isotopicSubstitutionMatrix: Definitions of isotopic substitutions

In rformassspectrometry/MetaboCoreUtils: Core Utils for Metabolomics Data

Definitions of isotopic substitutions

Description

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 is associated with an isotopic substitution (which can involve isotopes of several elements or different isotopes of the same element). In general for each isotopic substitution multiple rows are present in the data.frame. Each row provides parameters to compute bounds (for the ratio between the isotopologue peak and the monoisotopic one) on a certain mass range. 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:

• "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.

• "maxmass": the maximal mass of a compound for which the isotopic substitution was found. Peaks with a mass higher 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.

• "leftend": left endpoint of the mass interval.

• "rightend": right endpoint of the mass interval.

• "LBint": intercept of the lower bound line on the mass interval whose endpoints are "leftend" and "rightend".

• "LBslope": slope of the lower bound line on the mass interval.

• "UBint": intercept of the upper bound line on the mass interval.

• "UBslope": slope of the upper bound line on the mass interval.

Usage

isotopicSubstitutionMatrix(source = c("HMDB_NEUTRAL"))

Arguments

source

character(1) defining the set of predefined parameters and isotopologue definitions to return.

Value

data.frame with parameters to detect the defined isotopic substitutions

Available pre-calculated substitution matrices

• 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).

Author(s)

Andrea Vicini

Examples

## Get the substitution matrix calculated on HMDB
isotopicSubstitutionMatrix("HMDB_NEUTRAL")

rformassspectrometry/MetaboCoreUtils documentation built on Oct. 2, 2024, 5:13 a.m.