When creating a compound, adjust fit style by using the “Compound Details” dialog. By default all compounds use the peak-based fit style, which fit the exact areas and lineshapes of individual compounds while profiling an NMR spectrum. These peak-based compounds can be used to quickly and easily deconvolve (break down) overlapping regions in a spectrum and generate accurate profiled concentration values.
Sometimes, however, you may prefer to assign the region-based fit style to a newly created compound. Region-based compounds will automatically fit themselves to a spectrum while profiling, ignoring the shape of their own individual peaks and instead fitting the entire region around each of their clusters. This fit style is ideal for compounds whose individual peak shapes are not modelled accurately enough to provide a good fit.
Using the region-based fit style allows you to create new compounds very quickly and without worrying too much about how they are affected by changes to pH, magnet frequency, and other acquisition variables. But it has disadvantages, too.
For example, region-based compounds cannot overlap with other region-based compounds. Also, they are not associated with a sample concentration, so Profiler will never report a concentration value for them. Instead, Profiler calculates the area of a region-based compound by summing up the areas of your spectrum within each of the compound's cluster regions. This total area is proportional to the real underlying concentration of the compound, so it can still be used for various kinds of analysis.
Region-based compounds can also used for simple compound identification.
How to change the fit style of a compound
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Click Compound Details.
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Choose region-based fits or peak-based fits on the General tab.
Tips and Tricks
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You don't have to worry too much about the exact shape of each cluster in your region-based compounds. Just make sure that the peaks are far enough apart to capture each cluster's entire area.
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The “Generate Cluster for Region” and “iv) Optimize Selected Peak Shapes” features provide a quick and easy way to generate and fit cluster shapes for your region-based compounds.
Related Topics
Importing lets you use an existing spin simulation
(.xss) or legacy compound album
(.cca) to guide the construction of
a new compound signature.
| Menu Location | File > Import Simulation... |
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How to import a spin simulation or compound album
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Open the Import Compound dialog.
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Locate the folder containing the simulation or album file that you would like to import.
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Select the simulation or album file and click Open.
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Choose a calibration method.
If you are calibrating to a spectrum file (
.cnx), click the Browse button (...) and locate the spectrum file you would like to use.The spectrum that you choose is overlaid in the Spectrum View.
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Click OK.
Tips and Tricks
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Calibrate a signature to a real spectrum for accurate results when using the signature for an analysis. This will ensure that the simulation is run at the same magnet frequency as the calibration spectrum when it is imported.
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Calibrating to the Default Environment instead of a spectrum will run the simulation at 800 MHz while importing it. It will have a pH of 7.00, and CSI settings corresponding to DSS at 0.500 mM (height of 1 si, width of 1 sw).
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The magnet frequency and spectrum pH for the current spectrum overlay appear in the status bar at the bottom of the Compound Builder window. If there is no spectrum overlay, the displayed values correspond to the default environment.
Related Topics
You may wish to build a compound signature that will let you verify that the compound is present in a spectrum, without necessarily providing the full range of flexibility that a chemically accurate signature affords. You can quickly create these limited-use signatures using automatically generated clusters. Generated clusters lack the chemical accuracy of signatures that are backed by spin simulations, but provide a quick model of the lineshape of a compound under specific conditions.
| Menu Location | Tools > Generate Cluster for Region |
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How do I generate a cluster to match a region of the spectrum?
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Select the region of the spectrum that you would like to match with a generated cluster.
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Click Generate Cluster for Region.
Tips and Tricks
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Unlike Spin Simulated clusters, generated clusters have no formal theoretical basis. They simply contain a number of Lorentzian peaks that approximate the overall shape of part of the overlaid source spectrum. These generated peaks will not let you accurately account for significant changes in the spectrum based on magnet frequency, pH or other systematic variations.
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You should only expect a compound with generated clusters to fit accurately if you are profiling spectra that have been acquired under conditions very similar to the compound's source spectrum. This restriction makes compounds with generated clusters ideal candidates for the region-based fit style (see “Compound Fit Style”.)
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Generated clusters are already optimized. Using the Optimize Selected Peak Shapes feature on them will not give any better results.
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When you generate a cluster, Compound Builder will only use up to 100 peaks to match the selected region. If the region you are trying to match cannot be accurately modeled using 100 peaks, try selecting a smaller region, adding more peaks manually, or simulating the compound in Spin Simulator and importing the simulation.
| Menu Location | File > New Compound... |
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The New Compound feature creates a new compound file that contains the size, position, and shape of the clusters and peaks that make up a single compound's NMR signature. The new compound starts with default “Compound Details”, including a magnet frequency of 800 MHz and a sample concentration of 5 mM.
Tips and Tricks
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When you open or create a compound, it does not have a spectrum overlay by default. Add a spectrum overlay before you begin building the compound's signature.
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You can overlay one spectrum at a time in Compound Builder.
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You need to save the new compound (as an
.xcpdfile) to retain changes that you have made. -
Spectrum overlays are not retained when a compound is saved.
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If the compound that you've created is not always going to be a good fit when it is used to profile real NMR signatures, you might want to switch your compound's Fit Style from from peak-based to region-based (see “Compound Fit Style”).
Related Topics
Clusters have ID numbers that are normally not visible to the user. But if you create a new versions of an existing compound or multiple compound signatures for the same compound (for example, if you are going to make a pH sensitive compound) then it is important to make sure that the cluster ID for each cluster is the same in every compound signature.
| Menu Location | Tools > Manage Cluster IDs... |
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How do I change the cluster IDs in a signature?
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On the Tools menu, click Manage Cluster IDs....
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Click and drag the clusters in the list to change their order.
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Select a cluster in the list and use the green up and down arrows to change the position of the cluster in the list.
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Click OK.
Tips and Tricks
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Cluster IDs are used by the pH sensitivities dialog to determine which clusters should be considered as corresponding to the same signal across all of your selected data points. Make sure that the clusters appear in the proper order in each of your data points before applying pH sensitivities.
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A cluster that appears upfield from another cluster at one pH may appear downfield from the same cluster at a different pH. Consider overlaying all of your data point spectra (
.cnx) together in Processor or Profiler to more easily see the behavior of clusters across the full pH range. -
If you have already used a compound to profile spectra, replacing that compound in your library with a new version that has different cluster IDs will make your existing fits of that compound invalid.
Related Topics
You can make compound signatures that you create in Compound Builder sensitive to the pH of the spectrum that you are profiling. When used in Profiler, the clusters of pH sensitive compounds will automatically adapt their centers and transform windows based on the profiled spectrum's pH, ensuring that they start closer to their correct position and simplifying compound identification in complex regions of the spectrum.
| Menu Location | Tools > pH Sensitivities... |
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How do I make a compound signature pH sensitive?
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Make sure that you have a set of compound signatures (
.xcpdfiles) available touse as data points when calculating pH curves. You will create these signatures using Compound Builder. They must satisfy the following criteria:-
All of the compound signatures must have the same number of clusters, in the same order.
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Each signature must have its valid pH set to the pH value from the signature's originating sample, via the Compound Details dialog. Use a single value instead of a range.
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Select a signature to use as a 'master' signature. This signature will become the pH sensitive compound signature, and therefore should be very well fit to its associated spectrum file (
.cnx). The remaining signatures must have accurate cluster locations, but otherwise do not need to be perfectly fit to their associated spectra. -
Open the master signature file (
.xcpd) in Compound Builder, and overlay its associated spectrum file (.cnx). -
On the Tools menu, click pH Sensitivities....
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Click Load Data Points... and choose the your compound signatures.
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Click Optimize Lines.
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Review the resulting pH curves for each cluster by clicking the various tabs at the top of the pH Sensitivities dialog.
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Click Accept to apply the automatically generated cluster center and transform window expressions to the clusters in your master signature, and set the valid pH of the master signature to the range defined by the pH values of your individual data points.
Tips and Tricks
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Clusters that appear green in the Cluster Navigator are pH sensitive, meaning that their heights, positions, and widths all change with spectrum pH. If a compound signatures's cluster centers and transforms were set with the pH Sensitivities dialog, all of its clusters should be green.
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If you manually adjust any cluster after applying pH sensitivities to the compound, some or all of its automatically generated pH sensitivity expressions will be replaced with constant values. These clusters are no longer entirely pH sensitive, and will not appear green in the Cluster Navigator.
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If the clusters in your set of signatures appear in different orders in some of the files, use Manage Cluster IDs to rearrange the cluster IDs in the signatures so that they match.
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If the signatures you use as data points are at a different spectrometer frequency than your master signature, you may need to apply an offset to ensure accurate pH curves. Click Lock to Current Clusters in the pH Sensitivities dialog to calculate the offset before reviewing and accepting the pH curves.