Assign IMS data to a compounds object.

Assigns ion mobility and CCS values to the candidates in a compounds object.

# S4 method for class 'compounds'
assignMobilities(
  obj,
  fGroups,
  IMS = TRUE,
  from = NULL,
  matchFromBy = "InChIKey1",
  overwrite = FALSE,
  adduct = NULL,
  CCSParams = NULL,
  prefCalcChemProps = TRUE,
  neutralChemProps = FALSE,
  virtualenv = "patRoon-C3SDB"
)

# S4 method for class 'compoundsSet'
assignMobilities(obj, fGroups, IMS = TRUE, from = NULL, ...)

Arguments

obj

The compounds object for which IMS assignments should be performed.

fGroups

The featureGroups object for which the compound candidates (obj) were calculated.

IMS

(IMS workflow) Specifies which feature groups are considered for IMS assignments in IMS workflows. The following options are valid:

• "both": Selects IMS and non-IMS features.

• "maybe": Selects non-IMS features and IMS features without assigned IMS precursor.

• FALSE: Selects only non-IMS features.

• TRUE: Selects only IMS features.

from, matchFromBy, overwrite, CCSParams, prefCalcChemProps, neutralChemProps, virtualenv

Passed to the method for suspects

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.

...

(sets workflow) Further arguments passed to the non-sets workflow method.

Details

The assignMobilities method for compounds is used to (1) add predicted or known IMS data to annotation candidates and (2) convert (previously added) mobility <–> CCS values. Internally, the assignMobilities method for suspects is used to perform these operations, please see its documentation for more details.

If both adduct specific and non-adduct specific mobility and CCS data is available (and not NA), then the non-adduct specific data is assigned to the compound candidate. Otherwise, data corresponding to the adduct argument or the adduct assigned to the feature group is taken. The filter method can be used to filter out candidates with deviating IMS data.

Note

SIRIUS does currently not report InChIKey values, hence, matchFromBy="InChIKey" is not supported in this case.

If compound annotation is performed with generateCompoundsMetFrag with database="pubchemlite" then CCS data is already added, provided the local database has it. If you want to overwrite this data, set overwrite=TRUE.

Sets workflows

In a sets workflow the calculations are performed and stored independently for each set, as adducts, charges and m/z values typically differ.

The from argument may be a list that specifies the from values for each set. This is primarily intended when tables are used to set from.

See also

The assignMobilities method for suspects.