identifVarModif: Idenitfy Variable Modifications

Description

Take result from identifFixedModif and search for variable modifications (only on identified fixed modif), ie 2nd step for identif of var modifs. To reduce the complexity of the search space, only peptide fragments identified with fixed identifiactions will be considered for possible variable modifications.

Usage

identifVarModif(
  zz,
  modTy,
  expMa,
  maxMod,
  identMeas = "ppm",
  knownMods = NULL,
  limitIdent = 5,
  filtAmbiguous = FALSE,
  indexStart = 1,
  recalibFact = NULL,
  suplPepTab = NULL,
  massTy = "mono",
  silent = FALSE,
  callFrom = NULL,
  debug = TRUE
)

Value

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

Arguments

zz: (list) min input, result from identifFixedModif, must conatain elements 'nmassMatch','preMa','pepTab','recalibFact','recalibData'
modTy: (character) type of fixed and variable modifications
expMa: (matrix) experimental m/z values
maxMod: (integer) maximum number of residue modifications to be consiered in fragments (values >1 will increase complexity and RAM consumption)
identMeas: (character) comparison type (used in findCloseMatch(), default ="ppm"), used with limit 'limitIdent'
knownMods: (character) optional custom alternative to AAfragSettings(ou="all")$knownMods
limitIdent: (integer) limit applied to 'identMeas'
filtAmbiguous: (logical) toggle to remove all ambiguous identifications
indexStart: (integer) for keeping correct index at iterative use
recalibFact: (numeric, length=1)
suplPepTab: (matrix) predicted fragments (incl fixed and var modifs) to include to search (allowong to ensure overlap to include hits close to prev search)
massTy: (character) 'mono' or 'average'
silent: (logical) suppress messages
callFrom: (character) allow easier tracking of messages produced
debug: (logical) additional messages for debugging

Details

The main matching results are in output$massMatch : This list has one entry for each predicted mass where some matches were found. Thus, the names of the list-elements design the index from argument expMass. Each list-element contains a numeric vector giving the difference observed to predicted, the names design the unique predicted peptide index/number from output$preMa[,"no"]

Examples

Run this code

protP <- c(protP="PEPTIDE")
obsMassX <- cbind(a=c(199.1077,296.1605,397.2082,510.2922,625.3192),
  b=c(227.1026,324.1554,425.2031,538.2871,653.3141),
  x=c(729.2937,600.2511,503.1984,402.1507,289.0666),
  y=c(703.3145,574.2719,477.2191,376.1714,263.0874))
rownames(obsMassX) <- c("E","P","T","I","D")      # all 1 & 7 ions not included
identP10 <- identifFixedModif(prot=protP,expMass=as.numeric(obsMassX),minFragSize=2, 
  maxFragSize=7,modTy=list(basMod=c("b","y")))     # looks ok
identP10v <- identifVarModif(identP10,list(varMod="h"), as.numeric(obsMassX),2)
identP10v$massMatch                    # list of matches