Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics


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Documentation for package ‘protViz’ version 0.2.9

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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.
averagine averagine - a data set conatining isotope envelopes of averagine peptides
bymatrix Compute the b and y Fragment Ions of a Peptide Sequence
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.
fetuinLFQ fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.
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
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
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
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
NN_ find index of nearest neighbor
parentIonMass Compute Parent Ion Mass of a Peptide Sequence
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
peptidespectrummatching compute a matching between a peptide sequence and a MS2 spectrum
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
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.
psm compute a matching between a peptide sequence and a MS2 spectrum
PTM_MarkerFinder PTM MarkerFinder
PTM_MarkerFinder_util PTM MarkerFinder util plot
sigmamix MS dilution series of humen peptides.
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