FID Chromatogram - Peak Area

[pauljerry9]

Hello,

Still being a novice to the GC Image software, how can the peak area for compounds in an FID chromatogram be determined? As blobs/graphics of different sizes are drawn over the same compound peak, only the 'Peak Value' remains the same. How would this be converted to the actual peak area, as the peak value represents pixels?

[qtao]

The most common way is through Blobs. Area graphics are for manual integration.

Also, in Blob Table, Area is the number of data points of the peak. Volume is the total response of the peak. See here for the terms

[pauljerry9]

Sometimes when blob detection is done, it is not necessary that all blobs are detected. Then manually we would have to draw regions around the blob through blob mode (using oval, rectangular or free hand shapes). But this is the confusing part: if 'volume' represents the total response of the blob itself. How does the volume value change irrespective of different blob regions drawn over the same blob? The attached pictures have different blob regions enveloping the same blob and the volume changing in both cases. Why is the volume value not the same in both the cases?

[qtao]

When a blob is manually drawn, the software takes the exact region drawn as the integration window for the blob. So, the bigger the region was drawn, the larger the volume. With recent versions, there is a Detect/Edit Blob mode, which allows you to double click a peak location to perform a local blob detection.



Also, you may want to try Processing > Interactive Blob Detection to tune the settings, which may avoid manually drawing blobs. Here is a demo:
https://www.gcimage.com/docs/quick-star ... emo-2.html

[pauljerry9]

So basically, even after a blob region fully covers a blob and gives a certain volume, the value for volume keeps on increasing as blog region size is increased. Does this not point towards the fact that the volume value is user dependent (on the blob region defined) and the exact response (volume) of a blob cannot be accurately determined?

Shouldn't the total response/volume of a blob be a fixed value irrespective of the integration window?

[qtao]

If you let the software perform blob detection automatically, the blob boundary is automatically determined, and is reproducible if the same settings are used on the same data.

If you choose to draw blob boundary manually (aka, manual integration), the software takes it as-is.

If you only want to choose the peak location manually, but let the software determine the blob boundary automatically, use the Detect/Edit Blobs mode's double click operation.

WRT detecting the "real" boundary or response of a blob, it depends on the baseline, peak shape, and the peak detection algorithms, which is why all chromatography software have user-specified detection settings and allow manual integration.

[pauljerry9]

Is there a way to get the total area of all the peaks in a chromatogram directly without summing up from individual peaks after undergoing a peak detection? As I do not want to miss out any peak area which would not have been identified for by automatic peak detection and manual peak detection takes a significant time when analyzing a significant number of peaks present in a sample.

[qtao]

Blob Set Table has a Residual group that reports aggregated values for all peaks that are not part of user-defined groups. For total responses, Go to View > Blob Set Table menu to open the table, and check the Volume (Total) column.