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protViz (version 0.2.06)

Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Description

This R package helps with quality checks, visualizations and analysis of mass spectrometry data, coming from proteomics experiments. The package is developed, tested and used at the Functional Genomics Center Zurich. We use this package mainly for prototyping, teaching, and having fun with proteomics data. But it can also be used to do solid data analysis for small scale data sets.

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Version

Install

install.packages('protViz')

Monthly Downloads

400

Version

0.2.06

License

GPL-3

Maintainer

Christian Panse

Last Published

September 18th, 2014

Functions in protViz (0.2.06)

pgLFQfeature

pgLFQfeature - A data set with a featuremap export ProgenesisLCMS
pgLFQaov

iTRAQ two group analysis
PTM_MarkerFinder_util

PTM MarkerFinder util plot
massDeviationPlot

Mass Deviation Plot
findNN

find index of nearest neighbor
AA

AA - amino acid table
psm

compute a matching between a peptide sequence and a MS2 spectrum
pgImporter

Progenesis Importer Function
msms

A data set containing tandem mass spectra of an LCMS experiment.
aa2mass

determine the weight if a fiven amino acid sequence
pressureProfile

NanoLC pressure profile
iTRAQ

iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.
fragmentIon

Compute the b and y Fragment Ions of a Peptide Sequence
iTRAQ2GroupAnalysis

iTRAQ two group analysis
lcmsmap

LC-MS Map
averagine

averagine - a data set conatining isotope envelopes of averagine peptides
HexNAc

HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques
iRTpeptides

iRT peptides - independent retention time peptides
de_novo

de-novo on tandem ms
pgLFQtNpq

Label Free Quantification using the top N peptide approach
parentIonMass

Compute Parent Ion Mass of a Peptide Sequence
PTM_MarkerFinder

PTM MarkerFinder
genMod

Generates all possible modification of a given peptide seqence and modification pattern
peakplot

Labelling of Peptide Fragment Mass Spectra
pressureProfileSummary

A misc function for finding NN time slots in pressure profile data.
findNN_

find index of nearest neighbor
pressureProfilePlot

Plotting pressure profile data from Eksigent LC pumps
deisotoper

find isotop pattern in a given mass spectrum
fetuinLFQ

fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.
pgLFQprot

pgLFQprot - A data set with a featuremap export ProgenesisLCMS