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Preferences

For IR or RAMAN spectrum interpretation or Validation of spectrum and molecule some parameters might be set to take influence on analysis results. However, in most cases automatic selection of parameters will provide good results, because the automatic parameter detection will analyze each spectrum and adjust settings especially for the current spectrum. Of course all parameters can also be adjusted manually.

Parameters are stored in the Interpretation Rule Database!

Any parameters adjusted in this dialog will be stored together with the interpretation rules in the database. Thus modification of those parameters will modify the rule database. You will be prompted to save or discard changes, if you leave the application or switch to another rule database.

This also means, you may have different parameters for IR and RAMAN interpretation depending on the actual analysis mode.

Opening Interpretation Parameter Dialog

To open the interpretation parameter settings dialog , select the Preferences... command from the IR/RAMAN Interpretation menu. The dialog looks like this:

It provides parameters for the following items:

Peak Detection

For spectrum interpretation peaks need to be identified in advance. The parameters in this section are identical to those of the Find Peaks function in the "Mathematics" section of the software. Only identified peaks will be considered in the interpretation process.

  • Automatic
    If the automatic peak detection is enabled, various algorithms will find a suitable set of peaks for spectrum interpretation. Otherwise you may adjust the parameters below for peak detection.

  • Perform Auto-Baseline Correction
    If enabled, the baseline of the spectrum is automatically corrected to obtain more precise peak detection results. No particular parameters can be set here.

  • Peak Height
    This parameter controls the minimum absolute or relative peak height. Only signals with intensities beyond this value will be identified as peaks.

  • Use Absolute Peak Height
    This parameter controls the peak height detection mechanism, which is one of the following:

    • Absolute Peak Height (checked)
      The absolute peak height is determined from zero to the maximum peak intensity.

    • Relative Peak Height (unchecked)
      The relative peak height is determined from the imaginary baseline of the peak to the maximum peak intensity.

  • Peak Width
    This parameter controls the minimum peak width. Only signals with at least this minimum peak width denoted in wavenumber units will be identified.

An existing peak table overrides peak detection ...

If you are not satisfied with results derived from automatic peak detection or peak detection with height and width parameter, you can provide your own list of peaks for analysis. In this case, please find peaks yourself using the "Find Peaks" function from mathematics section before starting IR/Raman Interpretation.

An existing peak table overrides peak detection of the interpretation algorithm. In this case the existing peak table is considered for analysis.

Band Detection Tolerance

Interpretation rules represent the expected positions of bands in a spectrum. However because of physical or solvent effects sometimes bands are shifted and will not appear at original position. This might cause incorrect identification in some cases. If signal shifting is observed in the spectrum, you can correct for it by setting a particular deviation in wavenumber units. Bands will then be identified in their original expected range and also in an interval around.

  • Deviation
    This parameter controls the size of the tolerance interval for each IR or RAMAN band.

Intensity Threshold

The strength of a signal in the spectrum strongly depends on chemical environment and physical properties of the substance. In interpretation rules, expected signal strengths are stored being compared now to the current sample spectrum signal intensities. With intensity threshold settings below the analyst encodes the strength of signals in the analyzed spectrum from his personal feeling using the following categories:

  • Very weak

  • Weak

  • Medium

  • Strong

  • Very strong

The numbers behind these qualitative intensity categories represent the expected intensity ranges in absorbance units where very weak, weak, medium, strong and very strong signals are expected. Peaks appearing within one of the categories will be identified accordingly. Intensity values of these categories span from 0 to 1.5 absorbance units. Categories are allowed to overlap.

Normalization of the spectrum.

The intensity of the highest detected signal in the measured spectrum is automatically scaled to 1.5 absorbance units. The lowest intensity (usually the base line) in the spectrum is set to 0. All intensities in between will be scaled accordingly. This procedure is called normalization.

 

By default and as long as the Automatic checkbox is enabled, these intensity categories will be determined automatically by some algorithms in the software.

Interactive Parameter Settings

Step by step optimization of parameters and improvement of results is also possible and you can see the result changing directly without repeating all steps of the analysis.

  1. Adjust parameters for spectrum interpretation in the dialog.

  2. Click the Apply button for recalculation and update of interpretation results.