## ----echo=FALSE, eval = TRUE, fig = FALSE, echo=FALSE----- options(prompt = "R> ", continue = "+ ", width = 60, useFancyQuotes = FALSE, warn = -1) ## ----load------------------------------------------------- library(specL) packageVersion('specL') ## ----summry----------------------------------------------- summary(peptideStd) ## ----peptideStd------------------------------------------- # plot(peptideStd) plot(0,0, main='MISSING') ## ----pepttidePlot----------------------------------------- demoIdx <- 40 # str(peptideStd[[demoIdx]]) #res <- plot(peptideStd[[demoIdx]], ion.axes=TRUE) plot(0,0, main='MISSING') ## ----mascot2psmSet---------------------------------------- specL:::.mascot2psmSet ## ----irtFASTAseq------------------------------------------ irtFASTAseq <- paste(">zz|ZZ_FGCZCont0260|", "iRT_Protein_with_AAAAK_spacers concatenated Biognosys\n", "LGGNEQVTRAAAAKGAGSSEPVTGLDAKAAAAKVEATFGVDESNAKAAAAKYILAGVENS", "KAAAAKTPVISGGPYEYRAAAAKTPVITGAPYEYRAAAAKDGLDAASYYAPVRAAAAKAD", "VTPADFSEWSKAAAAKGTFIIDPGGVIRAAAAKGTFIIDPAAVIRAAAAKLFLQFGAQGS", "PFLK\n") Tfile <- file(); cat(irtFASTAseq, file = Tfile); fasta.irtFASTAseq <- read.fasta(Tfile, as.string=TRUE, seqtype="AA") close(Tfile) ## --------------------------------------------------------- peptideStd[[demoIdx]]$proteinInformation ## --------------------------------------------------------- peptideStd <- annotate.protein_id(peptideStd, fasta=fasta.irtFASTAseq) ## --------------------------------------------------------- (idx <- which(unlist(lapply(peptideStd, function(x){nchar(x$proteinInformation)>0})))) ## --------------------------------------------------------- peptideStd[[demoIdx]]$proteinInformation ## --------------------------------------------------------- digestPattern = "(([RK])|(^)|(^M))" ## --------------------------------------------------------- res.genSwathIonLib <- genSwathIonLib(data = peptideStd, data.fit = peptideStd.redundant) ## --------------------------------------------------------- summary(res.genSwathIonLib) ## --------------------------------------------------------- res.genSwathIonLib@ionlibrary[[demoIdx]] ## ----fig.retina=3----------------------------------------- plot(res.genSwathIonLib@ionlibrary[[demoIdx]]) ## ----fig.retina=3----------------------------------------- # define customized fragment ions # for demonstration lets consider only the top five singly charged y ions. r.genSwathIonLib.top5 <- genSwathIonLib(peptideStd, peptideStd.redundant, topN=5, fragmentIonFUN=function (b, y) { return( cbind(y1_=y) ) } ) plot(r.genSwathIonLib.top5@ionlibrary[[demoIdx]]) ## --------------------------------------------------------- iRTpeptides ## ----fit, eval=FALSE-------------------------------------- # fit <- lm(formula = rt ~ aggregateInputRT * fileName, data = m) ## ----eval=FALSE------------------------------------------- # data <- aggregate(df$rt, by = list(df$peptide, df$fileName), # FUN = mean) # data.fit <- aggregate(df.fit$rt, # by = list(df.fit$peptide, df.fit$fileName), # FUN = mean) ## ----merge, eval=FALSE------------------------------------ # m <- merge(iRT, data.fit, by.x='peptide', by.y='peptide') ## ----fig.retina=3----------------------------------------- # calls the plot method for a specLSet object op <- par(mfrow=c(2,3)) plot(res.genSwathIonLib) par(op) ## ----fig.retina=3----------------------------------------- idx.iRT <- which(unlist(lapply(peptideStd, function(x){ if(x$peptideSequence %in% iRTpeptides$peptide){0} else{1} })) == 0) # remove all iRTs and compute ion library res.genSwathIonLib.no_iRT <- genSwathIonLib(peptideStd[-idx.iRT]) summary(res.genSwathIonLib.no_iRT) op <- par(mfrow = c(2, 3)) plot(res.genSwathIonLib.no_iRT) par(op) ## --------------------------------------------------------- write.spectronaut(res.genSwathIonLib, file="specL-Spectronaut.txt") ## ----eval=FALSE------------------------------------------- # res <- genSwathIonLib(data, data.fit, # topN=10, # fragmentIonMzRange=c(200,2000), # fragmentIonRange=c(2,100)) ## ----sessionInfo, echo=FALSE------------------------------ sessionInfo()