Few small bugs with run.metfrag

[rhelmus]

Hello,

Using the following example:

library("metfRag")

settingsObject<-list()
settingsObject[["DatabaseSearchRelativeMassDeviation"]]<-5.0
settingsObject[["FragmentPeakMatchAbsoluteMassDeviation"]]<-0.002
settingsObject[["FragmentPeakMatchRelativeMassDeviation"]]<-5.0
settingsObject[["MetFragDatabaseType"]]<-"PubChem"
settingsObject[["IonizedPrecursorMass"]]<-111.0085
settingsObject[["PrecursorIonMode"]] <- -1
settingsObject[["IsPositiveIonMode"]] <- FALSE
settingsObject[["PeakList"]]<-matrix(c(
    59.01272, 844,
    66.03390, 1148,
    67.01822, 45440,
    68.02170, 1828,
    68.99536, 696,
    97.93084 , 1308,
    110.97631, 764,
    111.00851, 2860,
    114.93391, 4100), ncol=2, byrow=TRUE)
#settingsObject[["PrecursorCompoundIDs"]]<-c("86160156")
#
# pre and post-processing filter
#
# define filters to filter unconnected compounds (e.g. salts)
settingsObject[["MetFragPreProcessingCandidateFilter"]]<-c("UnconnectedCompoundFilter","IsotopeFilter")
settingsObject[["MetFragPostProcessingCandidateFilter"]]<-c("InChIKeyFilter")

settingsObject[["MetFragScoreTypes"]]<-c("FragmenterScore")
settingsObject[["MetFragScoreWeights"]]<-c(1.0)

#run MetFrag
scored.candidates<-run.metfrag(settingsObject)

Looking at the first two results we can see that...

• NoExplPeaks reports two for both, while the second result only lists one peak in other columns such as ExplPeaks.
• The explained formula for m/z 67.01822 differs by a hydrogen. This happens for quite a few results and I see that the webinterface marks these kind of differences as (de)protonated.

In addition, some results are reported more than once.

Regards, Rick