R/digestMod.R

In adductomicsR: Processing of adductomic mass spectral datasets

#' modified \code{\link[OrgMassSpecR]{Digest}} function
#' (from OrgMassSpecR package)
#' @description allows maxCharge to be set to calculate precursor m/z
#' @param sequence a character string representing the amino acid sequence.
#' @param enzyme is the enzyme to perform in silico digestion with
#' @param missed the maximum number of missed cleavages.
#' Must be an integer of 0 (default)
#' or greater. An error will result if the specified number of
#' missed cleavages is
#' greater than the maximum possible number of missed cleavages.
#' @param maxCharge numeric max charge charge for predicted precursor m/z
#' @param IAA logical. TRUE specifies iodoacetylated cysteine and FALSE
#'specifies unmodified
#' cysteine. Used only in determining the elemental formula,
#' not the three letter codes.
#' @param custom list of custom masses
#' @param N15 logical indicating if the nitrogen-15 isotope should be used
#' in place of the default
#' nitrogen-14 isotope.
#' calculation
#' @examples digestMod('MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIA',
#' enzyme = "trypsin", missed = 0, maxCharge = 8,IAA = TRUE, N15 = FALSE,
#' custom = list())
#' @details see \code{\link{Digest}} for details of further function arguments.
#' @return dataframe
#' @usage digestMod(sequence, enzyme = "trypsin", missed = 0,
#' maxCharge = 8,IAA = TRUE, N15 = FALSE, custom = list())
#' @export
digestMod <-
    function(sequence,
             enzyme = "trypsin",
             missed = 0,
             maxCharge = 8,
             IAA = TRUE,
             N15 = FALSE,
             custom = list()) {
        dsAAnos <- strsplit(gsub("[A-Z]|ds", "", sequence), "\\[|\\]")[[1]]
        dsAAnos <- dsAAnos[dsAAnos != ""]
        dsRes <- as.numeric(unique(strsplit(paste0(
            dsAAnos,
            collapse = "-"
        ), "-")[[1]]))
        sequence <- gsub("\\[ds|[0-9]|\\]|-", "", sequence)
        seq_vector <- strsplit(sequence, split = "")[[1]]
        end_position <- length(seq_vector)
        if (enzyme == "trypsin") {
            if (seq_vector[end_position] == "K" | seq_vector[end_position] ==
                "R") {
                seq_vector[end_position] <- "!"
                seq_string <- paste(seq_vector, collapse = "")
            } else
                seq_string <- sequence
            seq_string <- gsub("KP", "!P", seq_string)
            seq_string <- gsub("RP", "!P", seq_string)
            seq_vector <- strsplit(seq_string, split = "")[[1]]
            stop <- grep("K|R", seq_vector)
            start <- stop + 1
        }
        if (enzyme == "trypsin.strict") {
            if (seq_vector[end_position] == "K" | seq_vector[end_position] ==
                "R") {
                seq_vector[end_position] <- "!"
                seq_string <- paste(seq_vector, collapse = "")
            } else
                seq_string <- sequence
            seq_vector <- strsplit(seq_string, split = "")[[1]]
            stop <- grep("K|R", seq_vector)
            start <- stop + 1
        }
        if (enzyme == "pepsin") {
            if (seq_vector[end_position] == "F" |
                seq_vector[end_position] == "L" |
                seq_vector[end_position] ==
                "W" |
                seq_vector[end_position] == "Y" | seq_vector[end_position] ==
                "A" |
                seq_vector[end_position] == "E" |
                seq_vector[end_position] ==
                "Q") {
                seq_vector[end_position] <- "!"
            }
            stop <- grep("F|L|W|Y|A|E|Q", seq_vector)
            start <- stop + 1
        }
        if (enzyme != "trypsin" && enzyme != "trypsin.strict" &&
            enzyme != "pepsin")
            stop("undefined enzyme, defined enzymes are trypsin, 
                trypsin.strict, and pepsin")
        if (length(stop) == 0)
            warning("sequence does not contain cleavage sites")
        if (missed > length(stop))
            stop("number of specified missed cleavages is greater 
                than the maximum possible")
        cleave <-
            function(sequence, start, stop, misses) {
                peptide <- substring(sequence, start, stop)
                mc <- rep(misses, times = length(peptide))
                result <-
                    data.frame(peptide, start, stop, mc,
                            stringsAsFactors = FALSE)
                return(result)
            }
        start <- c(1, start)
        stop <- c(stop, end_position)
        results <- cleave(sequence, start, stop, 0)
        if (missed > 0) {
            for (i in seq_len(missed)) {
                start_tmp <- start[seq_len((length(start) - i))]
                stop_tmp <- stop[(1 + i):length(stop)]
                peptide <-
                    cleave(sequence, start_tmp, stop_tmp, i)
                results <- rbind(results, peptide)
            }
        }
        # add in whole protein sequence
        wholeProt <-
            data.frame(
                peptide = sequence,
                start = 1,
                stop = end_position,
                mc = "whole sequence"
            )
        results <- rbind(results, wholeProt)
        C <- 12
        H <- 1.0078250321
        O <- 15.9949146221
        S <- 31.97207069
        N <-
            ifelse(N15 == TRUE, 15.0001088984, 14.0030740052)
        proton <- 1.007276466
        residueMass <- function(residue) {
            if (residue == "A")
                mass = C * 3 + H * 5 + N + O
            if (residue == "R")
                mass = C * 6 + H * 12 + N * 4 + O
            if (residue == "N")
                mass = C * 4 + H * 6 + N * 2 + O * 2
            if (residue == "D")
                mass = C * 4 + H * 5 + N + O * 3
            if (residue == "E")
                mass = C * 5 + H * 7 + N + O * 3
            if (residue == "Q")
                mass = C * 5 + H * 8 + N * 2 + O * 2
            if (residue == "G")
                mass = C * 2 + H * 3 + N + O
            if (residue == "H")
                mass = C * 6 + H * 7 + N * 3 + O
            if (residue == "I")
                mass = C * 6 + H * 11 + N + O
            if (residue == "L")
                mass = C * 6 + H * 11 + N + O
            if (residue == "K")
                mass = C * 6 + H * 12 + N * 2 + O
            if (residue == "M")
                mass = C * 5 + H * 9 + N + O + S
            if (residue == "F")
                mass = C * 9 + H * 9 + N + O
            if (residue == "P")
                mass = C * 5 + H * 7 + N + O
            if (residue == "S")
                mass = C * 3 + H * 5 + N + O * 2
            if (residue == "T")
                mass = C * 4 + H * 7 + N + O * 2
            if (residue == "W")
                mass = C * 11 + H * 10 + N * 2 + O
            if (residue == "Y")
                mass = C * 9 + H * 9 + N + O * 2
            if (residue == "V")
                mass = C * 5 + H * 9 + N + O
            if (residue == "C" && IAA == FALSE)
                mass = C * 3 + H * 5 + N + O + S
            if (residue == "C" && IAA == TRUE)
                mass <-
                    ifelse(N15 == FALSE,
                            C * 5 + H * 8 + N *
                                2 + O * 2 + S,
                            C * 5 + H * 8 + N + 14.0030740052 +
                                O * 2 + S)
            if (length(custom) != 0)
                for (i in seq_along(custom$code))
                    if (residue == custom$code[i])
                        mass = custom$mass[i]
                    return(mass)
        }
        mz <- vector("list", length = nrow(results))
        for (i in seq_len(nrow(results))) {
            peptide_vector <- strsplit(results$peptide[i],
                                        split = "")[[1]]
            peptide_mass <-
                sum(vapply(peptide_vector,
                            residueMass,
                            FUN.VALUE = numeric(1)))
            mz[[i]] <-
                round((peptide_mass + H * 2 + O +
                            (c(
                                seq_len(maxCharge)
                            ) *
                                proton)) / c(seq_len(maxCharge)),
                        digits = 3)
        }
        mz <- as.data.frame(do.call("rbind", mz))
        names(mz) <-
            paste0("mz", seq_len(maxCharge))
        results <- cbind(results, mz)
        return(results)
    }