wrTopDownFrag (version 1.0.4)

.singleSpecModif: Add Single Specific Modifications

Description

Add single specific modification to peptide/protein fragments .

Usage

.singleSpecModif(
  pepTab,
  specModif,
  nMaxMod = 1,
  massTy = "mono",
  callFrom = NULL,
  silent = FALSE,
  debug = FALSE
)

Value

This function returns a list with $massMatch (list of exerimental peptides matching to one or more predicted), $preMa (predicted ions, including fixed modif), $pepTab (predicted neutral peptides, wo modifications), $expMa (experimental mass from input), $recalibFact (recalibration factor as from input), $docTi (time for calculations)

Arguments

pepTab

(matrix) matrix of fragments (cols 'no','seq','orig','ty','seqNa','beg','end','precAA','tailAA','ambig','mass')

specModif

(list) with elements 'modOrigin' (sequence), 'modPos' (position within sequence), 'modMass' (digits, ie mass to add), 'modName' (name of modif), 'modFixed' (fixed or , logical)

nMaxMod

(numeric) max number a given modification may occur

massTy

(character) 'mono' or 'average'

callFrom

(character) allow easier tracking of message(s) produced

silent

(logical) suppress messages

debug

(logical) additional messages and objects exportet to current session for debugging

See Also

makeFragments, identifVarModif, identifyPepFragments

Examples

pep1 <- c(pe1="KPEPTI")
# The table of possible terminal fragments (for simplicity terminal only)
pepTab1 <- makeFragments(pep1, min=3, max=7, internFra=FALSE)
specModif1 <- list(modOrigin=pep1, modPos=1, modMass=579.9663, modName="p", modFixed=FALSE)
.singleSpecModif(pepTab1, specModif1 )

protP <- c(protP="PEPTIDEKR")
pep1 <- c("PTI","KPE","EPTI")
papTab1 <- cbind(no=c(7,2,6),seq=pep1, orig=rep("KPEPTI",3), origNa=rep("pe1",3), 
  ty=paste0(c("C","N","C"),"ter"), beg=c(4,1,3), end=c(6,3,4),
  mass= wrProteo::convAASeq2mass(pep1, massTy="mono"), modSpec="")