protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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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 data analysis for small scale data sets.

Author
Christian Panse <cp@fgcz.ethz.ch>, Jonas Grossmann <jg@fgcz.ethz.ch>, Simon Barkow-Oesterreicher <sb@fgcz.ethz.ch>
Date of publication
2016-12-05 18:28:47
Maintainer
Christian Panse <cp@fgcz.ethz.ch>
License
GPL-3
Version
0.2.15
URLs

View on CRAN

Man pages

AA
AA - amino acid table
aa2mass
determine the weight if a fiven amino acid sequence
averagine
averagine - a data set conatining isotope envelopes of...
deisotoper
find isotop pattern in a given mass spectrum
de_novo
de-novo on tandem ms
fetuinLFQ
fetuinLFQ - A data set for evaluation of relative and...
findNN
find index of nearest neighbor
findNN_
find index of nearest neighbor
fragmentIons
Compute the b and y Fragment Ions of a Peptide Sequence
genMod
Generates all possible modification of a given peptide...
HexNAc
HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS,...
iRTpeptides
iRT peptides - independent retention time peptides
iTRAQ
iTRAQ - A small 8-plex iTRAQ data set with confident...
iTRAQ2GroupAnalysis
iTRAQ two group analysis
lcmsmap
LC-MS Map
mdp
Mass Deviation Plot
msms
A data set containing tandem mass spectra of an LCMS...
parentIonMass
Compute Parent Ion Mass of a Peptide Sequence
peakplot
Labelling of Peptide Fragment Mass Spectra
pgImporter
Progenesis Importer Function
pgLFQaov
iTRAQ two group analysis
pgLFQfeature
pgLFQfeature - A data set with a featuremap export...
pgLFQprot
pgLFQprot - A data set with a featuremap export...
pgLFQtNpq
Label Free Quantification using the top N peptide approach
ppp
Plotting pressure profile data from Eksigent LC pumps
pps
A misc function for finding NN time slots in pressure profile...
pressureProfile
NanoLC pressure profile
psm
compute a matching between a peptide sequence and a MS2...
PTM_MarkerFinder
PTM MarkerFinder
PTM_MarkerFinder_util
PTM MarkerFinder util plot
sigmamix
MS dilution series of humen peptides.

Files in this package

protViz
protViz/inst
protViz/inst/CITATION
protViz/inst/NEWS.Rd
protViz/inst/doc
protViz/inst/doc/PTM_MarkerFinder.Rnw
protViz/inst/doc/protViz.pdf
protViz/inst/doc/protViz.R
protViz/inst/doc/protViz.Rnw
protViz/inst/doc/PTM_MarkerFinder.pdf
protViz/inst/doc/PTM_MarkerFinder.R
protViz/inst/unitTests
protViz/inst/unitTests/test_findNN_.R
protViz/inst/unitTests/test_aa2mass_main__verus__parentIonMass.R
protViz/inst/unitTests/test_deisotoper.R
protViz/inst/unitTests/test_aa2mass_main.R
protViz/inst/unitTests/test_psm.R
protViz/inst/unitTests/test_fragmentIon.R
protViz/exec
protViz/exec/protViz_dat2R.bash
protViz/exec/protViz_fun.bash
protViz/exec/protViz_mgf2RData.pl
protViz/exec/protViz_extractPressureProfiles.bash
protViz/exec/protViz_annotateSpecLib_with_protID_split.bash
protViz/exec/protViz_mascotDat2RData.pl
protViz/exec/protViz_annotateSpecLib_with_protID.py
protViz/exec/protViz_bibliospec2RData.py
protViz/tests
protViz/tests/runTests.R
protViz/src
protViz/src/tryptic-digest.c
protViz/src/Makevars
protViz/src/computeFragmentIons.c
protViz/src/rcppdeisotoperenvelope.h
protViz/src/base
protViz/src/base/ms
protViz/src/base/ms/deisotoper.h
protViz/src/base/chemistry
protViz/src/base/chemistry/iisotopeenvelope.h
protViz/src/fcat.c
protViz/src/deisotoper.cpp
protViz/src/protMass.c
protViz/src/computeParentIonMass.c
protViz/src/findNN_.cpp
protViz/src/findNN.c
protViz/src/aa2mass.cpp
protViz/NAMESPACE
protViz/demo
protViz/demo/peakplot.R
protViz/demo/quantification.R
protViz/demo/pressureProfile.R
protViz/demo/PTM_MarkerFinder.R
protViz/demo/00Index
protViz/data
protViz/data/pgLFQprot.RData
protViz/data/HexNAc.RData
protViz/data/AA.RData
protViz/data/sigmamix.RData
protViz/data/averagine.RData
protViz/data/iRTpeptides.RData
protViz/data/iTRAQ.RData
protViz/data/fetuinLFQ.RData
protViz/data/pressureProfile.RData
protViz/data/msms.RData
protViz/data/datalist
protViz/data/pgLFQfeature.RData
protViz/R
protViz/R/pgLFQ.R
protViz/R/peakplot.R
protViz/R/lcmsmap.R
protViz/R/parentIonMass.R
protViz/R/sysdata.rda
protViz/R/iTRAQ2GroupAnalysis.R
protViz/R/pgImporter.R
protViz/R/de_novo.R
protViz/R/fragmentIon.R
protViz/R/PTM_MarkerFinder.R
protViz/R/deisotoper.R
protViz/R/aa2mass.R
protViz/R/findNN.R
protViz/R/findNN_.R
protViz/R/pp.R
protViz/R/psm.R
protViz/R/mdp.R
protViz/R/genMod.R
protViz/vignettes
protViz/vignettes/PTM_MarkerFinder.Rnw
protViz/vignettes/protViz.Rnw
protViz/vignettes/protViz.bib
protViz/README.md
protViz/MD5
protViz/build
protViz/build/vignette.rds
protViz/DESCRIPTION
protViz/man
protViz/man/pgLFQaov.Rd
protViz/man/HexNAc.Rd
protViz/man/ppp.Rd
protViz/man/lcmsmap.Rd
protViz/man/genMod.Rd
protViz/man/aa2mass.Rd
protViz/man/iTRAQ.Rd
protViz/man/fetuinLFQ.Rd
protViz/man/pgLFQfeature.Rd
protViz/man/averagine.Rd
protViz/man/psm.Rd
protViz/man/pgLFQtNpq.Rd
protViz/man/findNN.Rd
protViz/man/pps.Rd
protViz/man/mdp.Rd
protViz/man/msms.Rd
protViz/man/iRTpeptides.Rd
protViz/man/fragmentIons.Rd
protViz/man/PTM_MarkerFinder.Rd
protViz/man/de_novo.Rd
protViz/man/AA.Rd
protViz/man/pgLFQprot.Rd
protViz/man/deisotoper.Rd
protViz/man/pgImporter.Rd
protViz/man/peakplot.Rd
protViz/man/findNN_.Rd
protViz/man/iTRAQ2GroupAnalysis.Rd
protViz/man/sigmamix.Rd
protViz/man/pressureProfile.Rd
protViz/man/parentIonMass.Rd
protViz/man/PTM_MarkerFinder_util.Rd
protViz/.Rinstignore