| annotateAHO | annotate peptides using AhoCorasickTrie | 
| annotatePeptides | Annotate peptides with protein ids | 
| Cdsw | Compute dynamic swath windows | 
| Cdsw-class | Compute dynamic swath windows | 
| computeFDR | Compute FDR given a score | 
| computeFDRwithID | Compute FDR given a score | 
| createDecoyDB | Create db with decoys and contaminants | 
| create_fgcz_fasta_db | create fasta db from one or more fasta files | 
| fdrSample | Data frame score and proteinID | 
| greedy | given matrix (columns protein rows peptides), compute minimal protein set using greedy algorithm | 
| greedyRes2Matrix | converts result of greedy function to a matrix with 3 columns - peptide - charge and protein | 
| loadContaminantsFasta2019 | load list of contaminant sequences FGCZ 2019 | 
| loadContaminantsFasta2021 | load list of contaminant sequences FGCZ 2021 | 
| makeID | make id for chain in format sp|P30443|1A01_HUMANs25 | 
| makeIDUnip | make id for chain compatible with uniprot | 
| masses | MS masses A dataset containing approx 150000 MS1 precursor masses | 
| objectiveMS1Function | compute the deviation from optimum: equal number of MS1 per bin | 
| pepprot | Table containing peptide information | 
| plotFDR | plot FDR | 
| predictScoreFDR | Predict score given FDR | 
| prepareMatrix | given table of peptide protein assigments generate matrix | 
| protpepmetashort | Small version of pepprot dataset to speed up computation | 
| prozor | Minimal Protein Set Explaining Peptides | 
| readjustWindows | Readjust windows so that boundaries in regions of few peaks. | 
| readPeptideFasta | wrapper setting the correct parameters seqinr::read.fasta for reading peptide sequences | 
| removeSignalPeptide | remove signal peptides from main chain | 
| reverseSeq | create rev sequences to fasta list | 
| writeFasta | write fasta lists into file |