PCA – GC/MS data

OpenChrom offers rudimental functionalities to run a principal component analysis (PCA) on chromatographic/mass spectrometric data. This is especially helpful when analyzing data from analytical pyrolysis (Py-GC/MS).

Open a GC/MS file via the “Chromatogram File Explorer (MSD)“.

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Then detect and integrate peaks. You could alternatively use deconvolution techniques like AMDIS. In this case, we use the “First Derivative” peak detector.

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The detected peaks are marked with an inverted triangle.

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Please apply a peak integrator then, in this case the “Integrator Trapezoid“.

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Save the chromatogram in the OpenChrom *.ocb format. Please repeat this step for all chromatograms you’d like to process with PCA. This is a tedious task, that’s why OpenChrom offers a batch process to do this automatically.

OpenChrom Batch Process: https://wiki.openchrom.net/index.php/Batch_Processing

After doing a peak detection and integration on all your chromatograms, you’re prepared to run the PCA analysis. Please open the “PCA Evaluation” editor (Menu > Chromatogram > Processors > PCA Evaluation).

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Please select the number of principle components and the time window to bin the peaks.

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The next step is to select the chromatogram files you’ve just created.

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Now just press the button “Run PCA“. The PC1 vs. PC2 is displayed by default in the “Score Plot” tab item.

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The binned peaks are listed in the “Data Table” tab item.

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