AAfragSettings: Settings For AA Fragmentation

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

Settings For AA Fragmentation

Description

This function provides basic settings for what types of fragments may accomodate which type of modifications : $knownMods: information about which modifications may be considered, $specAAMod: specifc AA sites (if applicable), $specAAMod: specifc AA sites (if applicable). For example, here 'p' codes for gain of mass for HPO3 only at S, T and Y residues. Note: $knownMods$Nterm and $knownMods$Cterm are treated as mutually exclusive

Usage

AAfragSettings(outTy = "all", silent = FALSE, debug = FALSE, callFrom = NULL)

Arguments

outTy	(character) default "all" or any of the list-elements
silent	(logical) suppress messages
debug	(logical) additional messages for debugging
callFrom	(character) allows easier tracking of messages produced

Value

This function returns a list ($knownMods, $knspecAAMods, $modChem, $neutralLossOrGain)

See Also

makeFragments, fragmentSeq, massDeFormula

Examples

AAfragSettings()

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