# Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

## Documentation for package ‘protViz’ version 0.7.9

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Code demos. Use demo() to run them.
- Package NEWS
- Package README

## Help Pages

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