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.

AuthorChristian Panse <cp@fgcz.ethz.ch>, Jonas Grossmann <jg@fgcz.ethz.ch>, Simon Barkow-Oesterreicher <sb@fgcz.ethz.ch>
Date of publication2016-12-05 18:28:47
MaintainerChristian Panse <cp@fgcz.ethz.ch>
LicenseGPL-3
Version0.2.15
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.

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

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.