identifFixedModif {wrTopDownFrag}

Identify Fixed Modifications

Description

Identify peptide/protein fragment 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,
  filtChargeCatch = 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,
  chargeCatchFilter = TRUE,
  massTy = "mono",
  prefFragPat = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

prot

(character) amino-acid sequene of peptide or protein

expMass

(numeric) erperimental 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 cosiered

filtChargeCatch

(logical) by default removing of all fragments not containing a (polar) charge-cathing residue

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

chargeCatchFilter

(logical) optionally remove all peptides not containing charge-catch AAs (K, R, H, defined via .chargeCatchingAA() )

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

Value

list, ie result of massMatch() on 'pepTab' and 'expMass'

See Also

makeFragments

Examples

protP <- c(protP="PEPTIDEKR")
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
identP1 <- identifFixedModif(prot=protP, expMass=as.numeric(obsMassX), minFragSize=2, 
  maxFragSize=7,modTy=list(basMod=c("b","y")))     # looks ok
identP2 <- identifFixedModif(prot=protP, expMass=as.numeric(obsMassX), minFragSize=2, 
 maxFragSize=7, modTy=list(basMod=c("a","x"), varMod=c("h","o","r","m")))
 head(identP1$preMa,n=17)     # predicted masses incl fixed modif
 head(identP2$preMa,n=17)     # predicted masses incl fixed modif