Package: synapter 2.31.0

Laurent Gatto

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.

Authors:Laurent Gatto, Nick J. Bond, Pavel V. Shliaha and Sebastian Gibb.

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synapter.pdf |synapter.html✨
synapter/json (API)

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

Peer review:

Bug tracker:https://github.com/lgatto/synapter/issues

Datasets:
  • synapterTiny - Loads a small test data for the 'synapter' package

On BioConductor:synapter-2.31.0(bioc 3.21)synapter-2.30.0(bioc 3.20)

immunooncologymassspectrometryproteomicsqualitycontrol

6.03 score 4 stars 5 scripts 316 downloads 97 exports 141 dependencies

Last updated 23 days agofrom:4502012902. Checks:OK: 1 NOTE: 1 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winWARNINGNov 19 2024
R-4.5-linuxNOTENov 19 2024
R-4.4-winWARNINGNov 19 2024
R-4.4-macWARNINGNov 19 2024
R-4.3-winWARNINGNov 19 2024
R-4.3-macWARNINGNov 19 2024

Exports:allCombas.MSnSet.SynapterbestCombcreateUniquePeptideDbRdsestimateMasterFdrfileNamesfilterFragmentsfilterIdentPepScorefilterIdentPpmErrorfilterIdentProtFprfilterNonUniqueIdentMatchesfilterNonUniqueMatchesfilterPeptideLengthfilterQuantPepScorefilterQuantPpmErrorfilterQuantProtFprfilterUniqueDbPeptidesfilterUniqueIdentDbPeptidesfilterUniqueMatchesfilterUniqueQuantDbPeptidesfindEMRTsfragmentMatchingfragmentMatchingPerformancegetBestGridParamsgetBestGridValuegetEMRTtablegetFragmentMatchingPpmTolerancegetGridgetGridDetailsgetIdentificationFragmentsgetIdentPpmErrorgetImDiffgetLoggetLowessSpangetPepNumbersgetPepScoreFdrgetPpmErrorQsgetProtFprgetQuantitationSpectragetQuantPpmErrorgetRtNsdgetRtQsinputFilesinspectPeptideScoresmakeMastermasterFdrmergePeptidesmodelIntensitymodelRtperformanceperformance2plotplotCumulativeNumberOfFragmentsplotEMRTtableplotFdrplotFeaturesplotFragmentMatchingplotFragmentMatchingPerformanceplotGridplotIntensityplotPepScoresplotPpmErrorplotRtplotRtDiffsrequantifyrescaleForTop3rescueEMRTssearchGridsetBestGridParamssetFragmentMatchingPpmTolerancesetIdentPpmErrorsetImDiffsetLowessSpansetPepScoreFdrsetPpmErrorsetProtFprsetQuantPpmErrorsetRtNsdshowshowFdrStatsSynaptersynapterGuidesynapterPlgsAgreementsynapterTinyDatasynergisesynergise1synergise2synergizesynergize1synergize2updateObjectwriteFragmentLibrarywriteIdentPeptideswriteMasterPeptideswriteMatchedEMRTswriteMergedPeptideswriteQuantPeptides

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelBiostringsbitbit64bslibcachemcleaverclicliprclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMSnbaseMultiAssayExperimentmulttestmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesqvalueR6rappdirsRColorBrewerRcppreadrreshape2Rhdf5librlangrmarkdownS4ArraysS4VectorssassscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomvsnwithrxfunXMLXVectoryamlzlibbioc

Combining HDMSe/MSe data using synapter to optimise identification and quantitation

Laurent Gatto, Sebastian Gibb, Pavel V. Shliaha

Rendered fromsynapter.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2018-07-16
Started: 2017-01-16

Fragment matching using synapter

Laurent Gatto, Sebastian Gibb, Pavel V. Shliaha

Rendered fromfragmentmatching.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-09-27
Started: 2017-01-14

Synapter2 and synergise2

Laurent Gatto, Sebastian Gibb, Pavel V. Shliaha

Rendered fromsynapter2.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2018-01-17
Started: 2017-01-17

Readme and manuals

Help Manual

Help pageTopics
Combine label-free data for optimal identification and quantitationsynapter-package synapter
Create an RDS file for the 'Unique Peptides Database'createUniquePeptideDbRds
Computes FDR for all possible final peptide combinationsestimateMasterFdr
Inspect peptide scores.inspectPeptideScores
Merges final peptide filesmakeMaster writeFragmentLibrary writeFragmentLibrary,MasterPeptides,character-method writeMasterPeptides writeMasterPeptides,MasterPeptides,character-method
Class '"MasterFdrResults"'allComb allComb,MasterFdrResults-method bestComb bestComb,MasterFdrResults-method class:MasterFdrResults fileNames,MasterFdrResults-method masterFdr masterFdr,MasterFdrResults-method MasterFdrResults MasterFdrResults-class plot,MasterFdrResults,missing-method show,MasterFdrResults-method
Class '"MasterPeptides"'class:MasterPeptides MasterPeptides-class show,MasterPeptides-method
Plot fragment matching results.plotFragmentMatching plotFragmentMatching,Synapter-method
Intensity requantificationrequantify requantify,MSnSet-method
Rescale for TOP3rescaleForTop3 rescaleForTop3,MSnSet,MSnSet-method
Class "Synapter"as.MSnSet.Synapter class:Synapter dim,Synapter-method filterFragments filterFragments,Synapter-method filterIdentPepScore filterIdentPepScore,Synapter-method filterIdentPpmError filterIdentPpmError,Synapter-method filterIdentProtFpr filterIdentProtFpr,Synapter-method filterNonUniqueIdentMatches filterNonUniqueIdentMatches,Synapter-method filterNonUniqueMatches filterNonUniqueMatches,Synapter-method filterPeptideLength filterPeptideLength,Synapter-method filterQuantPepScore filterQuantPepScore,Synapter-method filterQuantPpmError filterQuantPpmError,Synapter-method filterQuantProtFpr filterQuantProtFpr,Synapter-method filterUniqueDbPeptides filterUniqueDbPeptides,Synapter-method filterUniqueIdentDbPeptides filterUniqueIdentDbPeptides,Synapter-method filterUniqueMatches filterUniqueMatches,Synapter-method filterUniqueQuantDbPeptides filterUniqueQuantDbPeptides,Synapter-method findEMRTs findEMRTs,Synapter-method fragmentMatching fragmentMatching,Synapter-method fragmentMatchingPerformance fragmentMatchingPerformance,Synapter-method getBestGridParams getBestGridParams,Synapter-method getBestGridValue getBestGridValue,Synapter-method getEMRTtable getEMRTtable,Synapter-method getFragmentMatchingPpmTolerance getFragmentMatchingPpmTolerance,Synapter-method getGrid getGrid,Synapter-method getGridDetails getGridDetails,Synapter-method getIdentificationFragments getIdentificationFragments,Synapter-method getIdentPpmError getIdentPpmError,Synapter-method getImDiff getImDiff,Synapter-method getLog getLog,Synapter-method getLowessSpan getLowessSpan,Synapter-method getPepNumbers getPepNumbers,Synapter-method getPepScoreFdr getPepScoreFdr,Synapter-method getPpmErrorQs getPpmErrorQs,Synapter-method getProtFpr getProtFpr,Synapter-method getQuantitationSpectra getQuantitationSpectra,Synapter-method getQuantPpmError getQuantPpmError,Synapter-method getRtNsd getRtNsd,Synapter-method getRtQs getRtQs,Synapter-method inputFiles inputFiles,Synapter-method isCurrent,Synapter-method mergePeptides mergePeptides,Synapter-method modelIntensity modelIntensity,Synapter-method modelRt modelRt,Synapter-method performance performance,Synapter-method performance2 performance2,Synapter-method plotCumulativeNumberOfFragments plotCumulativeNumberOfFragments,Synapter-method plotEMRTtable plotEMRTtable,Synapter-method plotFdr plotFdr,Synapter-method plotFeatures plotFeatures,Synapter-method plotFragmentMatchingPerformance plotFragmentMatchingPerformance,Synapter-method plotGrid plotGrid,Synapter-method plotIntensity plotIntensity,Synapter-method plotPepScores plotPepScores,Synapter-method plotPpmError plotPpmError,Synapter-method plotRt plotRt,Synapter-method plotRtDiffs plotRtDiffs,Synapter-method rescueEMRTs rescueEMRTs,Synapter-method searchGrid searchGrid,Synapter-method setBestGridParams setBestGridParams,Synapter-method setFragmentMatchingPpmTolerance setFragmentMatchingPpmTolerance,Synapter-method setIdentPpmError setIdentPpmError,Synapter-method setImDiff setImDiff,Synapter-method setLowessSpan setLowessSpan,Synapter-method setPepScoreFdr setPepScoreFdr,Synapter-method setPpmError setPpmError,Synapter-method setProtFpr setProtFpr,Synapter-method setQuantPpmError setQuantPpmError,Synapter-method setRtNsd setRtNsd,Synapter-method show,Synapter-method showFdrStats showFdrStats,Synapter-method Synapter updateObject,Synapter-method validObject,Synapter-method writeIdentPeptides writeIdentPeptides,Synapter-method writeMatchedEMRTs writeMatchedEMRTs,Synapter-method writeMergedPeptides writeMergedPeptides,Synapter-method writeQuantPeptides writeQuantPeptides,Synapter-method
Opens the 'synapter' vignettesynapterGuide
Synapter/PLGS AgreementsynapterPlgsAgreement synapterPlgsAgreement,MSnSet-method
Loads a small test data for the 'synapter' packagesynapterTiny synapterTinyData
Synergise identification and quantitation resultssynergise synergise1 synergize synergize1
Synergise identification and quantitation resultssynergise2 synergize2