synapter: Label-free data analysis pipeline for optimal identification and quantitation

The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("synapter")
AuthorLaurent Gatto, Nick J. Bond, Pavel V. Shliaha and Sebastian Gibb.
Bioconductor views MassSpectrometry Proteomics QualityControl
Date of publicationNone
MaintainerLaurent Gatto <lg390@cam.ac.uk> and Sebastian Gibb <mail@sebastiangibb.de>
LicenseGPL-2
Version2.0.0
https://lgatto.github.io/synapter/

View on Bioconductor

Functions

allComb Man page
allComb,MasterFdrResults-method Man page
as.MSnSet.Synapter Man page
bestComb Man page
bestComb,MasterFdrResults-method Man page
class:MasterFdrResults Man page
class:MasterPeptides Man page
class:Synapter Man page
createUniquePeptideDbRds Man page
dim,Synapter-method Man page
estimateMasterFdr Man page
fileNames,MasterFdrResults-method Man page
filterFragments Man page
filterFragments,Synapter-method Man page
filterIdentPepScore Man page
filterIdentPepScore,Synapter-method Man page
filterIdentPpmError Man page
filterIdentPpmError,Synapter-method Man page
filterIdentProtFpr Man page
filterIdentProtFpr,Synapter-method Man page
filterNonUniqueIdentMatches Man page
filterNonUniqueIdentMatches,Synapter-method Man page
filterNonUniqueMatches Man page
filterNonUniqueMatches,Synapter-method Man page
filterPeptideLength Man page
filterPeptideLength,Synapter-method Man page
filterQuantPepScore Man page
filterQuantPepScore,Synapter-method Man page
filterQuantPpmError Man page
filterQuantPpmError,Synapter-method Man page
filterQuantProtFpr Man page
filterQuantProtFpr,Synapter-method Man page
filterUniqueDbPeptides Man page
filterUniqueDbPeptides,Synapter-method Man page
filterUniqueIdentDbPeptides Man page
filterUniqueIdentDbPeptides,Synapter-method Man page
filterUniqueMatches Man page
filterUniqueMatches,Synapter-method Man page
filterUniqueQuantDbPeptides Man page
filterUniqueQuantDbPeptides,Synapter-method Man page
findEMRTs Man page
findEMRTs,Synapter-method Man page
fragmentMatching Man page
fragmentMatchingPerformance Man page
fragmentMatchingPerformance,Synapter-method Man page
fragmentMatching,Synapter-method Man page
getBestGridParams Man page
getBestGridParams,Synapter-method Man page
getBestGridValue Man page
getBestGridValue,Synapter-method Man page
getEMRTtable Man page
getEMRTtable,Synapter-method Man page
getFragmentMatchingPpmTolerance Man page
getFragmentMatchingPpmTolerance,Synapter-method Man page
getGrid Man page
getGridDetails Man page
getGridDetails,Synapter-method Man page
getGrid,Synapter-method Man page
getIdentificationFragments Man page
getIdentificationFragments,Synapter-method Man page
getIdentPpmError Man page
getIdentPpmError,Synapter-method Man page
getImDiff Man page
getImDiff,Synapter-method Man page
getLog Man page
getLog,Synapter-method Man page
getLowessSpan Man page
getLowessSpan,Synapter-method Man page
getPepNumbers Man page
getPepNumbers,Synapter-method Man page
getPepScoreFdr Man page
getPepScoreFdr,Synapter-method Man page
getPpmErrorQs Man page
getPpmErrorQs,Synapter-method Man page
getProtFpr Man page
getProtFpr,Synapter-method Man page
getQuantitationSpectra Man page
getQuantitationSpectra,Synapter-method Man page
getQuantPpmError Man page
getQuantPpmError,Synapter-method Man page
getRtNsd Man page
getRtNsd,Synapter-method Man page
getRtQs Man page
getRtQs,Synapter-method Man page
inputFiles Man page
inputFiles,Synapter-method Man page
inspectPeptideScores Man page
isCurrent,Synapter-method Man page
makeMaster Man page
masterFdr Man page
masterFdr,MasterFdrResults-method Man page
MasterFdrResults Man page
MasterFdrResults-class Man page
MasterPeptides-class Man page
mergePeptides Man page
mergePeptides,Synapter-method Man page
modelIntensity Man page
modelIntensity,Synapter-method Man page
modelRt Man page
modelRt,Synapter-method Man page
performance Man page
performance2 Man page
performance2,Synapter-method Man page
performance,Synapter-method Man page
plotCumulativeNumberOfFragments Man page
plotCumulativeNumberOfFragments,Synapter-method Man page
plotEMRTtable Man page
plotEMRTtable,Synapter-method Man page
plotFdr Man page
plotFdr,Synapter-method Man page
plotFeatures Man page
plotFeatures,Synapter-method Man page
plotFragmentMatching Man page
plotFragmentMatchingPerformance Man page
plotFragmentMatchingPerformance,Synapter-method Man page
plotFragmentMatching,Synapter-method Man page
plotGrid Man page
plotGrid,Synapter-method Man page
plotIntensity Man page
plotIntensity,Synapter-method Man page
plot,MasterFdrResults,missing-method Man page
plotPepScores Man page
plotPepScores,Synapter-method Man page
plotPpmError Man page
plotPpmError,Synapter-method Man page
plotRt Man page
plotRtDiffs Man page
plotRtDiffs,Synapter-method Man page
plotRt,Synapter-method Man page
requantify Man page
requantify,MSnSet-method Man page
rescaleForTop3 Man page
rescaleForTop3,MSnSet,MSnSet-method Man page
rescueEMRTs Man page
rescueEMRTs,Synapter-method Man page
searchGrid Man page
searchGrid,Synapter-method Man page
setBestGridParams Man page
setBestGridParams,Synapter-method Man page
setFragmentMatchingPpmTolerance Man page
setFragmentMatchingPpmTolerance,Synapter-method Man page
setIdentPpmError Man page
setIdentPpmError,Synapter-method Man page
setImDiff Man page
setImDiff,Synapter-method Man page
setLowessSpan Man page
setLowessSpan,Synapter-method Man page
setPepScoreFdr Man page
setPepScoreFdr,Synapter-method Man page
setPpmError Man page
setPpmError,Synapter-method Man page
setProtFpr Man page
setProtFpr,Synapter-method Man page
setQuantPpmError Man page
setQuantPpmError,Synapter-method Man page
setRtNsd Man page
setRtNsd,Synapter-method Man page
showFdrStats Man page
showFdrStats,Synapter-method Man page
show,MasterFdrResults-method Man page
show,MasterPeptides-method Man page
show,Synapter-method Man page
synapter Man page
Synapter Man page
synapter-defunct Man page
synapter-deprecated Man page
synapterGUI Man page
synapterGuide Man page
synapter-package Man page
synapterPlgsAgreement Man page
synapterPlgsAgreement,MSnSet-method Man page
synapterTiny Man page
synapterTinyData Man page
synergise Man page
synergise1 Man page
synergise2 Man page
synergize Man page
synergize1 Man page
synergize2 Man page
updateObject,Synapter-method Man page
validObject,Synapter-method Man page
writeFragmentLibrary Man page
writeFragmentLibrary,MasterPeptides,character-method Man page
writeIdentPeptides Man page
writeIdentPeptides,Synapter-method Man page
writeMasterPeptides Man page
writeMasterPeptides,MasterPeptides,character-method Man page
writeMatchedEMRTs Man page
writeMatchedEMRTs,Synapter-method Man page
writeMergedPeptides Man page
writeMergedPeptides,Synapter-method Man page
writeQuantPeptides Man page
writeQuantPeptides,Synapter-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R R/AllGenerics.R R/MSnbase-extensions.R R/exported_tools.R R/fasta.R R/figures.R R/fragmentlibrary-functions.R R/fragmentmatching-functions.R R/fragments-functions.R R/gui.R R/master.R R/readcsv-functions.R R/requantify-functions.R R/spectrum-functions.R R/synapter-class.R R/synapter-interface.R R/synergise.R R/update.R R/utils.R R/zzz.R
build
build/vignette.rds
data
data/synapterTiny.rda
inst
inst/CITATION
inst/doc
inst/doc/Bugs.md
inst/doc/Foreword.md
inst/doc/fragmentmatching.R
inst/doc/fragmentmatching.Rmd
inst/doc/fragmentmatching.html
inst/doc/synapter.R
inst/doc/synapter.Rmd
inst/doc/synapter.html
inst/doc/synapter2.R
inst/doc/synapter2.Rmd
inst/doc/synapter2.html
inst/extdata
inst/extdata/04_test_database.fasta
inst/extdata/synapter.css
inst/reports
inst/reports/scripts
inst/reports/scripts/synergise.R
inst/reports/synergise1.Rmd
inst/reports/synergise2.Rmd
inst/scripts
inst/scripts/run_test_report.R
man
man/MasterFdrResults-class.Rd man/MasterPeptides-class.Rd man/Synapter.Rd man/createUniquePeptideDbRds.Rd man/defunct.Rd man/estimateMasterFdr.Rd man/inspectPeptideScores.Rd man/makeMaster.Rd man/plotCrossMatching.Rd man/requantify.Rd man/rescaleForTop3.Rd man/synapter-package.Rd man/synapterGuide.Rd man/synapterPlgsAgreement.Rd man/synapterTinyData.Rd man/synergise.Rd man/synergise2.Rd
tests
tests/testthat
tests/testthat.R tests/testthat/test_MSnbase-extensions.R tests/testthat/test_fragmentlibrary-functions.R tests/testthat/test_fragments-functions.R tests/testthat/test_master-functions.R tests/testthat/test_readcsv-functions.R tests/testthat/test_requantify.R tests/testthat/test_spectrum-functions.R tests/testthat/test_utils.R
vignettes
vignettes/Bugs.md
vignettes/Dotfiles
vignettes/Dotfiles/synapter2workflow.dot
vignettes/Figures
vignettes/Figures/PLGS_create_databank1.jpg
vignettes/Figures/PLGS_create_databank2.jpg
vignettes/Figures/PLGS_db_search_options.jpg
vignettes/Figures/PLGS_output_files1.jpg
vignettes/Figures/PLGS_output_files2.jpg
vignettes/Figures/PLGS_output_files3.jpg
vignettes/Figures/synapter2workflow.png
vignettes/Foreword.md
vignettes/fragmentmatching.Rmd
vignettes/synapter.Rmd
vignettes/synapter.bib
vignettes/synapter2.Rmd

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