I'm working with two cells lines, the same origin but different metabolic activity.
Dear Pedro,
Depends on the goal, I think. But if this would be a poll, I vote for cell number.
Dear Pedro,
Use of cell number for normalization of data would be problematic when cells grow in clumps. In such a situation, it would be difficult to count them accurately. Also, the method used to determine cell number such as trypsinization, would introduce artifacts into the metabolomic data.
Protein quantification may show large variations. Also, at low cell number, the sensitivity might reduce.
For normalization of metabolomic data, you should go for DNA concentration. The advantages are as follows.
a) consistency.
b) DNA samples can be collected from the same dish as the metabolites. You may isolate and quantify DNA from metabolomics samples which are collected by cell scraping in the extraction solvent.
c) DNA concentration is almost proportional to cell number.
For more information, you may want to refer to the paper attached below.
https://doi.org/10.1021/ac401559v
Best.
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