Processor applies each processing step as a layer, altering the shape of your spectrum, but leaving the original spectral data untouched. The Processing History records each layer along with its associated parameters, like phase angles, baseline breakpoints and linewidth adjustments. You can review the layers, edit them, and even remove them if necessary, restoring your spectrum to an earlier state.
When you import a processed spectrum, all processing that you have
performed in other software appears in the Processing History as a layer
called External Processing; the details of the External Processing layer
indicate the format from which the processed data was imported. The
External Processing layer is not reversible, and cannot be removed. If
you need to work with the spectrum as it appeared before processing in
other software, import the raw data (fid,
.jdf, .fid) directly.
The following steps reflect best practices for using Chenomx NMR Suite. Please follow these steps in sequence for best results.
Line broadening is a mathematical operation that multiplies your fid by an exponential function before the fid is Fourier transformed. Line broadening effectively increases the linewidth in your spectrum while averaging out instrument noise.
You may not need to apply line broadening to every spectrum. If you choose to use line broadening, apply it after phase correction and baseline correction.
While importing a spectrum, you may choose to have Processor automatically apply line broadening of 0 to 1000 Hz. After importing a spectrum, you can apply line broadening manually. In either case, a Line Broadening layer appears in the Processing History; you can remove the layer if necessary.
| Menu Location | Processing > Line Broadening... |
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How do I apply line broadening to my spectrum?
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Switch to Line Broadening mode.
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Enter a value between 0 and 1000 Hz.
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Click the Accept button.
Tips and Tricks
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If you intend to apply shim correction to your spectrum, you can add line broadening at the same time. See “Fourth Step: Shim Correction” for details.
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To apply line broadening to more than one spectrum at a time, use the “Batch Process” tool.
Related Topics
Phase correction lets you correct phase shifts that may have occurred during data acquisition. Most spectra require some degree of phase correction. Phase should be adjusted before applying baseline correction or shim correction.
You can recognize phase shifts in a spectrum as an asymmetric baseline on either side of peaks and peak clusters in the spectrum. In some cases, you may see whole peaks inverted, pointing down from the baseline instead of up, while extreme phase shifts may also add a periodic oscillation or "rolling" to the baseline.
While importing a spectrum, you may choose to have Processor automatically apply phase correction. After importing a spectrum, you can apply automatic or manual phase correction. In either case, a Phase Correction layer appears in the Processing History; you can remove the layer if necessary.
| Menu Location | Processing > Phase Correction... |
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How do I apply phase correction to my spectrum?
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Switch to Phase Correction mode.
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Automatic: Click the Auto button to have Processor automatically calculate phase angles. Use the Auto Zero-order to only optimize the zero-order phase (the first-oder phase will be set to 0. Review the spectrum after automatic phase correction to ensure that the results are acceptable. If necessary, you can use the manual controls to adjust the phase angles before accepting them.
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Manual: Click and drag the Zero-order Phase and First-order Phase sliders, or type angles in the boxes beside each slider. Use the Fine Tune checkbox to adjust the spectrum more gradually while moving the sliders.
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Click the Accept button to apply your changes, or click the Cancel button to discard them.
Tips and Tricks
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Properly phase all of your spectra, as good phase correction is essential to accurately analyzing your data using Chenomx NMR Suite. Your spectrum is properly phased when its baseline is a smooth curve (or line) across the entire width of the spectrum.
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A good strategy for manual phasing is to pick a peak on either side of your spectrum, adjust the zero-order phase until the baseline on either side of the peak lines up, activate the Use pivot Point checkbox, move the red cursor on the location of that peak, and adjust the first-order phase. The use of a pivot point automatically adjusts the zero-phase upon modifcation of the first-order phase so that the resulting phase at the pivot point location stays constant.
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Only phase your spectrum once. If you do not like the results of phase correction, undo it or remove it using the Processing History, then try again.
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Always phase your spectrum before applying baseline correction or any other processing layers.
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Select one of the phase angle controls, and use the arrow keys to make fine adjustments to the phase angle. The arrow keys adjust in increments of 0.15° normally, and in 0.01° increments when the Fine Tune checkbox is selected.
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In spectra of aqueous samples, the water peak may be distorted relative to the rest of the spectrum; do not use the water peak to determine phase correction. Instead, try to obtain smooth baseline curves to either side of the water peak.
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During a phase correction session, you can clear your current adjustments by clicking the Reset button. After you have accepted your changes, you can clear previous adjustments through the Processing History panel.
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To apply phase correction to more than one spectrum at a time, use the “Batch Process” tool.
Baseline correction removes distortions in the baseline of the spectrum. You can recognize distorted baselines as a net curvature or slant of the regions of your spectrum that contain no signal ("noise" regions). Common forms of baseline distortions include "smiles" (outer regions of the spectrum turned up), "frowns" (outer regions of the spectrum turned down) and "wings" (left and right edges of the spectrum turned up or down, with the middle region flat). If you notice a periodic oscillation or "rolling" of the baseline, check the phase correction of your spectrum before proceeding with baseline correction.
Most spectra require some degree of baseline correction, particularly if you need accurate quantification in Profiler. Apply baseline correction after phase correction, but before shim correction.
While importing a spectrum, you may choose to have Processor automatically apply either simple linear baseline correction (drift correction) or a cubic spline baseline correction based on automatically-determined breakpoints. After importing a spectrum, you can apply automatic or manual baseline correction. In either case, a Baseline Correction layer appears in the Processing History panel; you can remove this layer if necessary.
For more direct control over the baseline correction applied to your spectrum, you can specify breakpoints manually.
| Menu Location | Processing > Baseline Correction... |
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How do I apply baseline correction to my spectrum?
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Switch to Baseline Correction mode.
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Select the type of baseline to be performed from the Automatic BaseLine Correction pull-down menu. Four different types of baseline are available:
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Linear (Drift): Simple drift correction by passing a baseline through the edges of the spectrum.
Or
Chenomx Spline: Cubic-spline-based baseline adjustment.
Or
Whitaker Spline: Whitaker filter followed by cubic interpolation of equally-spaced points.
Or
BXR Spline: BXR algorithm followed by cubic interpolation of equally-spaced points.
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You can control the number of automatically generated breakpoints, and in the case of the Whitaker and BXR splines, the smoothness of the produced baseline by clicking on the engineer wheel icon next to the pull-down menu.
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Last Applied Baseline: Loads the settings and the breakpoint locations from the last applied baseline. The baseline type and settings pulldown menus will be updated to show the parameters associated with that baseline. A new baseline calculated with those settings but for the currently loaded spectrum will be shown.
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From File: Loads the baseline from the processing history of a cnx file, if applicable. A baseline operation must be present in the processing history. If multiple baseline operations are contained in the chosen file (note that technically there should never be more than one baseline correction applied), only the first instance is considered. The baseline type and settings pulldown menus will be updated to show the parameters associated with that baseline. A new baseline calculated with those settings but for the currently loaded spectrum will be shown.
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Manual: Click on the spectrum to set breakpoints for a cubic spline fit. Click and drag existing breakpoints (including the endpoints) to move them. Hold down Control or Command to place breakpoints anywhere in the spectrum, instead of directly on the spectrum line itself. Hold down Shift while clicking on an existing breakpoint to delete it. Hold down Shift while delimiting a box inside the spectrum to delete multiple breakpoints at once.
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Click the Accept button to apply your changes, or click the Cancel button to discard them.
Tips and Tricks
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Only apply baseline correction after you are satisfied with the phase correction in your spectrum.
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Even if you intend to manually adjust baseline correction, you may find it helpful to use the Linear Drift function first. Linear Drift lets Processor first locate the "natural" endpoints of the spectrum, giving you a useful starting point for any more complex baseline fit.
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When setting breakpoints, be aware of the amount of curvature in the area you are trying to fit. You need to set more breakpoints to fit regions with very strong curvature, such as the areas near the water peak, than you would for a relatively flat region.
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To apply baseline correction to more than one spectrum at a time, use the “Batch Process” tool.
Shim correction is a method of reconstructing an ideal spectrum by removing lineshape distortions based on the shape of a reference peak. To successfully apply shim correction to a spectrum, you need to find a single, isolated peak, well-separated from the signals in the rest of the spectrum. If you have added DSS or TSP to your sample, the methyl signal from either of these is an ideal choice.
Shim correction is a linear process, using direct and inverse Fourier transforms, so quantitative relationships among compounds in the spectrum remain intact. Applying shim correction to a spectrum assumes that all lineshapes in the spectrum are affected by systematic distortions in the same way.
Many spectra can benefit from the use of shim correction, but it is not required. It is particularly useful in reducing the effects of varying shimming techniques, or when you need accurate quantification from regions with strong overlap of signals.
You need to apply shim correction manually after you have imported your spectrum. After you have applied shim correction, a Shim Correction layer appears in the Processing History panel; you can remove this layer if necessary.
| Menu Location | Processing > Shim Correction... |
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How do I apply shim correction to my spectrum?
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Switch to Shim Correction mode.
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Zoom in to the highlighted peak in the Spectrum Graph. If it is not properly fit to the peak that you are targeting for shim correction, adjust its fit as necessary.
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If you are using DSS or TSP as your target peak, select the Use DSS/TSP Satellites check box. Otherwise, clear the check box.
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Enter the desired target linewidth.
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Click the Accept button to apply your changes, or click the Cancel button to discard them.
Tips and Tricks
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Only apply shim correction after you are satisfied with the phase correction and baseline correction in your spectrum.
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The target linewidth text box initially contains the native linewidth of your spectrum, based on your CSI definition.
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Choosing a target linewidth larger than the native linewidth in your spectrum is equivalent to applying line broadening. Choosing a value smaller than the native linewidth may provide some resolution enhancement, at the expense of a reduced signal-to-noise ratio and possible spectral artifacts.
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To apply shim correction to more than one spectrum at a time, use the “Batch Process” tool.
Once you've finished processing your spectrum, you should calibrate it so that it can be analyzed in Profiler or used to create compound signatures and simulations in Compound Builder and Spin Simulator.
The chemical shape indicator (CSI) settings form the basis for all
fits performed in Profiler and Compound Builder. The accuracy of these
settings also have a direct impact on the accuracy of profiled spectra
(.cnx), exported data
(.txt), compound files (.xcpd)
and spin simulations (.xss). Calibrate CSI mode lets
you view, define and change these settings for the current
spectrum.
When you import a spectrum, Processor attempts to automatically locate the CSI, and determine its width and height. You can change these automatically determined parameters using Calibrate CSI mode if necessary.
| Menu Location | Tools > Calibrate CSI... |
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How do I modify the CSI settings?
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Switch to Calibrate CSI mode.
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Type the concentration of the CSI in your sample in the Concentration (mM) text entry box under Calibration Peak.
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Select the CSI present in your sample using the drop-down box under Chemical Shape Indicator (CSI). Chenomx NMR Suite includes CSI definitions for DSS, TSP, formate, fumarate and maleate. A custom CSI can also be defined.
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Automatic: Click the Calibrate Automatically button.
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Manual:
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Click and drag the calibration peak to match it with the spectrum line (black).
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Adjust the width by dragging the width control (red triangles to either side of the peak) or typing a number directly into the Width (Hz) text entry box.
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Use the up and down arrow keys to adjust peak height, and the left and right arrow keys to adjust peak position.
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How do I handle samples that have no CSI?
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Switch to Calibrate CSI mode.
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Using the drop-down box under Chemical Shape Indicator (CSI), select None.
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Click and drag the horizontal axis to set a chemical shift reference.
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Set an appropriate line width for the spectrum by typing a value in Hz under Calibration Peak.
Tips and Tricks
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Calibrate the CSI only after you have finished applying all necessary processing layers. If you change a spectrum's processing, you will need to recalibrate its CSI to ensure accurate quantification and generally good fits.
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Processor can only automatically calibrate the CSI if its signal has a chemical shift less than 0 or greater than 10. This includes all of the supported CSIs by default, and some Custom CSIs, as long as they are single peaks.
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If Processor cannot calibrate the CSI automatically when you use DSS or TSP, check the phase correction and baseline correction of your spectrum and try again. If Processor still cannot calibrate the CSI, you need to use the manual tools to locate it instead.
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If you have selected DSS as the CSI, then the indicated center position always reads 0 ppm. If you use any other CSIs, the center position varies based on the current pH value for the spectrum.
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If you would like to adjust the height or width of the calibration peak while keeping its total area constant, check the Preserve Peak Area box.
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When you select None as the CSI, the red calibration peak in the Spectrum Graph disappears. You can only adjust the chemical shift and width settings as described above.
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To make adjustments to the CSI in more than one spectrum at a time, use the “Batch Process” tool.
Related Topics
| Menu Location | File > Send to Profiler |
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When you finish processing a spectrum in Processor, your next task is often to start profiling the spectrum in Profiler. Send to Profiler closes the current spectrum in Processor, and re-opens it in Profiler.
Tips and Tricks
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Any changes that you have made to the spectrum in Processor are retained when you send the spectrum to Profiler, and are visible if you bring the spectrum back into Processor. However, you still need to save the spectrum, either in Processor or Profiler, to permanently save those changes to the spectrum file.