AA                      AA - amino acid table
ADPR                    ADP Ribosylated Peptide
Fasta                   FASTA format reader
HexNAc                  HexNAc - Analysis of N-HexNAc glycopeptides by
                        LC-MS/MS, using HCD and ETD fragmentation
                        techniques
PTM_MarkerFinder        PTM MarkerFinder
PTM_MarkerFinder_util   PTM MarkerFinder util plot
aa2mass                 determine the weight if a fiven amino acid
                        sequence
as.psmSet               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.
centroid                Centroid a spectrum acquired in profile mode
de_novo                 de-novo on tandem ms
deisotoper              find isotop pattern in a given mass spectrum
fetuinLFQ               fetuinLFQ - A data set for evaluation of
                        relative and absolute label-free quantification
                        methods.
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
iRTpeptides             iRT peptides - independent retention time
                        peptides
iTRAQ                   iTRAQ - A small 8-plex iTRAQ data set with
                        confident identified peptides from 5 proteins.
iTRAQ2GroupAnalysis     iTRAQ two group analysis
insertSamples           Insert sample on a given position
lcmsmap                 LC-MS Map
mascot                  Generic methods for mascot results
massDeviationPlot       Mass Deviation Plot
msms                    A data set containing tandem mass spectra of an
                        LCMS experiment.
parentIonMass           Compute Parent Ion Mass of a Peptide Sequence
peakplot                Labelling of Peptide Fragment Mass Spectra
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
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.
psm                     Compute a matching between a peptide sequence
                        and a MS2 spectrum
ssrc                    Sequence Specific Retention Calculator
