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)“.


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


The detected peaks are marked with an inverted triangle.


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


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).


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


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


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


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




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