6.3 Selecting adducts to improve grouping
The selectIons() and adduct() functions discussed before can also improve sets workflows. This is because the adduct annotations can be used to improve feature neutralization, which in turn will improve grouping features between positive and negative ionization data. Once adduct annotations are set the features will be re-neutralized and re-grouped.
A typical workflow with selectIons looks like this:
# as before ...
anaInfoPos <- patRoonData::exampleAnalysisInfo("positive")
anaInfoNeg <- patRoonData::exampleAnalysisInfo("negative")
fListPos <- findFeatures(anaInfoPos, "openms")
fListNeg <- findFeatures(anaInfoNeg, "openms")
fGroupsPos <- groupFeatures(fListPos, "openms")
fGroupsNeg <- groupFeatures(fListNeg, "openms")
fList <- makeSet(fListPos, fListNeg, adducts = c("[M+H]+", "[M-H]-"))
fGroups <- groupFeatures(fList, "openms")
fGroups <- filter(fGroups, absMinIntensity = 10000, relMinReplicateAbundance = 1, maxReplicateIntRSD = 0.75,
blankThreshold = 5, removeBlanks = TRUE)
components <- generateComponents(fGroups, "openms")
fGroups <- selectIons(fGroups, components, c("[M+H]+", "[M-H]-"))
# do rest of the workflow...The first part of the workflow is exactly the same as was introduced in the beginning of this chapter. Furthermore, note that for sets workflows, selectIons needs a preferential adduct for each set.
The adducts function can also be used to obtain and modify adduct annotations. For sets workflows, these functions operate per set:
If you want to modify annotations for multiple sets, it is best to delay the re-gouping step:
adducts(fGroups, set = "positive", reGroup = FALSE)[4] <- "[M+K]+"
adducts(fGroups, set = "negative", reGroup = TRUE)[10] <- "[M-H2O]-"Setting reGroup=FALSE will not perform any re-neutralization and re-grouping, which preserves feature group names and safes processing time. However, it is crucial that the re-grouping step is eventually performed at the end.