AAfragSettings {wrTopDownFrag}

Settings for AA fragments

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")

Arguments

outTy

(character) default "all" or any of the list-elements

Value

list ($knownMods, $knspecAAMods, $modChem, $neutralLossOrGain)

See Also

makeFragments, fragmentSeq, massDeFormula

Examples

AAfragSettings()