Carbon atom ball diagrams in metabolomics experiments
Represent carbon atoms labeled in metabolic pathways
If you've ever wondered how to create those metabolic maps that show the number of atoms labeled by a carbon isotope (e.g., C-13), we'll show you how. But before you begin, you need to know a few important details.
What is the Exchange Rate?
The Exchange Rate is a parameter that indicates the number of atoms exchanged between the uniformly carbon-labeled molecule to which your cells were initially exposed and the remaining fully or partially labeled metabolites detected in the Isotopic Profiling experiment, also called Isotopic Trace Analysis.
In articles, the Average Exchange Rate is often represented in diagrams with filled or empty balls, with the filled balls representing the average number of labeled carbon atoms in the metabolite in question and the empty balls representing the average number of unlabeled carbon atoms for the same metabolite.
What is an isotopologue?
If you did not receive information about the Exchange Rate, you probably received at least information about the percentage of labeling for each isotope, or "Exchange Rate [%]: i"; where i is the number of carbon atoms labeled in the stated ratio for each species or form of the metabolite or isotope detected.
An isotope is therefore each of the forms of a metabolite with a different C-labeling, with respect to the total number of carbon atoms. They are recognized as M+0 (unlabeled metabolite) and M+i, where i is the cumulative value of labeled carbon atoms in the molecule, expressed as a percentage. That is, the percentage M+1 represents the percentage of metabolite X with one labeled carbon atom, M+2 represents that of two labeled carbon atoms, and so on.
How to calculate the average exchange rate if it was not added to the list of metabolites obtained?
The Exchange Rate is obtained as a weighted average, once the percentage of isotopes is known, as follows:
=((0*"M+0")+(1*"M+1")+(2*"M+2")+(3*"M+3"))/100
where "M+i" is the "Exchange Rate [%]: i"
The result is rounded to the nearest unit (no decimals are used, since the drawing of each ball is either full or empty).
How to create connections between metabolites on the map 🗺️
Go to KEGG PATHWAY Database and search for the pathways of the selected metabolite. If you don't find any of the other metabolites in that primary pathway, continue searching consecutive pathways, from the widest to the narrowest.
Once you find a metabolite, search for the next one in the pathway, opening the pathways linked to the previous metabolite if necessary.
⛑️ Limitations of the Carbon-13 ball diagram ❌
Occasionally, a metabolite with fewer than 0.5 labeled carbon atoms has been found, so its nearest unit is 0, and metabolites with 0 labeled carbon atoms are usually not represented.
Therefore, when representing the results in the figures in your article, you will sometimes need to combine carbon balls plots (for metabolites with an average of more than 0.5 labeled carbon atoms) with bar charts or box plots (for detected metabolites with an average of less than 0.5 labeled carbon atoms).
J.
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