Obtain transformation products (TPs) with metabolic logic

Automatically calculate potential transformation products with metabolic logic.

generateTPsLogic(fGroups, minMass = 40, ...)

# S4 method for featureGroups
generateTPsLogic(fGroups, minMass = 40, adduct = NULL, transformations = NULL)

# S4 method for featureGroupsSet
generateTPsLogic(fGroups, minMass = 40, transformations = NULL)

Arguments

fGroups

A featureGroups object for which TPs should be calculated.

minMass

A numeric that specifies the minimum mass of calculated TPs. If below this mass it will be removed.

adduct

An adduct object (or something that can be converted to it with as.adduct). Examples: "[M-H]-", "[M+Na]+". If the featureGroups object has adduct annotations then these are used if adducts=NULL.

(sets workflow) The adduct argument is not supported for sets workflows, since the adduct annotations will then always be used.

transformations

A data.frame with transformation reactions to be used for calculating the TPs (see details below). If NULL, a default table from Schollee et al. is used (see references).

Value

A transformationProducts (derived) object containing all generated TPs.

Details

This function uses metabolic logic to obtain transformation products. This function is called when calling generateTPs with algorithm="logic".

With this algorithm TPs are predicted from common (environmental) chemical reactions, such as hydroxylation, demethylation etc. The generated TPs result from calculating the mass differences between a parent feature after it underwent the reaction. While this only results in little information on chemical properties of the TP, an advantage of this method is that it does not rely on structural information of the parent, which may be unknown in a full non-target analysis.

Transformation reactions

The transformations argument specifies custom rules to calculate transformation products. This should be a data.frame with the following columns:

transformation The name of the chemical transformation
add The elements that are added by this reaction (e.g. "O").
sub The elements that are removed by this reaction (e.g. "H2O").
retDir The expected retention time direction relative to the parent (assuming a reversed phase like LC separation). Valid values are: -1 (elutes before the parent), 1 (elutes after the parent) or 0 (no significant change or unknown).

Source

The algorithms using transformation reactions are directly based on the work done by Schollee et al. (see references).

References

Schollee JE, Schymanski EL, Avak SE, Loos M, Hollender J (2015). “Prioritizing Unknown Transformation Products from Biologically-Treated Wastewater Using High-Resolution Mass Spectrometry, Multivariate Statistics, and Metabolic Logic.” Analytical Chemistry, 87(24), 12121--12129. doi:10.1021/acs.analchem.5b02905 .