R/Protein.To.Peptide.R

In ManuelPerisDiaz/CysMpro: Mass Spectrometry-Based Structural Analysis of Metalloproteins

#' Proteolytic digestion of a partial chemical labelled protein.
#'
#' Generates a MS library containing peptides harbouring incomplete chemical Cys-labelled residues.
#'
#' @param sequence Protein sequence.
#' @param missed Missed cleavage sites produced by proteolytic enzyme. Default to 2.
#' @param enzym Proteolytic enzyme used in the experiment. Default to Trypsin.
#' @return List of peptides with incomplete chemically labelled Cys-protein residues.
#' @examples
#' \dontrun{
#' MT2a<-("MDPNCSCAAGDSCTCAGSCKCKECKCTSCKKSCCSCCPVGCAKCAQGCICKGASDKCSCCA")
#'TheoreticalMass<-Protein.to.Peptide(MT2a)
#'
#' }
#' @export


Protein.to.Peptide<-function (sequence,missed=3,enzym = "trypsin")
{
  Digest  = getFromNamespace("Digest", "OrgMassSpecR")

  mt3clv<-Digest(sequence, enzym ,missed,IAA=FALSE)

  result<-c()
 result<-vector("list",length(mt3clv[,1]))



  for (i in 1:length(mt3clv[,1])){
  seq<-mt3clv[i,1]
  name<-seq
  num<-i
  peptideVector <- strsplit(seq, split = "")[[1]]
  FindElement <- function(residue) {
    if (residue == "A")
      element <- c(C = 3, H = 5, N = 1, O = 1, S = 0)
    if (residue == "R")
      element <- c(C = 6, H = 12, N = 4, O = 1, S = 0)
    if (residue == "N")
      element <- c(C = 4, H = 6, N = 2, O = 2, S = 0)
    if (residue == "D")
      element <- c(C = 4, H = 5, N = 1, O = 3, S = 0)
    if (residue == "E")
      element <- c(C = 5, H = 7, N = 1, O = 3, S = 0)
    if (residue == "Q")
      element <- c(C = 5, H = 8, N = 2, O = 2, S = 0)
    if (residue == "G")
      element <- c(C = 2, H = 3, N = 1, O = 1, S = 0)
    if (residue == "H")
      element <- c(C = 6, H = 7, N = 3, O = 1, S = 0)
    if (residue == "I")
      element <- c(C = 6, H = 11, N = 1, O = 1, S = 0)
    if (residue == "L")
      element <- c(C = 6, H = 11, N = 1, O = 1, S = 0)
    if (residue == "K")
      element <- c(C = 6, H = 12, N = 2, O = 1, S = 0)
    if (residue == "M")
      element <- c(C = 5, H = 9, N = 1, O = 1, S = 1)
    if (residue == "F")
      element <- c(C = 9, H = 9, N = 1, O = 1, S = 0)
    if (residue == "P")
      element <- c(C = 5, H = 7, N = 1, O = 1, S = 0)
    if (residue == "S")
      element <- c(C = 3, H = 5, N = 1, O = 2, S = 0)
    if (residue == "T")
      element <- c(C = 4, H = 7, N = 1, O = 2, S = 0)
    if (residue == "W")
      element <- c(C = 11, H = 10, N = 2, O = 1, S = 0)
    if (residue == "Y")
      element <- c(C = 9, H = 9, N = 1, O = 2, S = 0)
    if (residue == "V")
      element <- c(C = 5, H = 9, N = 1, O = 1, S = 0)
    if (residue == "C")
      element <- c(C = 3, H = 5, N = 1, O = 1, S = 1)
    return(element)
  }
  resultsVector <- c(C = 0, H = 0, N = 0, O = 0, S = 0)

  for (i in 1:length(peptideVector)) {
    resultsVector <- FindElement(peptideVector[i]) +
      resultsVector
  }
  resultsVector <- resultsVector + c(C = 0, H = 2, N = 0,
                                     O = 1, S = 0)

  NCys<-sum(as.numeric(peptideVector=="C"))
   M2<-c()
   M<-c()
    for (i in 1:NCys){
      element<-c(C=2,H=3,N=1,O=1,S=0)
      M<- resultsVector+element*i
      M2[i]<-list(M)
    }


   MonoisotopicMass  = getFromNamespace("MonoisotopicMass", "OrgMassSpecR")

    mass<-c()
    massb<-c()
    for (i in 1:length(M2)){
      mass[i]<- MonoisotopicMass(M2[[i]],charge=1)
    }
    i<-num
    #hist(mass)
    NM<-MonoisotopicMass(resultsVector)
    Modifications=seq(0,NCys,1)
    mass<-c(NM,mass)
    massb<-cbind(Modifications=Modifications,mass)

   result[[i]]<-massb
   names(result)[[i]]<-paste(name)

  }

return(  result)

  }