Man pages for RMassBank
Workflow to process tandem MS files and build MassBank records

add.formulaCalculations on molecular formulas
addMBMassBank-record Addition
addPeaksAdd additional peaks to spectra
addPeaksManuallyAddition of manual peaklists
addPropertyAdd and initialize dataframe column
aggregateSpectraAggregate analyzed spectra
analyzeMsMsAnalyze MSMS spectra
annotator.defaultGenerate peak annotation from peaklist
archiveResultsBackup 'msmsWorkflow' results
checkIsotopesChecks for isotopes in a 'msmsWorkspace'
checkSpectraCheck if a spectra set is found, complete, empty
cleanElnoiseRemove electronic noise
combineMultiplicitiesCombine workspaces for multiplicity filtering
createMolfileCreate MOL file for a chemical structure
CTS.externalIdSubsetSelect a subset of external IDs from a CTS record.
CTS.externalIdTypesFind all available databases for a CTS record
dbeCalculate Double Bond Equivalents
deprofileDe-profile a high-resolution MS scan in profile mode.
dot-buildRecord.RmbSpectraSetCompile MassBank records
dot-parseTitleStringParse record title
dot-updateObject.RmbSpectrum2.formulaSourceAdd formulaSource column to spectrum.
exportMassbankExport internally stored MassBank data to files
fillbackFill back reanalyzed / refiltered peak info into spectra
filterLowaccResultsFilter peaks with low accuracy
filterPeakSatellitesFilter satellite peaks
filterPeaksMultiplicityMultiplicity filtering: Removes peaks which occur only once...
findEICExtract EICs
findMassCalculate exact mass
findMsMsHRExtract MS/MS spectra for specified precursor
findMsMsHR.directDiscontinued: find MS/MS spectrum from open raw file
findMsMsHRperxcmsRead in mz-files using XCMS
findMsMsHR.ticms2Extract an MS/MS spectrum from MS2 TIC
findMzFind compound information
findMz.formulaFind the exact mass +/- a given margin for a given formula or...
findProgressDetermine processed steps
flattenFlatten, or re-read, MassBank header blocks molecular formula representations
gatherDataRetrieve annotation data
gatherDataBabelRetrieve annotation data
gatherDataUnknownRetrieve annotation data
gatherPubChemRetrieve supplemental annotation data from Pubchem
getAnalyticalInfoCompose data block of MassBank record
getCactusRetrieve information from Cactus
getCompToxRetrieves DTXSID (if it exists) from EPA Comptox Dashboard
getCSIDRetrieve the Chemspider ID for a given compound
getCtsKeyConvert a single ID to another using CTS.
getCtsRecordRetrieve information from CTS
getDataGet data frame with all present peak data
getMoleculeCreate Rcdk molecule from SMILES
getPcIdSearch Pubchem CID
is.valid.formulaCheck validity of formula
loadInfolistsLoad MassBank compound information lists
loadListLoad compound list for RMassBank
makeMollistWrite list.tsv file
makePeaksCacheGenerate peaks cache
makeRecalibrationRecalibrate MS/MS spectra
mbWorkflowMassBank record creation workflow
mbWorkspace-classWorkspace for 'mbWorkflow' data
mergePeaks.dfMerge peaks for spectra merging, FT shoulder elimination etc.
msmsReadExtracts and processes spectra from a specified file list,...
msmsRead.RAWExtracts and processes spectra from a list of xcms-Objects
msmsWorkflowRMassBank mass spectrometry pipeline
msmsWorkspace-classWorkspace for 'msmsWorkflow' data
newMbWorkspaceCreate new workspace for 'mbWorkflow'
newMsmsWorkspaceCreate new empty workspace or load saved data for...
order.formulaOrder a chemical formula correctly
parseMassBankMassBank-record Parser
parseMbRecordMassBank-record Parser
peaksMatchedSelect matching/unmatching peaks from aggregate table
peaksUnmatchedSelect matching/unmatching peaks from aggregate table
plotMbWorkspacesPlots mbWorkspaces
plotRecalibrationPlot the recalibration graph.
ppmCalculate ppm values
problematicPeaksIdentify intense peaks (in a list of unmatched peaks)
processProblematicPeaksGenerate list of problematic peaks
progressBarHookStandard progress bar hook.
reanalyzeFailpeaksReanalyze unmatched peaks
recalibratePredefined recalibration functions.
recalibrate.addMS1dataReturn MS1 peaks to be used for recalibration
RmbDefaultSettingsRMassBank settings
RmbSettingsRMassBank settings
selectPeaksSelect peaks from aggregate table
selectSpectraSelect a subset of spectra matching properties
setDataSet 'RmbSpectrum2' data from data.frame
smiles2massCalculate the mass from a SMILES-String
spectraCountCount MS2 spectra per compound
to.limits.rcdkConvert formula to Rcdk limits
toMassbankWrite MassBank record into character array
toRMBConversion of XCMS-pseudospectra into RMassBank-spectra
updateSettingsUpdate settings to current version
validateValidate MassBank records with a set of Unit tests
RMassBank documentation built on Nov. 8, 2020, 6:06 p.m.