makeFragments: Make Terminal And Internal Fragments From Proteins

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

Make Terminal And Internal Fragments From Proteins

Description

Makes terminal and internal fragments based on protein-sequence and present as matrix including heading and/or tailing amino-acid or theoretical molecular mass of all fragments. As the number of theoretically possible fragments increases with the size of the peptide/protein treated it is recommended to adopt arguments like masFragSize to realistic values for the type of mass spectrometer used, since efficient filtering will reduce considerably the amount of memory (RAM) needed and will improve overal performance.

Usage

makeFragments(
  protTab,
  minFragSize = 6,
  maxFragSize = 300,
  internFra = TRUE,
  knownMods = NULL,
  redRedundSeq = FALSE,
  prefFragPat = NULL,
  remNonConfPrefFragm = TRUE,
  ambigLab = c(duplSequence = "duplSequence", isoMass = "isoMass"),
  massTy = "mono",
  specModif = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

protTab	(character or matrix) named vector of protein-seqences to fragment or or, matrix with 1st column 'ma' with mass and 2nd column 'se' with protein-/peptide-sequence (optionally sequence(s) also as rownames or 3rd column with 'trivial' names)
minFragSize	(integer) minimum number of amino-acids for being considered
maxFragSize	(integer) maximum number of amino-acids for being considered
internFra	(logical) toggle if internal framents will be produced or not
knownMods	(character) optional custom alternative to AAfragSettings(ou="all")$knownMods
redRedundSeq	(logical) reduce redundant sequences to 1st appearance in all further treatments
prefFragPat	(matrix) for preferential fragmentation rules (see also .prefFragPattern)
remNonConfPrefFragm	(logical) allows to remove (peptide-)fragments non conform with preferential fragmentation rules (using evalIsoFragm)
ambigLab	(character) text-labels for ambiguities (first for duplicated sequences second for iso-mass)
massTy	(character) default 'mono' for mono-isotopic masses (alterative 'average')
specModif	(list) supplemental custom fixed or variable modifications (eg Zn++ at given residue)
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allow easier tracking of messages produced

Value

matrix with fragment sequence, mass, start- and end-position, heading and tailing AA (or NA if terminal fragment)

See Also

makeFragments; evalIsoFragm, from package wrProteo convAASeq2mass, AAmass, massDeFormula

Examples

protP <- c(protP="PEPTIDE")
pepT1 <- makeFragments(protTab=protP, minFragSize=2, maxFragSize=9, internFra=TRUE)
tail(pepT1)

protP2 <- cbind(se="PEPTIDE", ma="1304.7088503626")
pepT2 <- makeFragments(protTab=protP2, minFragSize=2, maxFragSize=9, internFra=TRUE)
tail(pepT1)

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