## ----style, eval=TRUE, echo=FALSE, results="asis"--------------------------------------- BiocStyle::latex(use.unsrturl=FALSE) ## ----setup, include=FALSE, cache=FALSE-------------------------------------------------- library("knitr") opts_chunk$set(tidy.opts=list(width.cutoff=45, tidy=FALSE), fig.align='center', comment=NA, prompt=TRUE) ## ----libraries, echo=FALSE-------------------------------------------------------------- suppressPackageStartupMessages(library("UniProt.ws")) suppressPackageStartupMessages(library("BRAIN")) ## --------------------------------------------------------------------------------------- library("cleaver") ## ----eval=FALSE------------------------------------------------------------------------- # help("cleave") ## --------------------------------------------------------------------------------------- ## cleave it cleave("LAAGKVEDSD", enzym="trypsin") ## get the cleavage ranges cleavageRanges("LAAGKVEDSD", enzym="trypsin") ## get only cleavage sites cleavageSites("LAAGKVEDSD", enzym="trypsin") ## --------------------------------------------------------------------------------------- ## miss one cleavage position cleave("LAAGKVEDSD", enzym="trypsin", missedCleavages=1) cleavageRanges("LAAGKVEDSD", enzym="trypsin", missedCleavages=1) ## miss zero or one cleavage positions cleave("LAAGKVEDSD", enzym="trypsin", missedCleavages=0:1) cleavageRanges("LAAGKVEDSD", enzym="trypsin", missedCleavages=0:1) ## --------------------------------------------------------------------------------------- ## create AAStringSet object p <- AAStringSet(c(gaju="LAAGKVEDSD", pnm="AGEPKLDAGV")) ## cleave it cleave(p, enzym="trypsin") cleavageRanges(p, enzym="trypsin") cleavageSites(p, enzym="trypsin") ## --------------------------------------------------------------------------------------- ## load UniProt.ws library library("UniProt.ws") ## select species Homo sapiens UniProt.ws <- UniProt.ws(taxId=9606) ## download sequences of Insulin/Somatostatin s <- select(UniProt.ws, keys=c("P01308", "P61278"), columns=c("SEQUENCE")) ## fetch only sequences sequences <- setNames(s$SEQUENCE, s$UNIPROTKB) ## remove whitespaces sequences <- gsub(pattern="[[:space:]]", replacement="", x=sequences) ## --------------------------------------------------------------------------------------- cleave(sequences, enzym="pepsin") ## --------------------------------------------------------------------------------------- ## load BRAIN library library("BRAIN") ## cleave insulin cleavedInsulin <- cleave(sequences[1], enzym="trypsin")[[1]] ## create empty plot area plot(NA, xlim=c(150, 4300), ylim=c(0, 1), xlab="mass", ylab="relative intensity", main="tryptic digested insulin - isotopic distribution") ## loop through peptides for (i in seq(along=cleavedInsulin)) { ## count C, H, N, O, S atoms in current peptide atoms <- BRAIN::getAtomsFromSeq(cleavedInsulin[[i]]) ## calculate isotopic distribution d <- useBRAIN(atoms) ## draw peaks lines(d$masses, d$isoDistr, type="h", col=2) } ## ----sessioninfo, echo=FALSE, results="asis"-------------------------------------------- toLatex(sessionInfo())