# Definitions¶

Some important definitions are provided in this section.

## Isotopologues¶

Molecular entities that differ only in their isotopic composition (number of isotopic substitutions), according to its IUPAC definition. It consists of isotopic forms that either:

1. do not have the same isotopic composition but have the same nominal mass (e.g., 13CH3NH2and CH2DNH2)
2. or have neither the same isotopic composition nor the same nominal mass (e.g., CH4, CH3D, CH2D2). The ability of the MS analyzer to distinguish different isotopologues is determined only by the elemental formula of the molecule and the resolution of the MS analyzer.

## Tracer isotopologues¶

Isotopologues that differ only in their isotopic composition (number of isotopic substitutions) of the tracer element (e.g. CH3NH2, CH2DNH2 and CHD2NH2 are considered as tracer isotopologues in a 2H-labeling experiments). A molecular entity containing $$n$$ tracer atoms has $$n+1$$ tracer isotopologues. Tracer isotopologues have different nominal masses, hence they can be distinguished both at low and high MS resolution.

## Isotopic cluster¶

Group of MS peaks that originate from a unique molecular entity, i.e. with the same elemental composition but different isotopic compositions, according to its IUPAC definition. A given peak of the isotopic cluster typically contains several isotopologues. The number and the nature of isotopologues overlapped in each peak is determined only by the elemental formula of the molecule and the resolution of the MS analyzer. The intensity of each peak depends on the abundance of each isotopologue, and thus on the incorporation of tracer.

## Mass fractions¶

The intensity or area of the peaks of the isotopic cluster that contain information on the incorporation of tracer, i.e. of the MS peaks originating from the molecular entity containing $$0, 1, ..., n$$ tracer atoms, where $$n$$ is the number of atoms of tracer element in this entity. Mass fractions also contains the contribution of other isotopic species which must be removed. The set of overlapping isotopic species is determined only by the elemental formula of the molecule and the resolution of the MS analyzer.

## Isotopologue distribution¶

Abundance of tracer isotopologues relative to the total pool of the tracer isotopologues. It contains labeling information which is specific to the incorporation of tracer atoms. Isotopologue distribution, obtained after correcting mass fractions for naturally occuring isotopes, is the output of IsoCor.

## Resolution¶

Resolution measures of the ability of the MS analyzer to distinguish two peaks of slightly different mass-to-charge ratios $$\delta(M)$$ in a mass spectrum. It is classically described as a fixed value of $$M/\delta(M)$$ (the nominal resolution, defined as Full Width at Half Maximum (FWHM) at a particular m/z). In order for the isotopic peaks to be well separated, the mass difference should be greater than 1.66 FWHM.