| Menu Location | Processing > Region Deletion... |
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In many spectra of biofluids or cell extracts, the solvent peak (typically water) may be very large. In some cases, it is so large that seeing any other peaks while completely zoomed out is difficult. Region deletion is a simple processing layer that masks data points within a specified frequency range. It is designed to prevent the height of the solvent peak from dominating the vertical range of the spectrum display.
Using region deletion to remove the solvent peak is optional. Ensure that no peaks of interest occur close to the solvent peak before you apply region deletion, as such peaks may be masked by the region deletion layer.
While importing a spectrum from an aqueous sample, you may choose to have Processor automatically apply region deletion to the water peak. A Region Deletion layer appears in the Processing History panel; you can remove this layer if necessary.
How do I apply region deletion to my spectrum?
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Switch to Region Deletion mode.
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Enter the desired frequency range.
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Interact with the highlighted region in the graph to define the frequency range. You can drag the region by clicking inside of it, and expand or contract it by clicking on either edge of the region.
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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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Region deletion works best if it is applied after phase correction.
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Region deletion is not only useful for removing the solvent peak from your spectrum; it can be used to remove other peaks and clusters as well.
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To apply region deletion to more than one spectrum at a time, use the “Batch Process” tool.
| Menu Location | Processing > Reverse Spectrum |
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Reverse spectrum reverses the order of the data points in your spectrum in the frequency domain, effectively flipping the spectrum horizontally.
You only need to use reverse spectrum with certain types of spectra from Bruker spectrometers. If you have trouble locating the CSI peak (when you have a CSI in the sample), or even making any sense of your spectrum after importing it, you may need to reverse the spectrum.
While importing a spectrum, you may choose to have Processor reverse the spectrum automatically. After importing a spectrum, you can reverse the spectrum manually. In either case, a Reverse Spectrum layer appears in the Processing History panel; you can remove this layer if necessary.
Tips and Tricks
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If you notice that a spectrum from a particular spectrometer must be reversed, it is likely that all spectra from that instrument, especially those acquired with the same parameters, need to be reversed.
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If it is necessary, apply Reverse Spectrum first, as other processing layers may be difficult to apply correctly when the spectrum is backwards.
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To apply Reverse Spectrum to more than one spectrum at a time, use the “Batch Process” tool.
If you have spectra that were acquired with a CSI other than the five supported by Chenomx NMR Suite (DSS, TSP, formate, fumarate and maleate), you can define a custom CSI for use with Chenomx NMR Suite.
| Menu Location | Tools > Define Custom CSI... |
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How do I define the custom CSI?
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Open a spectrum of a sample that contains both your custom CSI and a Chenomx-supported CSI (DSS, TSP, formate, fumarate and maleate). This spectrum should already be calibrated using its Chenomx-supported CSI.
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Open the Define Custom CSI dialog.
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Adjust the custom CSI peak (red) to match the appropriate peak in the calibrated spectrum.
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Enter a name for your custom CSI.
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Click Accept.
Tips and Tricks
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You may only have one custom CSI defined at a time.
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The spectrum that you use to define the custom CSI should also contain a Chenomx-supported CSI (DSS, TSP, formate, fumarate and maleate). This reference spectrum must be calibrated using the Chenomx CSI before you use it to define the custom CSI.
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Once you have defined the custom CSI, you may not delete it. You can only edit its parameters.
The signal position and shape of compounds in aqueous solution can be very sensitive to pH. The accuracy of the pH that you set for a spectrum will have an impact on the quality and accuracy of fits that you perform on that spectrum in Profiler, Compound Builder or Spin Simulator. Calibrate pH mode lets you calculate or set the pH for the current spectrum.
If your sample contains any combination of creatinine, imidazole or DFTMP, Processor may be able to calculate the spectrum pH. If your sample does not contain these compounds, or if you prefer to use an externally measured pH, you may enter a pH value manually.
While importing a spectrum, Processor attempts to calculate the pH of the sample automatically using the frequencies of the imidazole, creatinine and DFTMP peaks. You can refine or change this calculated pH in Calibrate pH mode. If Processor cannot calculate the pH of your sample, you need to set it manually.
Whether you use automatic or manual methods to set the spectrum pH, you can also set an uncertainty for the pH value. The pH uncertainty helps to determine the size of the transform windows for pH-sensitive compound signatures in Profiler.
The predicted frequencies of the imidazole, creatinine and DFTMP peaks, based on the pH value that you currently have set, appear in the Spectrum Graph as a pair of blue (imidazole) and purple lines (histidine) at low frequencies (high ppm value)s, a pair of green lines(creatinine) at mid frequency, and a single orange line (DFTMP) at high frequency. You can use these lines during manual pH determination by aligning them with the corresponding peaks for creatinine, imidazole, histidine and DFTMP, when these compounds are present.
| Menu Location | Tools > Calibrate pH... |
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How do I set the spectrum pH?
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Switch to Calibrate pH mode.
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Set the desired pH using any one of the following methods:
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Click the Find Automatically button.
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Click and drag the pH slider bar to set the determined frequencies of imidazole, creatinine and DFTMP as close as possible to the actual frequencies of the peaks in the spectrum (if known). The resulting pH appears in the text box beside the slider bar.
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Select the pH slider control, and use the arrow keys to make fine adjustments to the pH (with the Fine Tune checkbox selected).
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Type the desired numeric pH into the text entry box to the right of the slider bar.
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Tips and Tricks
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Setting an accurate spectrum pH helps Profiler choose more accurate starting positions and transform windows for clusters.
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Once you have made coarse adjustments to the pH, you can zoom in to particular indicator lines to make finer adjustments. Select the Fine Tune check box to let you make more detailed adjustments over a smaller pH range.
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When aligning the displayed lines to peaks in your spectrum, it is not necessary to have the lines match the peak positions precisely. A common situation is to arrive at two pH values separated by 0.01, one of which places the indicator lines on one side of the peak, while the other places them on the other side of the peak. In such cases, you may use either value.
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If you have selected a CSI other than DSS, then changing the pH changes the position of the horizontal axis, since the frequencies of the TSP and formate peaks are pH-sensitive.
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To make adjustments to the pH in more than one spectrum at a time, use the “Batch Process” tool.
| Menu Location | File > Export > JCAMP-DX... |
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Processor has the ability to export your spectrum into the JCAMP-DX file format, which can be imported into most NMR spectral processing software packages.
The effect of processing layers that you have applied to your spectrum will be retained in the exported JCAMP-DX file, but other analysis data such as compound fits and concentration will not.
Several spectra can also be exported all at once using Batch Export JCAMP from the Tools menu.