identifyPepFragments: Identify terminal and internal protein/peptide-fragments as...

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

Identify terminal and internal protein/peptide-fragments as matches to experimental MS-peaks

Description

Function for predicting internal and terminal peptide-fragments and compare them with experimental monoisotopic masses. The accuracy of results is given in ppm and a false discovery rate (FDR) for the identification is estimated. The identifed fragments are also checked for preferential break sites, a score including this and other parameters is given with the results.

Usage

identifyPepFragments(
  expMass,
  pep,
  modTy = NULL,
  minFragSize = 6,
  maxFragSize = 75,
  identMeas = "ppm",
  limitIdent = 5,
  internFra = TRUE,
  specModif = NULL,
  massTy = "mono",
  chargeCatchFilter = TRUE,
  corMutShift = NULL,
  nProc = 1,
  parallDefault = TRUE,
  multParam = NULL,
  maxMod = c(p = 3, h = 1, k = 1, o = 1, m = 1, n = 1, u = 1, r = 1, s = 1),
  recalibrate = TRUE,
  filtAmbiguous = FALSE,
  prefFragmPat = NULL,
  sortOutputByMass = FALSE,
  silent = FALSE,
  callFrom = NULL,
  debug = FALSE
)

Arguments

expMass	(matrix or data.frame)
pep	(character) protein/peptide sequences to be used for fragmentation
modTy	(list) defining fixed and variable modifications
minFragSize	(integer) min length in AA of peptides to be considered (please see you spectrometers characteristics)
maxFragSize	(integer) max length in AA of peptides to be considered (please see you spectrometers characteristics)
identMeas	(character) comparison type (used in findCloseMatch(), default ="ppm"), used with limit 'limitIdent'
limitIdent	(integer) limit applied to 'identMeas'
internFra	(logical) switch from including all internal fragments to terminal fragments only (if F)
specModif	(list) optional custom single-site modifications (eg ions bound), will be processed using .singleSpecModif
massTy	(list) list of modifications/fragmentation-type(s) to consider, organipredMae as 'basMod' (any occurance) and 'varMod' (optional aoccurance), 'modPos' (position of modif, integer), 'modMass' (mass to be added), 'modName' (name), 'modFixed' (fixed or variable modif, logical)
chargeCatchFilter	(logical) filter (upfront) to consider only peptides containing AAs capable of catching extra charges (K, R, H, defined via .chargeCatchingAA())
corMutShift	(numeric) (numeric) vector of decoy-type possible mass shifts (eg from load("C:/E/projects/MassSpec/fragmIdentif/corMutShift.RData"))
nProc	(integer) number of preocessors to use
parallDefault	(logical) if 'parallDefault'=F no multiprocessor parameters set for BiocParallel
multParam	(list)
maxMod	(integer) maximum number of residue modifications to be consiered in fragments (values >1 will increase complexity and RAM consumption)
recalibrate	(logical) recalibrate based on region with highest density of experim values
filtAmbiguous	(logical)
prefFragmPat	(matrix) optional custum preferential fragmentation pattern (otherwise .prefFragPattern() will be used)
sortOutputByMass	(logical)
silent	(logical) suppress messages
callFrom	(character) allow easier tracking of messages produced
debug	(logical) additional messages for debugging

Value

matrix of idenitfied ions

See Also

makeFragments, identifVarModif, identifFixedModif, findCloseMatch, scoreProteinFragments

Examples

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
modTy1 <- list(basMod=c("b","y"), varMod=c("p","o","q"))
frag1 <- identifyPepFragments(ex=as.numeric(obsMassX), pe=protP, modTy=modTy1, 
  minFragSize=2, chargeCatchFilter=FALSE)
(frag1b <- if(length(unlist(frag1$identif)) >0) modifFragmTabOutput(frag1))

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