Package: RMassBank 3.17.0

RMassBank at Eawag

RMassBank: Workflow to process tandem MS files and build MassBank records

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Authors:Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, Paul Stahlhofen, Tobias Schulze with contributions of Hendrik Treutler

RMassBank_3.17.0.tar.gz
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RMassBank.pdf |RMassBank.html✨
RMassBank/json (API)
NEWS

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

Peer review:

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT

On BioConductor:RMassBank-3.17.0(bioc 3.21)RMassBank-3.16.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologybioinformaticsmassspectrometrymetabolomicssoftwareopenjdk

6.26 score 26 scripts 369 downloads 10 mentions 145 exports 164 dependencies

Last updated 2 months agofrom:8e633a1b45. Checks:OK: 1 NOTE: 3 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-winWARNINGNov 18 2024
R-4.5-linuxNOTEDec 19 2024
R-4.4-winWARNINGNov 18 2024
R-4.4-macNOTEDec 19 2024
R-4.3-winWARNINGNov 18 2024
R-4.3-macNOTEDec 19 2024

Exports:.msmsWorkspace.updateObject.RmbSpectrum2.formulaSourceadd.formulaaddMBaddPeaksaddPeaksManuallyaddPropertyaggregateSpectraanalyzeMsMsanalyzeMsMs.formulaanalyzeMsMs.intensityannotator.defaultarchiveResultsbuildRecordCAS2SMILEScheckIsotopescheckSpectracleanElnoisecombineMultiplicitiescompoundlist2SDFcreateCompoundlistcreateMolfileCTS.externalIdSubsetCTS.externalIdTypesdbedeprofiledeprofile.fwhmdeprofile.localMaxdeprofile.scandeprofile.splineexportMassbankfillbackfilterCompoundlistfilterMultiplicityfilterPeakSatellitesfilterPeaksMultiplicityfindCASfindEICfindFormulafindLevelfindMassfindMsMsHRfindMsMsHR.directfindMsMsHR.massfindMsMsHR.ticms2findMsMsHRperMspfindMsMsHRperxcmsfindMsMsHRperxcms.directfindMzfindMz.formulafindNamefindProgressfindRtfindSmilesflattenformulastring.to.listgatherCCTEgatherDatagatherDataBabelgatherDataUnknowngatherPubChemgetAnalyticalInfogetCactusgetCASRNgetCSIDgetCtsKeygetCtsRecordgetDatagetDTXCIDgetDTXSIDgetDTXSMILESgetFieldgetMoleculegetPcIdgetPrefNameis.valid.formulalist.to.formulaloadInfolistloadInfolistsloadListloadMsmsWorkspaceloadRmbSettingsloadRmbSettingsFromEnvmakeMollistmakePeaksCachemakeRecalibrationmbWorkflowmergePeaksmergeSpectramsmsReadmsmsRead.RAWmsmsWorkflowmultiply.formulanewMbWorkspacenewMsmsWorkspacenormalizeorder.formulaparseMassBankparseMbRecordpeaksMatchedpeaksUnmatchedplotMbWorkspacesplotRecalibrationplotRecalibration.directppmproblematicPeaksprocessProblematicPeaksprogressBarHookpropertyproperty<-readMbdatareanalyzeFailpeakreanalyzeFailpeaksrecalibraterecalibrate.addMS1datarecalibrate.identityrecalibrate.linearrecalibrate.loessrecalibrate.meanrecalibrateSingleSpecrecalibrateSpectraresetInfolistsresetListrmb_log_debugrmb_log_errorrmb_log_fatalrmb_log_informb_log_successrmb_log_tracermb_log_warnRmbDefaultSettingsRmbSettingsTemplateselectPeaksselectSpectrasetAccessionBuildersetDatashowsmiles2massspectraCountto.limits.rcdktoMassbanktoRMBupdateHeaderupdateSettingsvalidate

Dependencies:abindaffyaffyioAnnotationFilteraskpassassertthatbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbitbit64bitopsbslibcachemChemmineRclicliprclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tabledata.treeDBIDelayedArraydigestdoParalleldplyrDTenviPatevaluatefansifarverfastmapfingerprintfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphimputeIRangesisobanditeratorsitertoolsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmaloggermagrittrMALDIquantMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeMsCoreUtilsMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpngpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR.methodsS3R.ooR.utilsR6rappdirsrcdkrcdklibsRColorBrewerRcppRCurlreadJDXreadrreshape2Rhdf5librJavarjsonrlangrmarkdownrsvgrvestS4ArraysS4VectorssassscalesselectrsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8vctrsviridisLitevroomvsnwebchemwithrxfunXMLxml2XVectoryamlzlibbioc

RMassBank: Non-standard usage

Michael Stravs

Rendered fromRMassBankNonstandard.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2022-03-09
Started: 2020-10-19

RMassBank: The workflow by example

Michael Stravs, Emma Schymanski

Rendered fromRMassBank.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2022-03-09
Started: 2020-10-19

Readme and manuals

Help Manual

Help pageTopics
Add a negative mass shift to a list of spectra-,RmbSpectraSet,ANY-method
Add a negative mass shift to a list of spectra-,RmbSpectrum2List,ANY-method
Add a negative mass shift to a spectrum-,Spectrum,numeric-method
Parse record title.parseTitleString
Add formulaSource column to spectrum..updateObject.RmbSpectrum2.formulaSource
Add a mass shift to a list of spectra+,RmbSpectraSet,ANY-method
Add a mass shift to a list of spectra+,RmbSpectrum2List,ANY-method
Add a mass shift to a spectrum+,Spectrum,numeric-method
Calculations on molecular formulasadd.formula multiply.formula
MassBank-record AdditionaddMB
Add additional peaks to spectraaddPeaks
Addition of manual peaklistsaddPeaksManually
Add and initialize dataframe columnaddProperty addProperty,data.frame,character,character-method addProperty,RmbSpectrum2,character,character-method
Aggregate analyzed spectraaggregateSpectra
Analyze MSMS spectraanalyzeMsMs analyzeMsMs.formula analyzeMsMs.intensity
Generate peak annotation from peaklistannotator.default
Backup 'msmsWorkflow' resultsarchiveResults
Build MassBank recordsbuildRecord buildRecord,RmbSpectraSet-method buildRecord,RmbSpectrum2-method
Convert CAS to SMILESCAS2SMILES
Checks for isotopes in a 'msmsWorkspace'checkIsotopes
Check if a spectra set is found, complete, emptycheckSpectra checkSpectra,RmbSpectraSet,character-method
Remove electronic noisecleanElnoise cleanElnoise,data.frame,numeric,numeric-method cleanElnoise,RmbSpectraSet,numeric,numeric-method cleanElnoise,RmbSpectrum2,numeric,numeric-method cleanElnoise,RmbSpectrum2List,numeric,numeric-method
Combine workspaces for multiplicity filteringcombineMultiplicities
Convert a Compoundlist into an SDFcompoundlist2SDF
Create a Compoundlist from JCAMP filescreateCompoundlist
Create MOL file for a chemical structurecreateMolfile
Select a subset of external IDs from a CTS record.CTS.externalIdSubset
Find all available databases for a CTS recordCTS.externalIdTypes
Calculate Double Bond Equivalentsdbe
De-profile a high-resolution MS scan in profile mode.deprofile deprofile.fwhm deprofile.localMax deprofile.scan deprofile.spline
Export internally stored MassBank data to filesexportMassbank
Fill back reanalyzed / refiltered peak info into spectrafillback fillback,msmsWorkspace,missing,missing-method fillback,RmbSpectraSet,missing,data.frame-method fillback,RmbSpectrum2,character,data.frame-method
Filter a Compoundlist for missing SMILES valuesfilterCompoundlist
Filter peaks with low accuracyfilterLowaccResults
filterMultiplicityfilterMultiplicity
Filter satellite peaksfilterPeakSatellites
Multiplicity filtering: Removes peaks which occur only once in a n-spectra set.filterPeaksMultiplicity
Extract EICsfindEIC
Calculate exact massfindMass
Extract MS/MS spectra for specified precursorfindMsMsHR findMsMsHR.mass
Discontinued: find MS/MS spectrum from open raw filefindMsMsHR.direct
Extract an MS/MS spectrum from MS2 TICfindMsMsHR.ticMS2 findMsMsHR.ticms2
Retrieve spectra from msp filesfindMsMsHRperMsp findMsMsHRperMsp.direct
Read in mz-files using XCMSfindMsMsHRperxcms findMsMsHRperxcms.direct
Find compound informationfindCAS findFormula findLevel findMz findName findRt findSmiles
Find the exact mass +/- a given margin for a given formula or its ions and adducts.findMz.formula
Determine processed stepsfindProgress
Flatten, or re-read, MassBank header blocksflatten readMbdata
Interconvert molecular formula representationsformulastring.to.list list.to.formula
Retrieve supplemental annotation data from US EPAgatherCCTE
Retrieve annotation datagatherData
Retrieve annotation datagatherDataBabel
Retrieve annotation datagatherDataUnknown
Retrieve supplemental annotation data from PubchemgatherPubChem
Get analytical info for MassBank recordgetAnalyticalInfo
Retrieve information from CactusgetCactus
Search CCTE CAS registration numbergetCASRN
Retrieve the Chemspider ID for a given compoundgetCSID
Convert a single ID to another using CTS.getCtsKey
Retrieve information from CTSgetCtsRecord
Get data frame with all present peak datagetData getData,RmbSpectrum2-method
Search CCTE DTXCIDgetDTXCID
Search CCTE DTXSIDgetDTXSID
Search CCTE SMILESgetDTXSMILES
Get the content of a field in a JCAMP filegetField
Create Rcdk molecule from SMILESgetMolecule
Search Pubchem CIDgetPcId
Search CCTE Preferred NamegetPrefName
Check validity of formulais.valid.formula
Load MassBank compound information listsloadInfolist loadInfolists resetInfolists
Load compound list for RMassBankloadList resetList
Write list.tsv filemakeMollist
Generate peaks cachemakePeaksCache
Recalibrate MS/MS spectramakeRecalibration recalibrateSingleSpec recalibrateSpectra
MassBank record creation workflowmbWorkflow
Workspace for 'mbWorkflow' datambWorkspace-class show,mbWorkspace-method
Merge peaks for spectra merging, FT shoulder elimination etc.mergePeaks mergePeaks,data.frame-method mergePeaks,matrix-method mergePeaks,RmbSpectrum2-method mergePeaks,Spectrum-method
Merge multiple spectra into onemergeSpectra mergeSpectra,RmbSpectrum2List-method
Extracts and processes spectra from a specified file list, according to loaded options and given parameters.msmsRead
Extracts and processes spectra from a list of xcms-ObjectsmsmsRead.RAW
RMassBank mass spectrometry pipelinemsmsWorkflow
Workspace for 'msmsWorkflow' data.msmsWorkspace msmsWorkspace-class show,msmsWorkspace-method
Create new workspace for 'mbWorkflow'newMbWorkspace
Create new empty workspace or load saved data for 'msmsWorkflow'loadMsmsWorkspace newMsmsWorkspace
Scale spectrum to specified intensity rangenormalize,RmbSpectrum2-method
Normalize spectranormalize,RmbSpectrum2List-method
Order a chemical formula correctlyorder.formula
MassBank-record ParserparseMassBank
MassBank-record ParserparseMbRecord
Select matching/unmatching peaks from aggregate tablepeaksMatched peaksMatched,data.frame-method peaksMatched,msmsWorkspace-method
Select matching/unmatching peaks from aggregate tablepeaksUnmatched peaksUnmatched,data.frame-method peaksUnmatched,msmsWorkspace-method
Plots mbWorkspacesplotMbWorkspaces
Plot the recalibration graph.plotRecalibration plotRecalibration.direct
Calculate ppm valuesppm
Identify intense peaks (in a list of unmatched peaks)problematicPeaks
Generate list of problematic peaksprocessProblematicPeaks
Standard progress bar hook.progressBarHook
Get a property of an RmbSpectrum2 objectproperty property,RmbSpectrum2,character-method
Replacement function to set properties of an RmbSpectrum2 objectproperty<- property<-,RmbSpectrum2,character,logical,character-method property<-,RmbSpectrum2,character,logical,missing-method property<-,RmbSpectrum2,character,missing,character-method property<-,RmbSpectrum2,character,missing,missing-method
Reanalyze unmatched peaksreanalyzeFailpeak reanalyzeFailpeaks
Predefined recalibration functions.recalibrate recalibrate.identity recalibrate.linear recalibrate.loess recalibrate.mean
Return MS1 peaks to be used for recalibrationrecalibrate.addMS1data
Pass arguments to logger::log_debug using custom RMassBank-logging settingsrmb_log_debug
Pass arguments to logger::log_error using custom RMassBank-logging settingsrmb_log_error
Pass arguments to logger::log_fatal using custom RMassBank-logging settingsrmb_log_fatal
Pass arguments to logger::log_info using custom RMassBank-logging settingsrmb_log_info
Pass arguments to logger::log_success using custom RMassBank-logging settingsrmb_log_success
Pass arguments to logger::log_trace using custom RMassBank-logging settingsrmb_log_trace
Pass arguments to logger::log_warn using custom RMassBank-logging settingsrmb_log_warn
RMassBank settingsloadRmbSettings loadRmbSettingsFromEnv RmbDefaultSettings RmbSettingsTemplate
RMassBank settingsRmbSettings
Set of spectra pertaining to one compound.RmbSpectraSet RmbSpectraSet-class
RMassBank Representation of an MSMS Spectrum.RmbSpectrum2 RmbSpectrum2-class
SimpleList specializations.RmbSpectraSetList .RmbSpectrum2List RmbSpectraSetList RmbSpectraSetList-class RmbSpectrum2List-class
Select peaks from aggregate tableselectPeaks selectPeaks,data.frame-method selectPeaks,msmsWorkspace-method selectPeaks,RmbSpectraSet-method selectPeaks,RmbSpectraSetList-method selectPeaks,RmbSpectrum2-method selectPeaks,RmbSpectrum2List-method selectPeaks,Spectrum-method
Select a subset of spectra matching propertiesselectSpectra selectSpectra,msmsWorkspace,character-method selectSpectra,RmbSpectraSetList,character-method
Define a programmatic or gluey ACCESSION buildersetAccessionBuilder
Set 'RmbSpectrum2' data from data.framesetData setData,RmbSpectrum2,data.frame-method
Calculate the mass from a SMILES-Stringsmiles2mass
Count MS2 spectra per compoundspectraCount spectraCount,msmsWorkspace-method spectraCount,RmbSpectraSet-method spectraCount,RmbSpectraSetList-method
Convert formula to Rcdk limitsto.limits.rcdk
Write MassBank record into character arraytoMassbank toMassbank,RmbSpectraSet-method toMassbank,RmbSpectrum2-method
Conversion of XCMS-pseudospectra into RMassBank-spectratoRMB
Add a header to a Multiblock JCAMP fileupdateHeader
Update settings to current versionupdateSettings
Validate MassBank records with a set of Unit testsvalidate