Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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Documentation for package ‘protViz’ version 0.7.9

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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