identifFixedModif: 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
)

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

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.

Examples

Run this code

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)),]