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Topic: Merging different LCMS runs that have different QCs (Read 236 times) previous topic - next topic

Merging different LCMS runs that have different QCs

Hi there,

I am new to metabolomics and I have been using MS dial for the past months now.
I initially only had one run, then decided to run more samples in a separate LCMS run. Now I am attempting to merge and batch correct run 1 and run 2 in R having QCs that include different samples.

Is there a way to align samples to two different QC files in MS dial? Or is there a way to merge abf QC files from the two runs somehow?

Otherwise, does anyone have any suggestions for how I could merge these runs and batch correct them using e.g R packages?

So far I have tried:
1) running them separately on MS dial, aligning them to the QC used for each run, then importing into R, processing them separately, then merging on common features between runs, and batch correct (pmp package and QCRSC function).
2) Running both runs in MS dial, aligning to the QC from the second run, then importing into R and batch correct as above.

As you can imagine, because of the different QCs none of these have worked so far, on my pca plot, samples in each run are clustering with their run QCs in separate clusters.

Any suggestions you might have would be greatly appreciated! Thank you.