Quantify compounds based on their SIC areas

[Anoukje]

I would like to quantitate compounds based on selected ions and not based on the total ion count. But I cannot figure out how to achieve this.

I have created a template which includes my compounds, and I specified multiple quantifier/qualifier pairs for each of my compounds. I clicked the include button to include them in the report. Then I generate a report I see a blob table with Area (pixel) but I assume this is based on the total ion count. And in the template report I do not see any areas.

What am I doing wrong? And what do I have to change in what I am doing to obtain extracted ion peak areas?

Thanks

[qtao]

For raw responses, Configure > Blob Table > Quantifier/Qualifier Ions and add Volume properties to Blob Table. See here for all calculated response properties:
https://www.gcimage.com/gcxgc/usersguid ... onFeatures

For calibration with quantifier ions, follow the instructions here:
https://www.gcimage.com/gcxgc/usersguid ... l#quantIon

Calibrated results are reported as Amount in Blob Table.

Also, note that the term differences mentioned here
https://www.gcimage.com/forum/viewtopic.php?f=5&t=38

[Anoukje]

Thank you for your help! I have another question.

I have successfully created a template and I am able to determine the blob volume based on a quantifier ion.

I have one question about the blob detection: It seems that it is usually done using the total-ion signal. I am a bit concerned that some compound blobs coeluting with much larger matrix blobs are correctly recognized.

Is there perhaps a way to perform blob detection using (multiple) selected ion signals?

Thanks

[qtao]

If the target ions are known, you may View > SIC > draw a rectangle around the targeted retention region > Edit > Local Blob Detection:
https://www.gcimage.com/gcxgc/usersguid ... bDetection

If a single blob is at concern, Local Blob Detection and editing can be performed on the selected blob too:
https://www.gcimage.com/gcxgc/usersguid ... tBlobsMode

For comprehensive ion peak detection, you may use Processing > Extract Ion Peaks to Areas:
https://www.gcimage.com/gcxgc/usersguid ... kDetection

Note that the results of ion peak detection are limited for quantitative analysis. Also, the results are sensitive to noise and filter settings. The Spectral Filter settings allows filtering out small intensities and targeting specific ion ranges, which can be very useful.