add prototype for .neutralLoss; see #47:3

R/functions-fragments.R

@@ -102,3 +102,46 @@
   return(df)
 }
 
+#' adds neutral loss to data.frame generated by .calculateFragments
+#' @param df data.frame generated by. calculateFragments
+#' @return data.frame neutral loss rows added
+#' @noRd
+.neutralLoss <- function(df) {
+  ## see "Low energy peptide fragmentation pathways" by Hugh-G. Patterton, Ph.D.
+  ## http://cbio.ufs.ac.za/fgap/download/fragmentation_review.pdf
+  ## see also discussion #47: https://github.com/lgatto/MSnbase/issues/47
+
+  ## constants
+  mass <- get.atomic.mass()
+
+  add <- c("_"=-(mass["H"]+2*mass["O"]), # - H2O
+           "*"=-(mass["N"]+3*mass["H"])) # - NH3
+
+  ## water loss
+  ## C-term COOH (all x, y, z fragments)
+  isXYZ <- which(df$type %in% c("x", "y", "z"))
+
+  ## N-term D/E, internal S/T
+  isDEST <- grep("^[DE].|.[ST].", df$seq)
+  isDEST <- setdiff(isDEST, isXYZ)
+
+  ## ammonia loss
+  ## N-term/internal K/N/Q, internal R
+  isKNQR <- grep("^.*[KNQ].|.R.", df$seq)
+
+  n <- c(length(isXYZ), length(isDEST), length(isKNQR))
+
+  if (sum(n)) {
+    idx <- c(isXYZ, isDEST, isKNQR)
+    ion <- rep(c("_", "_", "*"), n)
+    mz <- rep(add[c(1, 1, 2)], n)
+
+    loss <- df[idx, ]
+    loss[, c("ion", "type")] <- paste0(c(loss$ion, loss$type), ion)
+    loss$mz <- loss$mz + mz
+    df <- rbind(df, loss)
+    rownames(df) <- NULL
+  }
+  df
+}
+