Annotate_annotateSpectrum: annotate spectrum

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

Description

annotate spectrum

Arguments

psm	peptide spectrum match table
modification	modification table
spectrum	spectrum table

Examples

library(bibliospec)
rm(list=ls())
 dbfile <- file.path(path.package("bibliospec"),
 "extdata/peptideStd.sqlite")

# call constructor
BS <- Bibliospec(dbfile=dbfile)
tmp <- BS$getAnnotationLists()
names(tmp)
tmp$psml[[1]]
tmp$mod[[1]]
tmp$spectruml[[1]]
ann <- Annotate()


ann$aa2mass(tmp$psml[[1]]$peptideSeq)

spectrum <- tmp$spectruml[[1]]$mz
masses <- ann$aa2mass(tmp$psm[[1]]$peptideSeq)
xx<-ann$fragmentBYIonsUpTO( masses , charge = (tmp$psm[[1]]$precursorCharge -1))
head(xx)
x<-ann$psmEasy(spectrum, xx$mass )
head(x)

matches <- ann$annotateSpectrum(psm = tmp$psml[[1]],
modification = tmp$modl[[1]], spectrum = tmp$spectruml[[1]])
head(matches)

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