## ----message=FALSE, warning=FALSE--------------------------------------------- library(NestLink) stopifnot(require(specL)) ## ----------------------------------------------------------------------------- aa_pool_x8 <- c(rep('A', 12), rep('S', 0), rep('T', 12), rep('N', 12), rep('Q', 12), rep('D', 8), rep('E', 0), rep('V', 12), rep('L', 0), rep('F', 0), rep('Y', 8), rep('W', 0), rep('G', 12), rep('P', 12)) aa_pool_1_2_9_10 <- c(rep('A', 8), rep('S', 7), rep('T', 7), rep('N', 6), rep('Q', 6), rep('D', 8), rep('E', 8), rep('V', 9), rep('L', 6), rep('F', 5), rep('Y', 9), rep('W', 6), rep('G', 15), rep('P', 0)) aa_pool_3_8 <- c(rep('A', 5), rep('S', 4), rep('T', 5), rep('N', 2), rep('Q', 2), rep('D', 8), rep('E', 8), rep('V', 7), rep('L', 5), rep('F', 4), rep('Y', 6), rep('W', 4), rep('G', 12), rep('P', 28)) ## ----------------------------------------------------------------------------- table(aa_pool_x8) length(aa_pool_x8) table(aa_pool_1_2_9_10) length(aa_pool_1_2_9_10) table(aa_pool_3_8) length(aa_pool_3_8) ## ----------------------------------------------------------------------------- replicate(10, compose_GPGx8cTerm(pool=aa_pool_x8)) ## ----------------------------------------------------------------------------- compose_GPx10R(aa_pool_1_2_9_10, aa_pool_3_8) ## ----------------------------------------------------------------------------- set.seed(2) (sample.size <- 3E+04) peptides.GPGx8cTerm <- replicate(sample.size, compose_GPGx8cTerm(pool=aa_pool_x8)) peptides.GPx10R <- replicate(sample.size, compose_GPx10R(aa_pool_1_2_9_10, aa_pool_3_8)) # write.table(peptides.GPGx8cTerm, file='/tmp/pp.txt') ## ----------------------------------------------------------------------------- library(protViz) (smp.peptide <- compose_GPGx8cTerm(aa_pool_x8)) parentIonMass(smp.peptide) pim.GPGx8cTerm <- unlist(lapply(peptides.GPGx8cTerm, function(x){parentIonMass(x)})) pim.GPx10R <- unlist(lapply(peptides.GPx10R, function(x){parentIonMass(x)})) pim.iRT <- unlist(lapply(as.character(iRTpeptides$peptide), function(x){parentIonMass(x)})) ## ----------------------------------------------------------------------------- (pim.min <- min(pim.GPGx8cTerm, pim.GPx10R)) (pim.max <- max(pim.GPGx8cTerm, pim.GPx10R)) (pim.breaks <- seq(round(pim.min - 1) , round(pim.max + 1) , length=75)) hist(pim.GPGx8cTerm, breaks=pim.breaks, probability = TRUE, col='#1111AAAA', xlab='peptide mass [Dalton]', ylim=c(0, 0.006)) hist(pim.GPx10R, breaks=pim.breaks, probability = TRUE, add=TRUE, col='#11AA1188') abline(v=pim.iRT, col='grey') legend("topleft", c('GPGx8cTerm', 'GPx10R', 'iRT'), fill=c('#1111AAAA', '#11AA1133', 'grey')) ## ----fig.retina=1------------------------------------------------------------- library(specL) ssrc <- sapply(peptideStd, function(x){ssrc(x$peptideSequence)}) rt <- unlist(lapply(peptideStd, function(x){x$rt})) plot(ssrc, rt); abline(ssrc.lm <- lm(rt ~ ssrc), col='red'); legend("topleft", paste("spearman", round(cor(ssrc, rt, method='spearman'),2))) ## ----fig.width=5, fig.height=5------------------------------------------------ hyd.GPGx8cTerm <- ssrc(peptides.GPGx8cTerm) hyd.GPx10R <- ssrc(peptides.GPx10R) hyd.iRT <- ssrc(as.character(iRTpeptides$peptide)) (hyd.min <- min(hyd.GPGx8cTerm, hyd.GPx10R)) (hyd.max <- max(hyd.GPGx8cTerm, hyd.GPx10R)) hyd.breaks <- seq(round(hyd.min - 1) , round(hyd.max + 1) , length=75) ## ----fig.retina=1------------------------------------------------------------- hist(hyd.GPGx8cTerm, breaks = hyd.breaks, probability = TRUE, col='#1111AAAA', xlab='hydrophobicity', ylim=c(0, 0.06), main='Histogram') hist(hyd.GPx10R, breaks = hyd.breaks, probability = TRUE, add=TRUE, col='#11AA1188') abline(v=hyd.iRT, col='grey') legend("topleft", c('GPGx8cTerm', 'GPx10R', 'iRT'), fill=c('#1111AAAA', '#11AA1133', 'grey')) ## ----------------------------------------------------------------------------- round(table(aa_pool_x8)/length(aa_pool_x8), 2) ## ----------------------------------------------------------------------------- peptide2aa <- function(seq, from=4, to=4+8){ unlist(lapply(seq, function(x){strsplit(substr(x, from, to), '')})) } peptides.GPGx8cTerm.aa <- peptide2aa(peptides.GPGx8cTerm) round(table(peptides.GPGx8cTerm.aa)/length(peptides.GPGx8cTerm.aa), 2) ## ----------------------------------------------------------------------------- peptides.GPx10R.aa <- peptide2aa(peptides.GPx10R, from=3, to=12) round(table(peptides.GPx10R.aa)/length(peptides.GPx10R.aa), 2) ## ----------------------------------------------------------------------------- sample.size length(grep('^GP(.*)GP(.*)R$', peptides.GPGx8cTerm)) length(grep('^GP(.*)GP(.*)R$', peptides.GPx10R)) ## ----------------------------------------------------------------------------- sample.size table(table(tt<-unlist(lapply(peptides.GPGx8cTerm, function(x){paste(sort(unlist(strsplit(x, ''))), collapse='')})))) # write.table(tt, file='GPGx8cTerm.txt') table(table(unlist(lapply(peptides.GPx10R, function(x){paste(sort(unlist(strsplit(x, ''))), collapse='')})))) ## ----fig.width=10, fig.height=10, fig.retina=1, echo=TRUE--------------------- par(mfrow=c(2, 2)) h <- NestLink:::.plot_in_silico_LCMS_map(peptides.GPGx8cTerm, main='GPGx8cTerm') h <- NestLink:::.plot_in_silico_LCMS_map(peptides.GPx10R, main='GPx10R') ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()