Peak detection modes
OpenChrom offers several methods to detect peaks.
- Automated peak detection
- Manual peak detection
- Peak detection via AMDIS deconvolution
Automated peak detection
3. You can adjust some settings for the peak detector (menu bar>Window>Preferences>Chromatography/Spectrometry>Peak detector>First derivative peak detector). E.g. if your peaks consist of a very high number of scans you may need to increase the "Moving average window size", because the detector performs smoothing before detection. You can also adjust the minimum S/N here to avoid the minor signals to be detected as peaks. The integration is separated from peak detection and the settings for the integrator allow further adjustments.
Manual peak detection
Peak detection via AMDIS deconvolution
There are two possibilities to utilize the AMDIS deconvolution and peak detection capabilities:
1. Automated triggering of AMDIS from within OpenChrom.
2. Extraction of peak detection results from previously generated AMDIS ELU files
Note, that the approach 1. currently only works with older AMDIS versions (e.g. the version "Aug 13 2008" contained in the NIST demo),
but in order to perform a batchwise processing there is a workaround, which is described below.
1. Before using the AMDIS connector to detect peaks via AMDIS you need to set the path to the "AMDIS32$.exe" of your AMDIS application (A) and to the the folder where the AMDIS ELU files are stored by AMDIS (B). Furthermore, it may be advisable to set a Signal-to-Noise (S/N) threshold (C), particularly if you use the old AMDIS versions which lack the Filter-settings (e.g. for S/N). Note, that the algorithm for S/N calculation within AMDIS differs from the S/N algorithm "Dyson", which is set by default within OpenChrom and used for the threshold. Therefore the S/N values given by AMDIS differ (i.e. are much higher) from those calculated by OpenChrom. The "Preferences" dialog can be accessed via the menu bar (Window>Preferences).
3. All peaks detected and above the S/N (D) threshold set in the preferences are listed in the peak list. Note, that the peaks still need to be integrated. The peak areas calculated by AMDIS are not extracted from the ELU files. In OpenChrom peak detection and integration are kept as separate processes.