isotopicSubstitutionMatrix {MetaboCoreUtils} | R Documentation |
In order to identify potential isotopologues based on only m/z and intensity
values with the isotopologues()
function, sets of pre-calculated parameters
are required. This function returns such parameter sets estimated on
different sources/databases. The nomenclature used to describe isotopes
follows the following convention: the number of neutrons is provided in [
as a prefix to the element and the number of atoms of the element as suffix.
[13]C2[37]Cl3
describes thus an isotopic substitution containing 2 [13]C
isotopes and 3 [37]Cl
isotopes.
Each row in the returned data.frame
characterizes an isotopic substitution
(which can involve isotopes of several elements or different isotopes of the
same element). The provided isotopic substitutions are in general the most
frequently observed substitutions in the database (e.g. HMDB) on which they
were defined. Parameters (columns) defined for each isotopic substitution
are:
"degree"
: the degree of the isotopic substitution. Isotopic
substitutions with a single element (such as [15]N1
or [13]C1
) are of
degree 1 while isotopic substitutions with more isotopes are of a higher
degree ([37]Cl5
and [34]S1[37]Cl4
are e.g. both of degree 5).
"minmass"
: the minimal mass of a compound for which the isotopic
substitution was found. Peaks with a mass lower than this will most likely
not have the respective isotopic substitution.
"md"
: the mass difference between the monoisotopic peak and a peak of an
isotopologue characterized by the respective isotopic substitution.
"min_slope"
: used to calculate the lower expected bound for the ratio
between the probabilities of isotopologues associated to a given
substitution and the corresponding monoisotopic isotopologues. If a linear
relationship between the number of each element in the substitution and
the monoisotopic mass of compounds having those elements can be assumed
then the previously mentioned ratio has a polynomial trend with degree
equal to the degree of the isotopic substitution. The ratios for each
compound and for a given substitution can be transformed by taking the root
corresponding to degree of the substitution. In that way a linear trend
in the monoisotopic mass can be obtained for the ratios. "min_slope"
represent the slope of a lower bound line for this trend. In other words,
for a given substitution we expect the ratio between the intensity of
an isotopologue of a given compound corresponding to that substitution and
the intensity of the monoisotopic isotopologue to be
>= (monoisotopic mass * min_slope)^degree
.
"max_slope"
: used to calculate the expected upper intensity ratio bound.
isotopicSubstitutionMatrix(source = c("HMDB"))
source |
|
data.frame
with parameters to detect the defined isotopic
substitutions
source = "HMDB"
: most common isotopic substitutions and parameters for
these have been calculated for all compounds from the
Human Metabolome Database (HMDB, July 2021). Note that
the substitutions were calculated on the neutral masses (i.e. the
chemical formulas of the compounds, not considering any adducts).
Andrea Vicini
## Get the substitution matrix calculated on HMDB isotopicSubstitutionMatrix("HMDB")