As I'm a newcomer to metabolomic data processing from the very raw data, I was wondering how to combine pos and neg mode data together, especially in the condition of acquiring from separate two-year samples.
I have two separate data acquired from two years in the same untargeted LC/MS method but different samples involved, and I want to combine them. Things turned difficult for me when I found there are some metabolites detected in different mode between the two years and not consistent in the two modes. For example, compound A was detected in year 1's pos mode but in year 2's neg mode , not in pos mode.
I'm not sure whether I can combine such compounds directly into one column and then normalize.
Junyu Wang: Please do not combine data obtained using TWO DIFFERENT LC-MS METHODS, from analysis separated by two years (or any time frame). That is unscientific and invalid.
An LC-MS method operated in positive mode generates data that is different than in negative mode. The data is orthogonal, not additive.
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Article MSCombine: A tool for merging untargeted metabolomic data fr...
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