Package: isobar 1.51.0

Florian P Breitwieser

isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Authors:Florian P Breitwieser <[email protected]> and Jacques Colinge <[email protected]>, with contributions from Alexey Stukalov <[email protected]>, Xavier Robin <[email protected]> and Florent Gluck <[email protected]>

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isobar.pdf |isobar.html✨
isobar/json (API)
NEWS

# Install 'isobar' in R:

install.packages('isobar', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/fbreitwieser/isobar/issues

Datasets:

ib_phospho - Isobar Data packages
ibspiked_set1 - Isobar Data packages
ibspiked_set2 - Isobar Data packages
noise.model.hcd - Isobar Data packages

On BioConductor:isobar-1.51.0(bioc 3.20)isobar-1.50.0(bioc 3.19)

bioconductor-package

175 exports 1.80 score 82 dependencies 4 mentions

Last updated 2 months agofrom:96447b8c6f

Exports:%inrange%adjust.ratio.pvalue as.data.frame.IBSpectra as.data.frame.ProteinGroup calc.delta.score calc.pep.delta.score calcCumulativeProbXGreaterThanY calcPeptidePosition calcProbXDiffNormals calcProbXGreaterThanY calculate.dNSAF calculate.emPAI calculate.mult.sample.pvalue calculate.ratio.pvalue calculate.sample.pvalue classLabels classLabels<-combn.matrix combn.protein.tbl connect.nodes correct.peptide.ratios correctIsotopeImpurities create.meta.reports create.reports distrprint do.log draw.boxplot draw.protein.group draw.proteingroup.row estimateRatio estimateRatioForPeptide estimateRatioForProtein estimateRatioNumeric exclude filterSpectraDeltaScore filterSpectraPhosphoRS fitCauchy fitGaussianMixture fitNorm fitNormalCauchyMixture fitTlsd fitWeightedNorm get_n_proteins get.log get.pep.group getMultUnifDensity getMultUnifPValues getPeptideModifContext getPhosphoRSProbabilities getProteinInfoFromBioDb getProteinInfoFromBiomart getProteinInfoFromEntrez getProteinInfoFromNextProt getProteinInfoFromTheInternet getProteinInfoFromUniprot getPtmInfoFromNextprot getPtmInfoFromPhosphoSitePlus groupMemberPeptides GROUPSPECIFIC human.protein.names ibSpectra.as.concise.data.frame IBSpectraTypes indistinguishableProteins initialize.env is.logged isotopeImpurities isotopeImpurities<-load.properties load.tex.properties lowIntensity lowIntensity<-maplot maplot.protein modif.site.count modif.sites modifs my.protein.info n.observable.peptides naRegion naRegion<-noiseFunction NoiseModel normalize number.ranges observable.peptides observedKnownSites parameter parameter<-paste0 peptide.count peptideInfo peptideNProtein peptideRatios peptideRatiosNotQuant peptides peptideSpecificity plot.NoiseModel plotRatio print_classlabels_tbl print_groupsize print_longtablehdr print_longtablehdr_peptide print_protein_grp_info print_protein_grp_tbl print_protein_notquant_tbl print_protein_quant_tbl print_sign_proteins_tbl property protein.ac protein.g proteinDescription proteinGeneName proteinGroup ProteinGroup proteinGroup.as.concise.data.frame proteinGroup<-proteinGroupTable proteinID proteinInfo proteinInfo<-proteinInfoIsOnSpliceVariants proteinNameAndDescription proteinRatios protGgdata raplot ratiosReshapeWide read.mzid readIBSpectra readPhosphoRSOutput readProteinGroup readProteinGroup2 reporter.protein reporterData reporterData<-reporterIntensities reporterIntensities<-reporterIntensityPlot reporterMasses reporterMasses<-reporterMassPrecision reporterProteins REPORTERSPECIFIC reporterTagMasses reporterTagNames sanitize sequence.coverage shared.ratios shared.ratios.sign SPECIFICITIES spectra.count spectra.count2 spectrumSel spectrumTitles spectrumToPeptide stddev subsetIBSpectra subtractAdditiveNoise summarize.ratios summary.ProteinGroup testPdflatex testPerl tikz.proteingroup Tlsd transform_pepmodif twodistr.plot UNSPECIFIC variance weightedMean weightedVariance write.tex.commands write.xls.report writeData writeHscoreData writeIBSpectra writePhosphoRSInput

Dependencies:AnnotationDbi askpass Biobase BiocFileCache BiocGenerics biomaRt Biostrings bit bit64 blob cachem cli colorspace cpp11 crayon curl DBI dbplyr digest distr dplyr fansi farver fastmap filelock generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable hms httr httr2 IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr plyr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp rlang RSQLite S4Vectors scales sfsmisc startupmsg stringi stringr sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr xml2 XVector zlibbioc

isobar for developers

Rendered fromisobar-devel.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2013-11-01
Started: 2013-11-01

isobar for quantification of PTM datasets

Rendered fromisobar-ptm.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2013-11-01
Started: 2013-11-01

isobar package for iTRAQ and TMT protein quantification

Rendered fromisobar.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2018-08-30
Started: 2013-11-01

Usecases for isobar package

Rendered fromisobar-usecases.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2014-11-29
Started: 2014-11-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analysis and quantitation of isobarically tagged MSMS proteomics data	isobar-package isobar
Calculate Delta Score from Ion Score	calc.delta.score calc.pep.delta.score filterSpectraDeltaScore
Recalculate peptide start positions based on protein sequence	calcPeptidePosition
Calculate and Adjust Ratio and Sample p-values.	adjust.ratio.pvalue calculate.mult.sample.pvalue calculate.ratio.pvalue calculate.sample.pvalue
dNSAF approximate abundance calculations.	calculate.dNSAF
emPAI approximate abundance calculations.	calculate.emPAI n.observable.peptides observable.peptides
Correct peptide ratios with protein ratios from a separate experiment.	correct.peptide.ratios
Functions for distribution calculations	AbscontDistribution-class calcCumulativeProbXGreaterThanY calcProbXDiffNormals calcProbXGreaterThanY Distribution-class distrprint Parameter-class twodistr.plot UnivariateDistribution-class
Fit weighted and unweighted Cauchy and Normal distributions	fitCauchy fitGaussianMixture fitNorm fitNormalCauchyMixture fitTlsd fitWeightedNorm
Get context of modification	getPeptideModifContext
Generate input files for PhosphoRS, call it, and get modification site probabilities	filterSpectraPhosphoRS getPhosphoRSProbabilities readPhosphoRSOutput writePhosphoRSInput
Get PTM site information for idenfied proteins from public databases.	getPtmInfoFromNextprot getPtmInfoFromPhosphoSitePlus
Peptide info for protein group members	groupMemberPeptides
Info on proteins	human.protein.names my.protein.info
IBSpectra Class for Isobarically Tagged Quantitative MS Proteomics Data	as.data.frame,IBSpectra-method as.data.frame.IBSpectra class:IBSpectra classLabels classLabels,IBSpectra-method classLabels<- classLabels<-,IBSpectra-method coerce,IBSpectra,data.frame-method IBSpectra IBSpectra-class ibSpectra.as.concise.data.frame IBSpectraTypes initialize,IBSpectra-method isotopeImpurities isotopeImpurities,IBSpectra-method isotopeImpurities<- isotopeImpurities<-,IBSpectra-method iTRAQ4plexSpectra iTRAQ4plexSpectra-class iTRAQ8plexSpectra iTRAQ8plexSpectra-class iTRAQSpectra iTRAQSpectra-class proteinGroup proteinGroup,IBSpectra-method proteinGroup<- proteinGroup<-,IBSpectra-method reporterData reporterData,IBSpectra-method reporterData<- reporterData<-,IBSpectra-method reporterIntensities reporterIntensities,IBSpectra-method reporterIntensities<- reporterIntensities<-,IBSpectra-method reporterMasses reporterMasses,IBSpectra-method reporterMasses<- reporterMasses<-,IBSpectra-method reporterTagMasses reporterTagMasses,IBSpectra-method reporterTagNames reporterTagNames,IBSpectra-method show,IBSpectra-method spectrumSel spectrumSel,IBSpectra,character,missing-method spectrumSel,IBSpectra,data.frame,missing-method spectrumSel,IBSpectra,matrix,missing-method spectrumSel,IBSpectra,missing,character-method spectrumSel,IBSpectra,missing,missing-method spectrumTitles spectrumTitles,IBSpectra-method TMT10plexSpectra TMT10plexSpectra-class TMT2plexSpectra TMT2plexSpectra-class TMT6plexSpectra TMT6plexSpectra-class TMT6plexSpectra2 TMT6plexSpectra2-class TMTSpectra TMTSpectra-class VARMETADATA writeData writeData,IBSpectra-method
Log functions for IBSpectra objects	do.log do.log,IBSpectra,character-method get.log get.log,IBSpectra,character-method is.logged is.logged,IBSpectra,character-method
Isobar util functions	%inrange% paste0
IBSpectra analysis: Protein and peptide ratio calculation	estimateRatio estimateRatio,IBSpectra,ANY,character,character,character,missing-method estimateRatio,IBSpectra,ANY,character,character,character,NULL-method estimateRatio,IBSpectra,ANY,character,character,missing,character-method estimateRatio,IBSpectra,ANY,character,character,missing,data.frame-method estimateRatio,IBSpectra,ANY,character,character,missing,matrix-method estimateRatio,IBSpectra,ANY,character,character,NULL,character-method estimateRatio,IBSpectra,ANY,character,character,NULL,data.frame-method estimateRatio,IBSpectra,ANY,character,character,NULL,matrix-method estimateRatio,IBSpectra,ANY,missing,missing,character,missing-method estimateRatio,IBSpectra,ANY,missing,missing,missing,character-method estimateRatioForPeptide estimateRatioForProtein estimateRatioNumeric estimateRatioNumeric,numeric,numeric,missing-method estimateRatioNumeric,numeric,numeric,NoiseModel-method estimateRatioNumeric,numeric,numeric,NULL-method getMultUnifDensity getMultUnifPValues isobar-analysis
Loading data into IBSpectra objects using readIBSpectra	isobar-import read.mzid readIBSpectra readIBSpectra,character,character,character-method readIBSpectra,character,character,missing-method readIBSpectra,character,character-method readIBSpectra,character,data.frame,character-method readIBSpectra,character,data.frame,missing-method
IBSpectra plots	isobar-plots maplot maplot,IBSpectra,character,character-method maplot,IBSpectra,missing,missing-method maplot,missing,numeric,numeric-method maplot2 maplot2,ANY,character,character-method maplot2,list,character,character-method plotRatio plotRatio,IBSpectra,character,character,character-method protGgdata protGgdata,ANY,character,character-method raplot raplot,IBSpectra-method reporterIntensityPlot reporterIntensityPlot,IBSpectra-method reporterIntensityPlot-methods reporterMassPrecision reporterMassPrecision,IBSpectra,logical-method reporterMassPrecision,IBSpectra,missing-method
IBSpectra preprocessing	correctIsotopeImpurities correctIsotopeImpurities,IBSpectra-method exclude exclude,IBSpectra,character-method isobar-preprocessing normalize subtractAdditiveNoise subtractAdditiveNoise,IBSpectra-method
Isobar reports	connect.nodes create.meta.reports create.reports draw.boxplot draw.protein.group draw.proteingroup.row get_n_proteins initialize.env isobar-reports load.properties load.tex.properties modifs print_classlabels_tbl print_groupsize print_longtablehdr print_longtablehdr_peptide print_protein_grp_info print_protein_grp_tbl print_protein_notquant_tbl print_protein_quant_tbl print_sign_proteins_tbl property testPdflatex testPerl tikz.proteingroup transform_pepmodif write.tex.commands write.xls.report
Isobar Data packages	ibspiked_set1 ibspiked_set2 ib_phospho noise.model.hcd
Ratio intensity plot for individual proteins	maplot.protein
NoiseModel objects	class:NoiseModel ExponentialNoANoiseModel-class ExponentialNoiseModel-class GeneralNoiseModel-class initialize,NoiseModel-method InverseNoANoiseModel-class InverseNoiseModel-class lowIntensity lowIntensity,NoiseModel-method lowIntensity<- lowIntensity<-,NoiseModel-method naRegion naRegion,NoiseModel-method naRegion<- naRegion<-,NoiseModel-method noiseFunction noiseFunction,NoiseModel-method NoiseModel NoiseModel,IBSpectra-method NoiseModel-class parameter parameter,NoiseModel-method parameter<- parameter<-,NoiseModel-method plot.NoiseModel show,NoiseModel-method stddev stddev,NoiseModel-method variance variance,NoiseModel,numeric,missing-method variance,NoiseModel,numeric,numeric-method
Helper function to transform number lists to ranges	number.ranges
Observed modification sites.	modif.site.count modif.sites observedKnownSites
Peptide counts, spectral counts and sequence coverage for ProteinGroup objects.	peptide.count sequence.coverage spectra.count
Calculating and Summarizing Protein and Peptide Ratios	combn.matrix combn.protein.tbl peptideRatios peptideRatiosNotQuant proteinRatios summarize.ratios weightedMean weightedMean,numeric,numeric-method weightedVariance weightedVariance,numeric,numeric,missing-method weightedVariance,numeric,numeric,numeric-method
ProteinGroup objects	as.data.frame,ProteinGroup-method as.data.frame.ProteinGroup class:ProteinGroup coerce,data.frame,ProteinGroup-method get.pep.group indistinguishableProteins indistinguishableProteins,ProteinGroup,ANY,ANY-method indistinguishableProteins,ProteinGroup,character,missing-method indistinguishableProteins,ProteinGroup,missing,character-method indistinguishableProteins,ProteinGroup,missing,missing-method indistinguishableProteins,ProteinGroup-method peptideInfo peptideInfo,ProteinGroup-method peptideInfo-methods peptideNProtein peptideNProtein,ProteinGroup-method peptides peptides,ProteinGroup,character-method peptides,ProteinGroup,missing-method peptideSpecificity peptideSpecificity,ProteinGroup-method protein.ac protein.ac,ProteinGroup,character-method protein.ac,ProteinGroup,missing-method protein.g protein.g,ProteinGroup,character,character-method protein.g,ProteinGroup,character-method ProteinGroup ProteinGroup,data.frame,missing-method ProteinGroup,data.frame,NULL-method ProteinGroup,data.frame,ProteinGroup-method ProteinGroup-class proteinGroup.as.concise.data.frame proteinGroupTable proteinGroupTable,ProteinGroup-method readProteinGroup readProteinGroup2 reporterProteins reporterProteins,ProteinGroup-method show,ProteinGroup-method spectrumToPeptide spectrumToPeptide,ProteinGroup-method summary.ProteinGroup
Methods for Function proteinInfo	getProteinInfoFromBioDb getProteinInfoFromBiomart getProteinInfoFromEntrez getProteinInfoFromNextProt getProteinInfoFromTheInternet getProteinInfoFromUniprot proteinInfo proteinInfo,ProteinGroup,character,missing-method proteinInfo,ProteinGroup,missing,character-method proteinInfo,ProteinGroup,missing,missing-method proteinInfo,ProteinGroup-method proteinInfo-methods proteinInfo<- proteinInfo<-,ProteinGroup-method proteinInfoIsOnSpliceVariants
Get protein gene names and description from protein info of protein group.	proteinDescription proteinGeneName proteinID proteinNameAndDescription
Reshape output of proteinRatios into wide format	ratiosReshapeWide
Get reporter protein group identifier for protein group identifier	reporter.protein reporter.protein,ProteinGroup,character-method reporter.protein-methods
Helper function for LaTeX export	sanitize
Shared ratio calculation	shared.ratios
Plot and get significantly shared ratios.	shared.ratios.sign
Peptide specificities	group-specific GROUPSPECIFIC reporter-specific REPORTERSPECIFIC SPECIFICITIES specificities UNSPECIFIC unspecific
Spectral count for peptides and proteins in ProteinGroup objects.	spectra.count2
Subset IBSpectra objects	subsetIBSpectra
Class '"Tlsd"'	Tlsd Tlsd-class
Class '"TlsParameter"'	TlsParameter-class
Write identifications into a format suitable for Hscore.	writeHscoreData
Write IBSpectra file as CSV in a format readable by readIBSpectra.	writeIBSpectra