Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics


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Documentation for package ‘protViz’ version 0.1.01

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apex fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.
bymatrix Compute b and y Fragment Ions of a Peptide Sequence
defaultIons Compute b and y Fragment Ions of a Peptide Sequence
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
fragmentIons Compute b and y Fragment Ions of a Peptide Sequence
ionseries Compute b and y Fragment Ions of a Peptide Sequence
iTRAQ iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.
iTRAQ2GroupAnalysis iTRAQ two group analysis
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
pepmass Compute Parent Ion Mass of a Peptide Sequence
peptidesequencematching compute a matching between a peptide sequence and a MS2
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
pim Compute Parent Ion Mass of a Peptide Sequence
pressureProfile NanoLC pressure profile
pressureProfilePlot plotting pressure profile data
pressureProfileSummary A misc function for finding NN time slots in pressure profile data.
psm compute a matching between a peptide sequence and a MS2
t3pq fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.