I'm analyzing a dataset generated with LC-MS from cells that were fed $\ce{^13C}$-Glucose. There are 3 groups in total each with a different media conditions. My goal is to identify differences between these groups. When I look at the distribution of labeling (MDV) I don't see any difference across the different metabolites but when I look at the relative abundance I see large differences. How can I interpret this, when the labeling patterns are the same but the relative abundance is significantly different? Thanks.

  • $\begingroup$ We need more information to provide better answers. For example, what types of medium and what types of cells? How many sources of carbon were there in each aside form glucose? Were those carbon sources labeled? Also, what is MDV? $\endgroup$ – Curt F. Apr 2 '19 at 18:59
  • $\begingroup$ E.g., one potential explanation of the data is that in different media, cells have different levels of metabolites. And in none of the media did they use any of the labeled glucose you fed them. $\endgroup$ – Curt F. Apr 2 '19 at 19:00

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