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XCMS / Inconsistent integration borders in EICs
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This is my current best method, which I still want to improve. *Edit: added the Profparam*
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Right now I have a dataset of 15 runs I wish to analyse, there are three runs of the base sample, two runs of each of 4 concentrations of an added internal standard mixture, and four single runs of a concentration variation of the sample itself. My hope is to do quantification on the majority of analytes in the sample.
My issue is this: I'm seeing inconsistent integration borders in the EICs, and it results in outlier values in the integration. I've attached two images to show this phenomenon. These are not important analytes, but on other data it may happen on the main analytes. YES my data is noisy, but xcms mostly manages to find good peak borders, it just messes up a few. The issue is that I need this to work reliably, without me having to double check every peak. I'm confused where this behaviour could come from.
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