Automatically generate a transformation product library with formula data.

Functionality to automatically generate a TP library with formula data from a set of transformation rules, which can be used with generateTPsLibraryFormula. TP calculation will be skipped if the transformation involves subtraction of elements not present in the parent.

Usage

genFormulaTPLibrary(
  parents,
  transformations = NULL,
  minMass = 40,
  generations = 1,
  skipInvalid = TRUE,
  prefCalcChemProps = TRUE,
  neutralChemProps = FALSE
)

Arguments

parents: The parents to which the given transformation rules should be used to generate the TP library. Should be either a suspect list (see suspect screening for more information) or the resulting output of screenSuspects.
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, that can be obtained with TPLogicTransformations.
minMass: The minimum mass for a TP to be kept.
generations: An integer that specifies the number of transformation generations that should be calculated. If generations>1 then TPs are calculated by applying the transformation rules to the TPs generated in the previous generation.
skipInvalid: Set to TRUE to skip parents without formula information. Otherwise an error is thrown.
prefCalcChemProps: If TRUE then calculated chemical properties such as the formula and InChIKey are preferred over what is already present in the parent suspect list. For efficiency reasons it is recommended to set this to TRUE. See the Validating and calculating chemical properties section for more details.
neutralChemProps: If TRUE then the neutral form of the molecule is considered to calculate SMILES, formulae etc. Enabling this may improve feature matching when considering common adducts (e.g. [M+H]+, [M-H]-). See the Validating and calculating chemical properties section for more details.

Value

A data.table that is suitable for the TPLibrary argument to generateTPsLibraryFormula.

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 order direction.

Source

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

Validating and calculating chemical properties

Chemical properties such as SMILES, InChIKey and formulae in the parent suspect list are automatically validated and calculated if missing/invalid.

The internal validation/calculation process performs the following steps:

Validation of SMILES, InChI, InChIKey and formula data (if present). Invalid entries will be set to NA.
If neutralChemProps=TRUE then chemical data (SMILES, formulae etc.) is neutralized by (de-)protonation (using the –neutralized option of OpenBabel). An additional column molNeutralized is added to mark those molecules that were neutralized. Note that neutralization requires either SMILES or InChI data to be available.
The SMILES and InChI data are used to calculate missing or invalid SMILES, InChI, InChIKey and formula data. If prefCalcChemProps=TRUE then existing InChIKey and formula data is overwritten by calculated values whenever possible.
The chemical formulae which were not calculated are verified and normalized. This process may be time consuming, and is potentially largely avoided by setting prefCalcChemProps=TRUE.
Neutral masses are calculated for missing values (prefCalcChemProps=FALSE) or whenever possible (prefCalcChemProps=TRUE).

Note that calculation of formulae for molecules that are isotopically labelled is currently only supported for deuterium (2H) elements.

This functionality relies heavily on OpenBabel, please make sure it is installed.

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 .

OBoyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011). “Open Babel: An open chemical toolbox.” Journal of Cheminformatics, 3(1). doi:10.1186/1758-2946-3-33 .