MasterFdrResults-class
                        Class '"MasterFdrResults"'
MasterPeptides-class    Class '"MasterPeptides"'
Synapter                Class "Synapter"
createUniquePeptideDbRds
                        Create an RDS file for the 'Unique Peptides
                        Database'
estimateMasterFdr       Computes FDR for all possible final peptide
                        combinations
inspectPeptideScores    Inspect peptide scores.
makeMaster              Merges final peptide files
plotFragmentMatching    Plot fragment matching results.
requantify,MSnSet-method
                        Intensity requantification
rescaleForTop3,MSnSet,MSnSet-method
                        Rescale for TOP3
synapter-package        Combine label-free data for optimal
                        identification and quantitation
synapterGuide           Opens the 'synapter' vignette
synapterPlgsAgreement,MSnSet-method
                        Synapter/PLGS Agreement
synapterTinyData        Loads a small test data for the 'synapter'
                        package
synergise               Synergise identification and quantitation
                        results
synergise2              Synergise identification and quantitation
                        results
