Question on the parameter "correct_NA_tracer"

[liaochen1988]

I recently encountered IsoCor and it fits my need so well! However, I am confused about the parameter correct_NA_tracer in the function isocor.mscorrectors.LowResMetaboliteCorrector. Suppose I want to correct the observed MID of mz 233 in the mass spectrum of malic acid (3TMS). The fragment formula is C9H21O3Si2. The formula of the metabolite moiety is C3H3O3 and the formula of the derivative moiety is C6H18Si2. According to the IsoCor tutorial, I used the following code

corrector_LR = isocor.mscorrectors.LowResMetaboliteCorrector(
formula='C3H3O3', # elemental formula of the metabolite moiety
tracer="13C",
derivative_formula='C6H18Si2', # elemental formula of the derivative moiety
tracer_purity=[0.0, 1.0],
data_isotopes=isocor.mscorrectors.LowResMetaboliteCorrector.DEFAULT_ISODATA,
correct_NA_tracer=False/True
)

Here is my question. If I want to correct the observed MID, shall I set correct_NA_tracer to True or False? What does this parameter do exactly?

[pierremillard]

Thanks for your nice feedback!

When set to True, the argument correct_NA_tracer removes the contribution of natural abundance for the isotopic tracer at unlabeled positions.

For instance, if no labeled substrate participate in the biosynthesis of malic acid, this compound will be at natural abundance (i.e. 1.07% of 13C for each carbon). If you do not correct for natural abundance of the tracer element, you will end up with an MID at natural abundance for C, i.e. about [0.952, 0.044, 0.004, 0] (back of the enveloppe calculation, so not really accurate, just for the example). If you enable this correction, you will end up with [1, 0, 0, 0], meaning that this compound has not incorporated any tracer atom of the labeled substrate. Hope this is clear, let me know if you have additional questions or points to discuss.

Best,
Pierre

[liaochen1988]

Yes, it is crystal clear! Thank you very much!