identifFixedModif: Identify Fixed Modifications

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

Identify Fixed Modifications

Description

Identify peptide/protein fragments based on experimental m/z values 'expMass' for given range of aa-length. Internally all possible fragments will be predicted and their mass compared to the experimental values (argument expMass).

Usage

identifFixedModif(
  prot,
  expMass,
  minFragSize = 5,
  maxFragSize = 60,
  indexStart = 1,
  suplPepTab = NULL,
  internFra = TRUE,
  chargeCatchFilter = TRUE,
  maxMod = c(p = 3, h = 1, k = 1, o = 1, m = 1, n = 1, u = 1, r = 1, s = 1),
  modTy = NULL,
  specModif = NULL,
  knownMods = NULL,
  identMeas = "ppm",
  limitIdent = 5,
  filtAmbiguous = FALSE,
  recalibrate = FALSE,
  massTy = "mono",
  prefFragPat = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

prot	(character) amino-acid sequene of peptide or protein
expMass	(numeric) experimental masses to identify peptides from
minFragSize	(integer) min number of AA residues for considering peptide fragments
maxFragSize	(integer) max number of AA residues for considering peptide fragments
indexStart	(integer) for starting at correct index (if not 1)
suplPepTab	(matrix) additional peptides to be add to theoretical peptides
internFra	(logical) decide whether internal fragments should be consiered
chargeCatchFilter	(logical) by default remove all peptides not containing charge-catching (polar) AAs (K, R, H, defined via .chargeCatchingAA() )
maxMod	(integer) maximum number of residue modifications to be consiered in fragments (values >1 will increase complexity and RAM consumption)
modTy	(character) type of fixed and variable modifications
specModif	(list) supplemental custom fixed or variable modifications (eg Zn++ at given residue)
knownMods	(character) optional custom alternative to AAfragSettings(ou="all")$knownMods
identMeas	(character) default 'ppm'
limitIdent	(character) thershold for identification in 'identMeas' units
filtAmbiguous	(logical) allows filtering/removing ambiguous results (ie same mass peptides)
recalibrate	(logical or numeric) may be direct recalibration-factor (numeric,length=1), if 'TRUE' fresh determination of 'recalibFact' or 'FALSE' (no action); final recalibration-factor used exported in result as $recalibFact
massTy	(character) 'mono' or 'average'
prefFragPat	(numeric) pattern for preferential fragmentation (see also Haverland 2017), if NULL default will be taken (in function evalIsoFragm) from .prefFragPattern()
silent	(logical) suppress messages
debug	(logical) additional messages and objects exportet to current session for debugging
callFrom	(character) allow easier tracking of message(s) produced

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"]

The main element of the output is the $massMatch -list, which is in the format of findCloseMatch. Thus, the list-elements names represent the line-number of mass-predictions and the values the delta-mass and their names the position of the initial query.

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)

See Also

makeFragments, identifVarModif, identifyPepFragments, findCloseMatch

Examples

pro3 <- "HLVDEPQNLIK"
exp3 <- c( b4=465.2451, b5=594.2877, b6=691.3404,  y7=841.4772, y6=712.4347, y5=615.3819)
ident3 <- identifFixedModif(prot=pro3, expMass=exp3, minFragSize=4, 
  maxFragSize=60, modTy=list(basMod=c("b","y")))
ident3$massMatch                                                                                              
## as human readable table:
ident3$preMa[ ident3$preMa[,"no"] %in% (names(ident3$massMatch)),]

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