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Topic: Difficulties in blank subtraction (Read 169 times) previous topic - next topic

Difficulties in blank subtraction

While analyzing the LCMS data for untargeted metabolomics, I wanted to do blank subtraction. But when I separately analyze the blank samples and control and then do blank subtraction, it is not working because of the small changes in m/z coming in both the analysis. And when I analyze blank samples together with samples in the same pipeline, I am getting false detections of peaks in the sample.
So how can we efficiently do blank subtraction for untargeted metabolomics?

 

Re: Difficulties in blank subtraction

Reply #1
Not tried suggestion if you are using XCMS:
* have the blanks in their own group for the grouping step
* Use the subset parameter in PeakGroupsParam to exclude the blanks from retention time correction models
* ...
* remove peaks only found in blanks
* blank correction
Blog: stanstrup.github.io