Bibliospec_annotatePeaksWithFragments: Annotate the MS2 with fragment ion inforamtion, creates a new...

In protViz/bibliospec: Reading and Analyzing Mass Spectrometric Search Results

Description

Annotate the MS2 with fragment ion inforamtion, creates a new table "AnnotatedPeaks".

Arguments

error	error size
ppm	error type (default TRUE ppm, if FALSE than DA)
neutralloss	named vector with netral losses to add
excludeAA	remove all entries with special amino acids (default = "B|X|Z")

Examples

dbfile <- file.path(path.package("bibliospec"),
 "extdata/peptideStd.sqlite")

#call constructor
BS <- Bibliospec(dbfile=dbfile)
BS$annotatePeaksWithFragments()
annotPeaksTable <- (BS$getAnnotedPeaks())
head(annotPeaksTable)

psml <- BS$getAnnotationLists()$psml
xx <- plyr::rbind.fill(psml)
head(xx)
xdf <- merge(xx, annotPeaksTable, by="RefSpectraId")
head(xdf)

protViz/bibliospec documentation built on May 26, 2019, 9:37 a.m.