.CtermPepCut            Make Named Character Vector Of Sequential
                        C-Terminal Fragments
.NtermPepCut            Make Named Character Vector Of Sequential
                        C-Terminal Fragments
.chColNa                Check Column Names from Matrix Or data.frame
.chargeCatchingAA       Cite Charge Catching Amino-Acids
.checkModTy             Check Modification Type
.countLET               Count Letters
.countModif             Count For All Proteins The Occurance Of
                        Modification Types
.evalIsoFra             Evaluate Selected Lines Of PepTab
.exNamesTyDeList        Reorganize List Of Peptide Fragments To Matrix
.multMatByColNa         Multiply Values Of Matrix By Its Colnames And
                        Sum By Row
.parCombinateAllAndSum
                        Multiprocessor Version For Full Combinatorial
                        And Cumulative Values
.prefFragPattern        Return data.frame with pattern of perferential
                        fragmentation sites
.singleSpecModif        Add Single Specific Modifications
.termPepCut             Make Named Character Vector Of Sequential
                        Terminal Fragments
AAfragSettings          Settings For AA Fragmentation
addMassModif            Add Modifications To Peptide Mass
checkModTy              Check & complete mixed of variable and fixed
                        modifications
combinatIntTable        Planing For Making All Multiplicative
                        Combinations
combinateAllAndSum      Full Combinatorial And Cumulative Values
corInDelShift           Corrective Values For Random Sequences For
                        In/Dels
corMutShift             Corrective Values For Random Sequences For
                        Mutations
countChildrenParent     Identify Children/Parent Settings As a+b=c
countPotModifAAs        Make Table With Counts of Potential
                        Modification Sites
evalIsoFragm            Evaluate Selected Lines Of PepTab (iso-mass)
                        For Preferential Cutting Sites
fragmentSeq             Fragment Protein Or Peptide Sequence
identifFixedModif       Identify Fixed Modifications
identifVarModif         Idenitfy Variable Modifications
identifyPepFragments    Identify terminal and internal
                        protein/peptide-fragments as matches to
                        experimental MS-peaks
makeFragments           Make Terminal And Internal Fragments From
                        Proteins
modifFragmTabOutput     Change fragment identification output format
                        (for biologists)
plotFragmLoc            Plot Identified Fragments Relative To Their
                        Location
plotMgfLike             Draw simplified (deconvoluted) spectrum of mgf
                        type and highlight peaks with matches found to
                        theoretical data
plotNTheor              Plot the number of theoretical random fragments
plotPrefFragPat         plot preferential fragmenation pattern Plot
                        preferential fragmenation pattern equivalent to
                        Fig 1b of Haverland et al 2017 (J Am Soc Mass
                        Spectrom)
randMassByMut           Make decoy mass by full randomization
randMassByStochastic    Make Decoy Mass By Full Randomization
scoreChargeCatch        Scoring Of Charge Catching Potential For
                        Peptides
scoreFragments          Scoring For Single Protein : Individual
                        Components
scorePrefFrag           Identifcation and scoring of preferential
                        cuting sites
scoreProteinFragments   Scoring Of Identifications (For Multi-Protein
                        Queries)
