Package: protViz 0.7.9

protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

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 <https://fgcz.ch>. 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.

Authors:Christian Panse [aut, cre], Jonas Grossmann [aut], Simon Barkow-Oesterreicher [ctb]

protViz_0.7.9.tar.gz
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protViz.pdf |protViz.html✨
protViz/json (API)
NEWS

# Install 'protViz' in R:
install.packages('protViz', repos = c('https://cpanse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cpanse/protviz/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • AA - AA - amino acid table
  • ADPR.annotation - ADP Ribosylated Peptide
  • ADPR.lim - ADP Ribosylated Peptide
  • ADPR.ms2 - ADP Ribosylated Peptide
  • HexNAc - HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniques
  • averagine - Averagine - a data set conatining isotope envelopes of averagine peptides
  • fetuinLFQ - FetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.
  • iRTpeptides - IRT peptides - independent retention time peptides
  • iTRAQ - ITRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.
  • msms - A data set containing tandem mass spectra of an LCMS experiment.
  • pgLFQfeature - PgLFQfeature - A data set with a featuremap export ProgenesisLCMS
  • pgLFQprot - PgLFQprot - A data set with a featuremap export ProgenesisLCMS
  • pressureProfile - NanoLC pressure profile

On CRAN:

funmass-spectrometrypeptide-identificationproteomicsquantificationvisualization

7.88 score 11 stars 2 packages 72 scripts 577 downloads 4 mentions 47 exports 1 dependencies

Last updated 12 months agofrom:fd0091823a. Checks:OK: 3 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-win-x86_64OKNov 01 2024
R-4.5-linux-x86_64OKNov 01 2024
R-4.4-win-x86_64NOTENov 01 2024
R-4.4-mac-x86_64NOTENov 01 2024
R-4.4-mac-aarch64NOTENov 01 2024
R-4.3-win-x86_64NOTENov 01 2024
R-4.3-mac-x86_64NOTENov 01 2024
R-4.3-mac-aarch64NOTENov 01 2024

Exports:aa2massas.data.frame.fragmentIonSetas.data.frame.mascotas.data.frame.psmSetas.psm.mascot_queryas.psmSetassignPlatePositionblockRandomcentroidde_novodefaultIondeisotoperFastafindMzfindMz.mascotfindMz.psmSetfindNNfindNN_fragmentIongenModinsertSamplesis.mascotis.mascot_queryis.psmis.psmSetiTRAQ2GroupAnalysislcmsmaplower_bound_mdpparentIonMasspeakplotpgImporterpgLFQaovpgLFQtNpqplot.mascotplot.mascot_queryplot.psmplot.psmSetpppppspsmPTM_MarkerFinderPTM_MarkerFinder_utilssrcsummary.cometdecoysummary.mascotsummary.psmSet

Dependencies:Rcpp

ADP Ribosylated Peptides

Rendered fromADP-Ribosylated-peptides.Rnwusingutils::Sweaveon Nov 01 2024.

Last update: 2022-05-25
Started: 2022-04-04

Howto find putative ptm marker ion?

Rendered fromPTM_MarkerFinder.Rnwusingutils::Sweaveon Nov 01 2024.

Last update: 2019-11-18
Started: 2014-12-19

primer - protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

Rendered fromprotViz.Rnwusingutils::Sweaveon Nov 01 2024.

Last update: 2022-04-14
Started: 2014-12-19

protViz package poster (in portrait)

Rendered fromposter.Rnwusingutils::Sweaveon Nov 01 2024.

Last update: 2019-01-04
Started: 2017-06-19

Readme and manuals

Help Manual

Help pageTopics
AA - amino acid tableAA
determine the weight if a fiven amino acid sequenceaa2mass
ADP Ribosylated PeptideADPR ADPR.annotation ADPR.lim ADPR.ms2
psmSet - a set of peptide spectrum matchesas.psmSet as.psmSet.mascot is.psmSet
Assign an instrument queue configuration to a plateassignPlatePosition
averagine - a data set conatining isotope envelopes of averagine peptidesaveragine
Derive a randomization of a table.blockRandom
Centroid a spectrum acquired in profile modecentroid profile
de-novo on tandem msde_novo
find isotop pattern in a given mass spectrumdeisotoper
FASTA format readerFASTA Fasta fasta
fetuinLFQ - A data set for evaluation of relative and absolute label-free quantification methods.apex empai fetuinLFQ t3pq
find index of nearest neighborfindNN findNN_ lower_bound_ NN
Compute the b and y Fragment Ions of a Peptide Sequenceas.data.frame.fragmentIonSet bymatrix defaultIon fragmentIon ionseries
Generates all possible modification of a given peptide seqence and modification patterngenMod
HexNAc - Analysis of N-HexNAc glycopeptides by LC-MS/MS, using HCD and ETD fragmentation techniquesHexNAc
Insert sample on a given positioninsertSamples
iRT peptides - independent retention time peptidesiRT irt iRTpeptides
iTRAQ - A small 8-plex iTRAQ data set with confident identified peptides from 5 proteins.iTRAQ
iTRAQ two group analysisiTRAQ2GroupAnalysis
LC-MS Maplcmsmap lcmsoverview pep3d plot.psmSet
Generic methods for mascot resultsas.data.frame.mascot as.psm.mascot_query is.mascot is.mascot_query mascot plot.mascot plot.mascot_query summary.cometdecoy summary.mascot
Mass Deviation PlotmassDeviationPlot mdp
A data set containing tandem mass spectra of an LCMS experiment.msms
Compute Parent Ion Mass of a Peptide SequenceparentIonMass pepmass pim
Labelling of Peptide Fragment Mass Spectrapeaklist peaklistSet peakplot peakplot.label peakplot.pie peakplot.putlabel plot.psm protViz
Progenesis Importer FunctionpgImporter
iTRAQ two group analysispgLFQaov
pgLFQfeature - A data set with a featuremap export ProgenesisLCMSpgLFQfeature
pgLFQprot - A data set with a featuremap export ProgenesisLCMSpgLFQprot
Label Free Quantification using the top N peptide approachpgLFQtNpq tNpq
NanoLC pressure profilepressureProfile
Plotting pressure profile data from Eksigent LC pumpsppp pressureProfilePlot
A misc function for finding NN time slots in pressure profile data.pps pressureProfileSummary
Compute a matching between a peptide sequence and a MS2 spectrumas.data.frame.psmSet is.psm psm summary.psmSet
PTM MarkerFinderfindMz findMz.mascot findMz.psmSet pPTM PTM_MarkerFinder
PTM MarkerFinder util plotPTM_MarkerFinder_util
Sequence Specific Retention Calculatorhydrophobicity ssrc