scorePrefFrag: Identifcation and scoring of preferential cuting sites

In wrTopDownFrag: Internal Fragment Identification from Top-Down Mass Spectrometry

Identifcation and scoring of preferential cuting sites

Description

Search for preferential fragmentation sites from 'pepTab' among the 3 colums specified via 'useCol' (for full AA sequence, preceeding AA, tailing AA) and return sum of scores (from 3rd column of prefFragPat) for both ends. Note : proteins must be witten as single lettre code.

Usage

scorePrefFrag(
  pepTab,
  useCol = c("seq", "precAA", "tailAA"),
  prefFragPat = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

pepTab	(matrix) peptide-fragments with lines for peptides, cols as sequence/preceedingAA/tailingAA
useCol	(character) column names for peptide-sequence,preceeding and tailing AA
prefFragPat	(matrix) for preferential fragmentation rules (see .prefFragPattern())
silent	(logical) suppress messages
debug	(logical) additional messages and objects exportet to current session for debugging
callFrom	(character) allow easier tracking of messages produced

Value

This function returns a matrix with fragment sequence, mass, start- and end-position, heading and tailing AA (or NA if terminal fragment)

See Also

makeFragments

Examples

pepT <- cbind(precAA=c("A","D","D","A","D"),seq=c("AKA","PKA","AKA","PKD","PKD"),
  tailAA=c("A","A","D","P","P"))
scorePrefFrag(pepT)

wrTopDownFrag documentation built on June 8, 2025, 1:34 p.m.