suspect-screening: Target and suspect screening

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Target and suspect screening

Description

Utilities to screen for analytes with known or suspected identity.

Usage

screenSuspects(
  fGroups,
  suspects,
  rtWindow = 12,
  mzWindow = 0.005,
  adduct = NULL,
  skipInvalid = TRUE,
  prefCalcChemProps = TRUE,
  neutralChemProps = FALSE,
  onlyHits = FALSE,
  ...
)

## S4 method for signature 'featureGroups'
screenSuspects(
  fGroups,
  suspects,
  rtWindow,
  mzWindow,
  adduct,
  skipInvalid,
  prefCalcChemProps,
  neutralChemProps,
  onlyHits
)

## S4 method for signature 'featureGroupsScreening'
screenSuspects(
  fGroups,
  suspects,
  rtWindow,
  mzWindow,
  adduct,
  skipInvalid,
  onlyHits,
  amend = FALSE
)

numericIDLevel(level)

genIDLevelRulesFile(out, inLevels = NULL, exLevels = NULL)

## S4 method for signature 'featureGroupsSet'
screenSuspects(
  fGroups,
  suspects,
  rtWindow,
  mzWindow,
  adduct,
  skipInvalid,
  prefCalcChemProps,
  neutralChemProps,
  onlyHits
)

## S4 method for signature 'featureGroupsScreeningSet'
screenSuspects(
  fGroups,
  suspects,
  rtWindow,
  mzWindow,
  adduct,
  skipInvalid,
  prefCalcChemProps,
  neutralChemProps,
  onlyHits,
  amend = FALSE
)

Arguments

fGroups	The featureGroups object that should be screened.
suspects	A data.frame with suspect information. See the ⁠Suspect list format⁠ section below. \setsWF Can also be a list with suspect lists to be used for each set (otherwise the same suspect lists is used for all sets). The list can be named with the sets names to mark which suspect list is to be used with which set (e.g. suspects=list(positive=suspsPos, negative=suspsNeg)).
rtWindow, mzWindow	The retention time window (in seconds) and m/z window that will be used for matching a suspect (+/- feature data).
adduct	An adduct object (or something that can be converted to it with as.adduct). Examples: "[M-H]-", "[M+Na]+". May be NULL, see ⁠Suspect list format⁠ and ⁠Matching of suspect masses⁠ sections below.
skipInvalid	If set to TRUE then suspects with invalid data (e.g. missing names or other missing data) will be ignored with a warning. Similarly, any suspects for which mass calculation failed (when no mz column is present in the suspect list), for instance, due to invalid SMILES, will be ignored with a warning.
prefCalcChemProps	If TRUE then calculated chemical properties such as the formula and InChIKey are preferred over what is already present in the 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.
onlyHits	If TRUE then all feature groups not matched by any of the suspects will be removed.
...	Further arguments specified to the methods.
amend	If TRUE then screening results will be amended to the original object.
level	The identification level to be converted.
out	The file path to the target file.
inLevels, exLevels	A regular expression for the identification levels to include or exclude, respectively. For instance, exLevels="4|5" would exclude level 4 and 5 from the output file. Set to NULL to ignore.

Details

Besides 'full non-target analysis', where compounds may be identified with little to no prior knowledge, a common strategy is to screen for compounds with known or suspected identity. This may be a generally favorable approach if possible, as it can significantly reduce the load on data interpretation.

screenSuspects is used to perform suspect screening. The input featureGroups object will be screened for suspects by m/z values and optionally retention times. Afterwards, any feature groups not matched may be kept or removed, depending whether a full non-target analysis is desired.

numericIDLevel Extracts the numeric part of a given identification level (e.g. "3a" becomes ‘⁠3⁠’).

genIDLevelRulesFile Generates a template YAML file that is used to configure the rules for automatic estimation of identification levels. This file can then be used as input for annotateSuspects.

Value

screenSuspects returns a featureGroupsScreening object, which is a copy of the input fGroups object amended with additional screening information.

Sets workflows

In a sets workflow, screenSuspects performs suspect screening for each set separately, and the screening results are combined afterwards. The sets column in the screenInfo data marks in which sets the suspect hit was found.

Suspect list format

the suspects argument for screenSuspects should be a data.frame with the following mandatory and optional columns:

• name The suspect name. Must be file-compatible. (mandatory)

• rt The retention time (in seconds) for the suspect. If specified the suspect will only be matched if its retention matches the experimental value (tolerance defined by the rtWindow argument). (optional)

• neutralMass,formula,SMILES,InChI The neutral monoisotopic mass, chemical formula, SMILES or InChI for the suspect. (data from one of these columns are mandatory in case no value from the mz column is available for a suspect)

• mz The ionized m/z of the suspect. (mandatory unless it can be calculated from one of the aforementioned columns)

• adduct A character that can be converted with as.adduct. Can be used to automatically calculate values for the mz column. (mandatory unless data from the mz column is available, the adduct argument is set or fGroups has adduct annotations)

• fragments_mz,fragments_formula One or more MS/MS fragments (specified as m/z or formulae, respectively). Multiple values can be specified by separating them with a semicolon (⁠;⁠). This data is used by annotateSuspects to report detected MS/MS fragments and calculate identification levels. (optional)

Matching of suspect masses

How the mass of a suspect is matched with the mass of a feature depends on the available data:

• If the suspect has data from the mz column of the suspect list, then this data is matched with the detected feature m/z.

• Otherwise, if the suspect has data in the adduct column of the suspect list, this data is used to calculate its mz value, which is then used like above.

• In the last case, the neutral mass of the suspect is matched with the neutral mass of the feature. Hence, either the adduct argument needs to be specified, or the featureGroups input object must have adduct annotations.

Validating and calculating chemical properties

Chemical properties such as SMILES, InChIKey and formula in the 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.

Note

Both screenSuspects may use the suspect names to base file names used for reporting, logging etc. Therefore, it is important that these are file-compatible names. For this purpose, screenSuspects will automatically try to convert long, non-unique and/or otherwise incompatible suspect names.

References

\insertRef

OBoyle2011patRoon

See Also

featureGroupsScreening

rickhelmus/patRoon documentation built on Nov. 22, 2024, 3:11 p.m.