| AA | AA - amino acid table |
| aa2mass | determine the weight if a fiven amino acid sequence |
| 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 |
| averagine | averagine - a data set conatining isotope envelopes of averagine peptides |
| 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 |
| 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 |