.chargeCatchingAA | Cite Charge Catching Amino-Acids |
.chColNa | Check Column Names from Matrix Or data.frame |
.checkModTy | Check Modification Type |
.countLET | Count Letters |
.countModif | Count For All Proteins The Occurance Of Modification Types |
.CtermPepCut | Make Named Character Vector Of Sequential C-Terminal Fragments |
.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 |
.NtermPepCut | Make Named Character Vector Of Sequential C-Terminal Fragments |
.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 |
combinateAllAndSum | Full Combinatorial And Cumulative Values |
combinatIntTable | Planing For Making All Multiplicative Combinations |
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) |