure 9. Stacked spectra showing several similar matches

How can I improve my analysis results?

If no clear match appears, there are a number of options to consider that may improve your results. (Some setting adjustments will require a new background measurement.)

For starters, you can return to the dashboard and adjust the Resolution setting for the unknown sample. For example, you can acquire the spectrum at a higher resolution by using a lower Resolution setting. If the sample peaks are sharper or more numerous, you may get a better analysis result. You can also acquire more scans to reduce spectral noise, which can also affect the results.

If the sample spectrum has a tilted or curved baseline, try applying Automatic Baseline Correction (Process menu) to your sample spectrum. Then restart the analysis by choosing Identify (menu) > Correlation Search, or click the Search button on the toolbar.

How to Specify the Spectral Region for the Analysis

If your sample spectrum has a peak that is so large it is off the Y-axis scale, you may want to exclude that peak from your analysis. Here is an example:

Figure 10. Example of a totally absorbing peak

These “flat topped” peaks are referred to as “totally absorbing” and can contain excessive spectral noise, which affects the analysis results.

To exclude a totally absorbing peak, choose Identify (menu) > Search Setup and use the tools to select the regions to search.

First, clear the “Use Full Spectral Range” check box to enable the region tools.

Figure 11. Tools for selecting the regions to search

Then position the vertical bars to select the first region to search.

To add a search region, click the Add button and use the second set of vertical bars to select the next region. Here we used the first set of vertical bars to select the region to the left of the fully-absorbing peak. And then we added a region and used the second set of vertical bars to select the region to the right of the fully-absorbing peak.

When you are finished selecting regions, click Save to return to the Dashboard view, and then click the Search button on the toolbar to re-run the search.

Identify an Unknown Sample with ATR

Your FTIR spectrometer and OMNIC Paradigm Software can help you determine what’s in an unknown sample. This article demonstrates how to measure and analyze a sample using the Attenuated Total Reflection, or ATR, sampling technique. It is a common and “mess-free” technique for acquiring FTIR data from a sample material. This article includes a number of examples to help you build confidence in interpreting your analysis results.

You will learn how to:

Prepare the ATR accessory
Set up and run the analysis, and
Evaluate and confirm the results

Follow these instructions to measure and analyze an unknown pure sample using the ATR sampling technique.

Prepare the ATR accessory

To begin, make sure your ATR accessory is inserted in the spectrometer sample compartment and that it has an appropriate crystal installed. Each crystal material provides some kind of sampling advantage such as a wider spectral range, a higher energy throughput, or more durability. The correct choice depends on what crystals are available, which one works best with your sample material, and which one produces the needed information. See the information that came with your ATR accessory for more information.

Here is the Thermo Scientific™ Everest ATR Accessory with a diamond crystal installed in our Nicolet™ Summit FTIR spectrometer.

Make sure the crystal is clean so the spectrometer can take an accurate background measurement when it’s ready. To clean the crystal, dab it with a soft cloth. If the crystal requires more rigorous cleaning, check the user guide that came with your ATR accessory. The guide should list appropriate cleaning solvents for each crystal type.

Set up the analysis

The next step is to set up the OMNIC Paradigm software. After you open the software, you see the dashboard in the main window. The important measurement settings are at the top.

First, make sure the Sampling Accessory readout shows the installed accessory. If it doesn’t, reseat the accessory. Notice that the factory presets for that accessory appear under “Settings.”

Then enter a measurement name, or you can leave the suggested name, which is the exact date and time of the measurement.

Next make sure the Analysis Type is set to Search. This performs a point-by-point comparison of the sample spectrum against FTIR library spectra. The quality of the output depends on the source and quality of the spectra in the selected libraries.

Finally, check the acquisition settings (sample scans, resolution and final format). The settings shown above are all good starting values for this analysis.

Consider Your spectral libraries

All existing spectral libraries are selected automatically by default. Choose Search Setup in the Identify menu to view or change your library selections.

For this demonstration, we are using the free libraries provided with OMNIC Paradigm software.

Choose Cancel to close the Search Setup window.

The library spectra are normally the same quality or higher quality than the sample spectrum. It is also helpful if they are acquired using the same sampling technique (ATR in this case). If your library spectra were acquired using the transmission technique, OMNIC Paradigm software has a correction that can be applied to the sample spectrum to improve the results. You’ll learn more about that later in this article.

There is no need to perform conversions such as final format, resolution or spectral range on the sample data before performing a search—the software does that for you.

Measure and analyze the sample

To start the analysis, click Preview and Measure Sample.

The analysis starts with a background measurement. The only requirement for an ATR background is to make sure the crystal is clean. The background spectrum is used to eliminate any signals in the sample data that are due to the spectrometer, the ATR crystal, or the background environment.

The software shows a preview of the current background spectrum in the spectral pane. The background shape shown below is typical for a diamond crystal.

Click Start Background Measurement.

When the background measurement is completed, its image appears in the results panel and in the spectral pane.

If your sample is a liquid, raise the pressure tower and rotate it out of the way. Use a clean pipette to place a single drop on the crystal. Keep in mind that crystal types vary in size and some may require more sample. Use just enough sample to cover the crystal completely.

Figure 1. Measure a liquid with ATR

The pressure tower should not be used when analyzing a liquid sample

For a solid sample, rotate the knob on the pressure tower counterclockwise to raise the arm. Then place the sample on the crystal and rotate the knob clockwise to lower the arm. Continue to rotate the knob until clicks. For this demonstration, we are measuring a plastic card.

Figure 2. Measure a solid with ATR

Once a sample is in place, click Preview Sample to preview the sample data in the spectral pane. If the peaks in the preview spectrum are very small, use a more concentrated liquid sample. If you are measuring a solid, reposition the sample on the ATR crystal and reapply pressure.

If the spectrum has no sample peaks, check that the sample material absorbs energy in the infrared region of the light spectrum. If you observe extra peaks in the spectrum, make sure the crystal is clean.

What’s in my sample?

Figure 3. Sample and top search result displayed together using the same Y-axis scale

Sample spectrum (red)
Best match (yellow)
Results panel
Stack button

The match values tell you how well each library spectrum matches the unknown sample. The closer this value is to 100, the better the match.

In this example, the top two matches (the same compound from two different libraries) have match values that are above 90, which indicates a good match. The match value for the next spectrum in the list is well below that.

Figure 4. Match values showing a clear best match

If we look at the overlaid spectra in the spectral pane, the positions of the main peaks line up along the X-axis, and they differ only in their peak heights.

Figure 5. Overlaid spectra showing a clear match

Click the Stack button to see the two spectra scaled to fill each Y-axis. Again, the spectra are well matched except for the raised baseline in the sample spectrum’s low frequency region. As a result, we can conclude that the sample is polyethylene and the analysis is complete.

Figure 6. Stacked spectra showing a minor difference in the low frequency region

To get more information about a spectrum in the match list, including the library it came from and its ID number, hover over the spectrum’s grey arrow in the results panel.

Figure 7. Information button for a library spectrum

What if there isn’t a clear (single) match?

Figure 8. Stacked spectra showing several similar matches

How can I improve my analysis results?

If no clear match appears, there are a number of options to consider that may improve your results. (Some setting adjustments will require a new background measurement.)

Figure 9. Search results with changeable measurement settings displayed

You can also acquire more scans (see image above) to reduce spectral noise, which can also affect the results. Then restart the analysis by choosing Identify (menu) > Correlation Search or click the Search button on the toolbar.

If the sample spectrum has a tilted or curved baseline, try applying Automatic Baseline Correction (Process menu) to your sample spectrum and then restart the analysis.

If you need to search against transmission spectra, try using the Advanced ATR Correction (Process menu) and then repeat the analysis. This correction adjusts an ATR spectrum so that it looks more like a transmission spectrum, which can improve the results.

How to specify the spectral region for the analysis

If your sample spectrum has a peak that is so large it is off the Y-axis scale, you may want to exclude that peak from your analysis. Here is an example:

Figure 10. Example of a totally absorbing peak

These “flat topped” peaks are referred to as “totally absorbing” and can contain excessive spectral noise, which affects the analysis results. To exclude a totally absorbing peak, open the search settings, de-select "Use full spectral range", and specify the regions to search that exclude the totally absorbing region.

Figure 11. Using Add Region to exclude a peak from the search

Verify Sample Composition with QCheck

Verify your sample quality with a QCheck analysis. With QCheck, your sample is compared to a known reference, and the results report a correlation value between your sample and the reference, giving you quick verification that your sample meets your specifications.

This guide walks you through an example QCheck analysis.

Prerequisites

This guide assumes that you have already set up your instrument and sampling accessory. For instructions on installing a sampling accessory, see the documentation that came with your instrument.

You will also need at least one spectrum to use as a reference. You can specify any spectrum in your database as the reference spectrum. To use a spectrum from a library, first extract the spectrum from the library so that it is available in the database. For details, see Extract a Spectrum from a Library

Performing a QCheck Analysis

Running a QCheck analysis requires you to set up your analysis and measurement settings, measure the background, measure your sample, and interpret your results. Finally, when your analysis is complete, you can create and save a report.

To verify your sample composition with QCheck

1. Set up the analysis.

Before measuring your sample, review your analysis settings.

a. Navigate to Identify > QCheck Setup.

b. Review the QCheck Setup options.

Setting	Description
High Sensitivity	Select high sensitivity for more exact results between a sample that is very similar to the reference. You may want to de-select high sensitivity if you are measuring samples with some natural variation.
Pass/fail threshold	Set a threshold for pass or failure. Enter an integer between 0 and 100. A correlation value of 100 indicates a perfect match. If you de-select this option, all results will show Pass.
Maximum spectra in QCheck results	Sets the number of results shown in the results panel. For example, if you set the value to 2, only the two best matches will be shown in the results panel.
Prompt for reference	Select to choose a reference during the measurement. De-select to specify one or more reference spectra in advance. If you are planning to compare several samples to the same references, it is convenient to set them in advance to avoid having to keep selecting the same reference every time you measure a sample.
Blank diamond ATR region (2200 - 1955)	Select to exclude data in the region from 2200 wavenumbers to 1955 wavenumbers, where diamond ATR crystals absorb radiation
Blank CO₂ region (2390 - 2240)	Select to exclude data in the region from 2390 wavenumbers to 2240 wavenumbers, where carbon dioxide absorbs radiation.
Use full spectral range	Select to use the full range in the analysis. De-select to specify only a limited range to use for the analysis.

c. To save your settings and return to the dashboard, click Save.

d. On the dashboard, review your measurement settings, and confirm that the listed sampling accessory matches the accessory you are using.

e. From the Analysis Type list, select QCheck.

Once you are satisfied with your measurement and analysis settings, you are ready to measure the background.

2.Measure the background.

Before measuring your sample, you need to have a current measurement of the background.

The background spectrum is used to eliminate any signals in the sample data that are due to the spectrometer, the sampling accessory, or the background environment.

a. Click Preview and Measure Background..

b. Click Start Background Measurement. When the background measurement is complete, the spectrum is added to the results panel.

3. Measure your sample.

a. Load your sample. For instructions on loading a sample, see the documentation that came with your instrument or sampling accessory.

b. Click Preview Sample. The Sample Preview displays a live preview of your sample spectrum. The preview gives you the opportunity to correct any potential issues before measuring the sample.

c. When you are ready to continue, click Start Sample Measurement.

If Prompt for Reference is selected in your analysis settings, the Select Reference Spectrum dialog opens after the measurement is complete.

d. Select one or more reference spectra to use in the analysis and click OK.

Hold Ctrl and click to add a spectrum to your selection.

Hold Shift and click to add a group of spectra to the selection.

4. Interpret your results.

When the measurement and analysis are complete, your results are displayed in the results panel. Hover over the gray arrow for additional details.

5. Create a report

When you are finished with your analysis, create a report to export your results to Microsoft™ Word™, PowerPoint™ or Excel™ or to print or save your results.

a. Navigate to File > Create Report.

b. Give your report a title.

c. Select a format from the Format list and choose the QCheck template. A preview of the report is shown in the right panel.

d. Click Create.

Improving Your Results

If your correlation value is lower than expected, there are several options to consider that may improve your results.

Return to the dashboard and adjust the Resolution settings for your measurement. For example, you can measure the sample at a higher resolution by selecting a smaller value, such as 1 or 2. If the sample peaks are sharper or more numerous, you may get a more accurate analysis result.
Increase the number of scans in your measurement, which may reduce spectral noise.
If the sample spectrum has a tilted or curved baseline, try applying Automatic Baseline Correction to your sample and then restart the analysis from the Identify menu.
Exclude selected regions from the analysis. If your sample spectrum has a peak that is so large it is off the Y-axis scale, you may want to exclude that peak from your analysis. These “flat topped” peaks are referred to as “totally absorbing” and may affect the analysis results. Open QCheck Setup, de-select Use Full Spectral Range, and select ranges that exclude the sample spectrum’s totally absorbing peak. Then, rerun the QCheck analysis.

Extract a Spectrum from a Library

Extract a spectrum from a library to use it as a reference in a QCheck analysis. Spectra extracted from commercial libraries can be used for analysis, but cannot be renamed, tagged, or exported.

To extract a spectrum from a library

1. From the dashboard of the desktop interface of OMNIC Paradigm software, navigate to Identify > Library Manager.

2. Select a compound to extract.

3. Click Extract. A confirmation message states that the spectrum was successfully extracted.

Next Steps

In this guide, you set up and ran a QCheck analysis to verify that your sample matched a known reference within a pre-set threshold.

Next, see Create and Run Your First Workflow for a guided tutorial on using workflows to create routine, repeatable procedures.

Quantify Sample Composition

Find the concentrations of components in your sample using a Quantify analysis. A Quantify analysis uses a previously created quantitative analysis method and reports the concentration of components in the sample or other kind of information, such as peak height or match value.

This guide walks you through setting up and running a Quantify analysis using the desktop interface of OMNIC Paradigm software.

Prerequisites

This guide assumes that you have already set up your instrument and sampling accessory. For instructions on installing a sampling accessory, see the documentation that came with your instrument.

You will also need a valid quantification method saved as a QNT file. The quantitative analysis method must be calibrated using Thermo Scientific TQ Analyst software. See the documentation that came with that software for information on calibrating quantitative analysis methods.

Performing a Quantify Analysis

Running a Quantify analysis requires you to import a QNT file, review your measurement settings, measure the background, and finally measure your sample. When analysis is complete, you can create a report to save or share your results.

To perform a Quantify analysis

1.Set up the analysis.

a. On the dashboard of the desktop interface of OMNIC Paradigm software, confirm that the settings display your sampling accessory.

b. Navigate to Identify > Quantify Setup and browse to the QNT file you would like to use in the analysis.

The file explorer displays additional information about the QNT file that you have selected, such as the method title, method type, and whether the method has been calibrated.

c. To import the method, click Open.

d. In the Analysis type list, select Quantify. A symbol indicates that you have imported a valid QNT file. A red circle with an X [] indicates that a valid method has not been imported.

When selecting a QNT file, the file explorer displays additional information to help you make a selection, including the method title and type and whether the method has been calibrated. Only methods that have been calibrated with TQ Analyst software are valid.

2.Measure the background.

Before measuring your sample, you need to have a current measurement of the background.

The background spectrum is used to eliminate any signals in the sample data that are due to the spectrometer, the sampling accessory, or the background environment.

a. Click Preview and Measure Background..

b. Click Start Background Measurement. When the background measurement is complete, the spectrum is added to the results panel.

3. Measure your sample.

a. Load your sample. For instructions on loading a sample, see the documentation that came with your instrument or sampling accessory.

b. Click Preview Sample. The Sample Preview displays a live preview of your sample spectrum. The preview gives you the opportunity to correct any potential issues before measuring the sample.

c. When you are ready to continue, click Start Sample Measurement.

4. Interpret your results.

When the sample measurement is complete, the Quantify dialog box displays results of the analysis. The results shown depend on the settings in the quantitative analysis method used in the analysis. The results shown below show a measurement only result indicating a passing value.

After clicking OK to close the Quantify dialog box, you can view the analysis results by clicking the information icon [] next to the spectrum in the results panel. In the Spectrum Information dialog, navigate to the History tab and see the Quantify Results section.

5. Create a report

When you are finished with your analysis, create a report to export your results to Microsoft™ Word™, PowerPoint™ or Excel™ or to print or save your results.

a. Navigate to File > Create Report.

b. Give your report a title.

c. Select a format from the Format list and choose the Quantify template. A preview of the report is shown in the right panel.

d. Click Create.

Improving Your Results

If your results are unclear or problematic, there are several options to consider that may improve your data.

Return to the dashboard and adjust the Resolution settings for your measurement. For example, you can measure the sample at a higher resolution by selecting a smaller value, such as 1 or 2. If the sample peaks are sharper or more numerous, you may get a more accurate analysis result.
Increase the number of scans in your measurement, which may reduce spectral noise.
If the sample spectrum has a tilted or curved baseline, try applying Automatic Baseline Correction to your sample and then restart the analysis from the Identify menu.

Next Steps

In this guide, you set up and ran a Quantify analysis.

Next, see Create and Run Your First Workflow for a guided tutorial on using workflows to create routine, repeatable procedures.

Duplicate Measurement

Create a copy of a measurement by using Duplicate as New Measurement. You can duplicate a measurement from its current state or from an earlier step in its history.

Tip Duplicate can be useful as an alternative to Revert. For example, while reverting discards the current data and returns the measurement to an earlier state, with Duplicate, you can copy the measurement from an earlier state and keep your current data.

You might also use Duplicate to save a copy of your measurement at specific stages while you work. For example, you might duplicate your measurement immediately after collecting data to save a copy of the measurement without any further processing, and then work with only one copy of the measurement.

When you duplicate a measurement, not all of the measurement information is copied to the new measurement. Most information is duplicated, but there are some differences:

If the original measurement has tags, the tags will not be copied to the new measurement.
The measurement history is copied, but the history panel in the spectral view does not display any steps prior to the point at which the measurement was duplicated. Open the Measurement Information and view the History tab to review the measurement history.

To duplicate a measurement

From the dashboard

Duplicate from the dashboard to copy the measurement in its current state.

Right-click a measurement in the Measurements pane.
Select Duplicate as New Measurement.
Enter a name for the new measurement or keep the default name.
Click OK.

Duplicate from the measurement history

Duplicate from the Spectral View to copy the measurement from a previous point.

In the Spectral View, select the measurement in the Results pane.
With the measurement selected, navigate to the history panel.

Click any item in the history to preview the spectrum at that point.

Right-click the step at which you want to duplicate the measurement.

Events that did not change the spectrum, such as Add to Library or Create Report, cannot be duplicated as a new measurement.

Select Duplicate as New Measurement.
Enter a name for the new measurement or keep the default name.
Click OK.

Revert Measurement

Use Revert to undo one or more steps when processing or analyzing a measurement. For example, if a processing step degraded the quality of your measurement data, instead of starting over and collecting a new sample measurement, use Revert to return to an earlier step.

When you revert to an earlier state, any actions taken after the step you are reverting to are lost. In other words, there is no way to undo a revert.

If you are in a secure environment, Revert is not available. However, you can instead use the Duplicate tool to create a copy of the measurement as it was at an earlier step. You can then work with the duplicated measurement without having to remeasure your sample. See "Duplicate Measurement" for details.

To revert to an earlier step

In the Spectral View, select your measurement from the results panel.
Click the clock icon to view the history panel.

Click any item in the history to preview the measurement at that stage.

In the list of events, right-click the step you want to revert to.
In the context menu, select Revert.

Click Yes to revert or No to cancel.

View Measurement History

View the measurement history to visually compare a spectrum at different stages of processing and analysis. For example, after applying automatic baseline correction, view the measurement history to quickly see how the spectrum changed.

To view the measurement history

From the Spectral View, navigate to the history panel.
Right-click any item in the history and select Measurement History.

The historical data displays the spectrum at each stage in your processing and analysis.

To create a report of the historical data, open the File menu and select Create Report. Select the Historical Spectrum template, edit your report settings, and click Create.
To exit the measurement history, click Close Measurement History.

Search Setup

Configure settings for correlation search and multi-component search using Search Setup. These settings are used automatically when you select Correlation Search or Multi-component Search from the Identify menu in the desktop interface or from the main menu in the touchscreen interface.

Using the desktop interface, you can also use Search Setup to specify the location of additional libraries on your system. See "Add Library Locations" for details.

Correlation Search Settings

A correlation search compares your measurement to compounds in your libraries and returns the closest matches. The results include the match value for each compound with a value between 0 and 100, with 100 indicating a perfect match.

Setting	Description
Match historical search results	Select to have search results match those of legacy OMNIC applications. The improved algorithm used in OMNIC Paradigm software scales large peaks to reduce the effects of totally absorbing spectra. Select only if you are comparing new measurements with older data collected using legacy OMNIC software.
Maximum spectra in search results	Limit the number of search results. For example, with a maximum of 5, the search will return only the 5 best matches. You can enter a value from 1 to 20.
Show compounds with match values above ____	Set a threshold for which matches are returned by the search. For example, with a value of 60, the correlation search will return only matches with a match value above 60.
Search all libraries	Select to search all of your libraries. Clear the selection to specify only specific libraries to use for the search.
Use full spectral range	Select to use the full spectral range for the search. Clear the selection to specify one or more limited ranges for the search. You can use multiple regions to exclude another region from the search. For example, include a region on either side of a totally absorbing peak to exclude it from the search.

Multi-component search settings

Use multi-component search to identify the components making up your sample.

OMNIC Paradigm multi-component search setup

Setting	Description
Maximum number of search results	Limit the number of composite search results.
Number of components	Set the number of components to return for each composite.
Search all libraries	Select to search all of your libraries. Clear the selection to specify only specific libraries to use for the search.
Use full spectral range	Select to use the full spectral range for the search. Clear the selection to specify one or more limited ranges for the search. You can use multiple regions to exclude another region from the search. For example, include a region on either side of a totally absorbing peak to exclude it from the search.

QCheck Setup

Use QCheck Setup to configure your QCheck analysis. Your saved QCheck settings will be used automatically when you select QCheck as your analysis type before measuring a sample or when you select QCheck from the Identify menu.

For more on using QCheck, see "Verify Sample Composition with QCheck".

Setting	Description
High Sensitivity	Select high sensitivity for more exact results between a sample that is very similar to the reference. You may want to deselect high sensitivity if you are measuring samples with some natural variation.
Pass/fail threshold	Set a threshold for pass or failure. Enter an integer between 0 and 100. A correlation value of 100 indicates a perfect match. If you de-select this option, all results will show Pass.
Maximum spectra in QCheck results	Sets the number of results shown in the results panel. For example, if you set the value to 2, only the two best matches will be shown in the results panel.
Prompt for reference	Select to choose a reference during the measurement. De-select to specify one or more reference spectra in advance. If you are planning to compare several samples to the same references, it is convenient to set them in advance to avoid having to keep selecting the same reference every time you measure a sample. To use a compound from a library as your reference, first extract the compound so that it is available in your database.
Blank diamond ATR region (2200 - 1955)	Select to exclude data in the region from 2200 wavenumbers to 1955 wavenumbers, where diamond ATR crystals absorb radiation.
Blank CO2 region (2390 - 2240)	Select to exclude data in the region from 2390 wavenumbers to 2240 wavenumbers, where carbon dioxide absorbs radiation.
Use full spectral range	Select to use the full range in the analysis. De-select to specify only a limited range to use for the analysis.