## ----environment, echo=FALSE, message=FALSE, warning=FALSE-------------------- library("cleaver") library("UniProt.ws") 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 up <- UniProt.ws(taxId=9606) ## download sequences of Insulin/Somatostatin s <- select(up, keys=c("P01308", "P61278"), columns=c("sequence"), keytype="UniProtKB" ) ## fetch only sequences sequences <- setNames(s$Sequence, s$Entry) ## 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-------------------------------------------------- sessionInfo()