protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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.

Install the latest version of this package by entering the following in R:
install.packages("protViz")
AuthorChristian Panse <cp@fgcz.ethz.ch>, Jonas Grossmann <jg@fgcz.ethz.ch>, Simon Barkow-Oesterreicher
Date of publication2017-01-30 21:17:01
MaintainerChristian Panse <cp@fgcz.ethz.ch>
LicenseGPL-3
Version0.2.28
https://github.com/protViz/protViz/

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.

Functions

AA Man page
aa2mass Man page
apex Man page
averagine Man page
bymatrix Man page
defaultIon Man page
deisotoper Man page
de_novo Man page
empai Man page
fetuinLFQ Man page
findNN Man page
findNN_ Man page
fragmentIon Man page
genMod Man page
HexNAc Man page
ionseries Man page
irt Man page
iRT Man page
iRTpeptides Man page
iTRAQ Man page
iTRAQ2GroupAnalysis Man page
lcmsmap Man page
lcmsoverview Man page
massDeviationPlot Man page
mdp Man page
msms Man page
NN Man page
NN_ Man page
parentIonMass Man page
peakplot Man page
peakplot.label Man page
peakplot.pie Man page
peakplot.putlabel Man page
pep3d Man page
pepmass Man page
peptidespectrummatching Man page
pgImporter Man page
pgLFQaov Man page
pgLFQfeature Man page
pgLFQprot Man page
pgLFQtNpq Man page
pim Man page
ppp Man page
pps Man page
pPTM Man page
pressureProfile Man page
pressureProfilePlot Man page
pressureProfileSummary Man page
protViz Man page
psm Man page
PTM_MarkerFinder Man page
PTM_MarkerFinder_util Man page
sigmamix Man page
t3pq Man page
tNpq Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.