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?
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