| AA | AA - amino acid table | 
| aa2mass | determine the weight if a fiven amino acid sequence | 
| ADPR | ADP Ribosylated Peptide | 
| ADPR.annotation | ADP Ribosylated Peptide | 
| ADPR.lim | ADP Ribosylated Peptide | 
| ADPR.ms2 | ADP Ribosylated Peptide | 
| apex | fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods. | 
| as.data.frame.fragmentIonSet | Compute the b and y Fragment Ions of a Peptide Sequence | 
| as.data.frame.mascot | Generic methods for mascot results | 
| as.data.frame.psmSet | Compute a matching between a peptide sequence and a MS2 spectrum | 
| as.psm.mascot_query | Generic methods for mascot results | 
| as.psmSet | psmSet - a set of peptide spectrum matches | 
| as.psmSet.mascot | psmSet - a set of peptide spectrum matches | 
| assignPlatePosition | Assign an instrument queue configuration to a plate | 
| averagine | averagine - a data set conatining isotope envelopes of averagine peptides | 
| blockRandom | Derive a randomization of a table. | 
| bymatrix | Compute the b and y Fragment Ions of a Peptide Sequence | 
| centroid | Centroid a spectrum acquired in profile mode | 
| defaultIon | Compute the b and y Fragment Ions of a Peptide Sequence | 
| deisotoper | find isotop pattern in a given mass spectrum | 
| de_novo | de-novo on tandem ms | 
| empai | fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods. | 
| FASTA | FASTA format reader | 
| Fasta | FASTA format reader | 
| fasta | FASTA format reader | 
| fetuinLFQ | fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods. | 
| findMz | PTM MarkerFinder | 
| findMz.mascot | PTM MarkerFinder | 
| findMz.psmSet | PTM MarkerFinder | 
| findNN | find index of nearest neighbor | 
| findNN_ | find index of nearest neighbor | 
| fragmentIon | Compute the b and y Fragment Ions of a Peptide Sequence | 
| genMod | Generates all possible modification of a given peptide seqence and modification pattern | 
| HexNAc | HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques | 
| hydrophobicity | Sequence Specific Retention Calculator | 
| insertSamples | Insert sample on a given position | 
| ionseries | Compute the b and y Fragment Ions of a Peptide Sequence | 
| iRT | iRT peptides - independent retention time peptides | 
| irt | iRT peptides - independent retention time peptides | 
| iRTpeptides | iRT peptides - independent retention time peptides | 
| is.mascot | Generic methods for mascot results | 
| is.mascot_query | Generic methods for mascot results | 
| is.psm | Compute a matching between a peptide sequence and a MS2 spectrum | 
| is.psmSet | psmSet - a set of peptide spectrum matches | 
| iTRAQ | iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins. | 
| iTRAQ2GroupAnalysis | iTRAQ two group analysis | 
| lcmsmap | LC-MS Map | 
| lcmsoverview | LC-MS Map | 
| lower_bound_ | find index of nearest neighbor | 
| mascot | Generic methods for mascot results | 
| massDeviationPlot | Mass Deviation Plot | 
| mdp | Mass Deviation Plot | 
| msms | A data set containing tandem mass spectra of an LCMS experiment. | 
| NN | find index of nearest neighbor | 
| parentIonMass | Compute Parent Ion Mass of a Peptide Sequence | 
| peaklist | Labelling of Peptide Fragment Mass Spectra | 
| peaklistSet | Labelling of Peptide Fragment Mass Spectra | 
| peakplot | Labelling of Peptide Fragment Mass Spectra | 
| peakplot.label | Labelling of Peptide Fragment Mass Spectra | 
| peakplot.pie | Labelling of Peptide Fragment Mass Spectra | 
| peakplot.putlabel | Labelling of Peptide Fragment Mass Spectra | 
| pep3d | LC-MS Map | 
| pepmass | Compute Parent Ion Mass of a Peptide Sequence | 
| pgImporter | Progenesis Importer Function | 
| pgLFQaov | iTRAQ two group analysis | 
| pgLFQfeature | pgLFQfeature - A data set with a featuremap export ProgenesisLCMS | 
| pgLFQprot | pgLFQprot - A data set with a featuremap export ProgenesisLCMS | 
| pgLFQtNpq | Label Free Quantification using the top N peptide approach | 
| pim | Compute Parent Ion Mass of a Peptide Sequence | 
| plot.mascot | Generic methods for mascot results | 
| plot.mascot_query | Generic methods for mascot results | 
| plot.psm | Labelling of Peptide Fragment Mass Spectra | 
| plot.psmSet | LC-MS Map | 
| ppp | Plotting pressure profile data from Eksigent LC pumps | 
| pps | A misc function for finding NN time slots in pressure profile data. | 
| pPTM | PTM MarkerFinder | 
| pressureProfile | NanoLC pressure profile | 
| pressureProfilePlot | Plotting pressure profile data from Eksigent LC pumps | 
| pressureProfileSummary | A misc function for finding NN time slots in pressure profile data. | 
| profile | Centroid a spectrum acquired in profile mode | 
| protViz | Labelling of Peptide Fragment Mass Spectra | 
| psm | Compute a matching between a peptide sequence and a MS2 spectrum | 
| PTM_MarkerFinder | PTM MarkerFinder | 
| PTM_MarkerFinder_util | PTM MarkerFinder util plot | 
| ssrc | Sequence Specific Retention Calculator | 
| summary.cometdecoy | Generic methods for mascot results | 
| summary.mascot | Generic methods for mascot results | 
| summary.psmSet | Compute a matching between a peptide sequence and a MS2 spectrum | 
| t3pq | fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods. | 
| tNpq | Label Free Quantification using the top N peptide approach |