| AAfragSettings | Settings for AA fragments |
| addMassModif | Add modifications to peptide mass |
| checkModTy | Check & complete mixed of variable and fixed modifications |
| combinateAllAndSum | Full combinatorial and cumulative values |
| 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 |
| makeFragments | Make terminal and internal fragments from proteins |
| plotNTheor | Plot the number of theoretical random fragments |
| scoreChargeCatch | Scoring of charge catching potential for peptides |