+,RmbSpectraSet,ANY-method
                        Add a mass shift to a list of spectra
+,RmbSpectrum2List,ANY-method
                        Add a mass shift to a list of spectra
+,Spectrum,numeric-method
                        Add a mass shift to a spectrum
-,RmbSpectraSet,ANY-method
                        Add a negative mass shift to a list of spectra
-,RmbSpectrum2List,ANY-method
                        Add a negative mass shift to a list of spectra
-,Spectrum,numeric-method
                        Add a negative mass shift to a spectrum
.parseTitleString       Parse record title
.updateObject.RmbSpectrum2.formulaSource
                        Add formulaSource column to spectrum.
CAS2SMILES              Convert CAS to SMILES
CTS.externalIdSubset    Select a subset of external IDs from a CTS
                        record.
CTS.externalIdTypes     Find all available databases for a CTS record
RmbDefaultSettings      RMassBank settings
RmbSettings             RMassBank settings
RmbSpectraSet-class     Set of spectra pertaining to one compound
RmbSpectrum2-class      RMassBank Representation of an MSMS Spectrum
RmbSpectrum2List-class
                        SimpleList specializations
add.formula             Calculations on molecular formulas
addMB                   MassBank-record Addition
addPeaks                Add additional peaks to spectra
addPeaksManually        Addition of manual peaklists
addProperty             Add and initialize dataframe column
aggregateSpectra        Aggregate analyzed spectra
analyzeMsMs             Analyze MSMS spectra
annotator.default       Generate peak annotation from peaklist
archiveResults          Backup 'msmsWorkflow' results
buildRecord             Build MassBank records
checkIsotopes           Checks for isotopes in a 'msmsWorkspace'
checkSpectra            Check if a spectra set is found, complete,
                        empty
cleanElnoise            Remove electronic noise
combineMultiplicities   Combine workspaces for multiplicity filtering
compoundlist2SDF        Convert a Compoundlist into an SDF
createCompoundlist      Create a Compoundlist from JCAMP files
createMolfile           Create MOL file for a chemical structure
dbe                     Calculate Double Bond Equivalents
deprofile               De-profile a high-resolution MS scan in profile
                        mode.
exportMassbank          Export internally stored MassBank data to files
fillback                Fill back reanalyzed / refiltered peak info
                        into spectra
filterCompoundlist      Filter a Compoundlist for missing SMILES values
filterLowaccResults     Filter peaks with low accuracy
filterMultiplicity      filterMultiplicity
filterPeakSatellites    Filter satellite peaks
filterPeaksMultiplicity
                        Multiplicity filtering: Removes peaks which
                        occur only once in a n-spectra set.
findEIC                 Extract EICs
findMass                Calculate exact mass
findMsMsHR              Extract MS/MS spectra for specified precursor
findMsMsHR.direct       Discontinued: find MS/MS spectrum from open raw
                        file
findMsMsHR.ticms2       Extract an MS/MS spectrum from MS2 TIC
findMsMsHRperMsp        Retrieve spectra from msp files
findMsMsHRperxcms       Read in mz-files using XCMS
findMz                  Find compound information
findMz.formula          Find the exact mass +/- a given margin for a
                        given formula or its ions and adducts.
findProgress            Determine processed steps
flatten                 Flatten, or re-read, MassBank header blocks
formulastring.to.list   Interconvert molecular formula representations
gatherCCTE              Retrieve supplemental annotation data from US
                        EPA
gatherData              Retrieve annotation data
gatherDataBabel         Retrieve annotation data
gatherDataUnknown       Retrieve annotation data
gatherPubChem           Retrieve supplemental annotation data from
                        Pubchem
getAnalyticalInfo       Get analytical info for MassBank record
getCASRN                Search CCTE CAS registration number
getCSID                 Retrieve the Chemspider ID for a given compound
getCactus               Retrieve information from Cactus
getCtsKey               Convert a single ID to another using CTS.
getCtsRecord            Retrieve information from CTS
getDTXCID               Search CCTE DTXCID
getDTXSID               Search CCTE DTXSID
getDTXSMILES            Search CCTE SMILES
getData                 Get data frame with all present peak data
getField                Get the content of a field in a JCAMP file
getMolecule             Create Rcdk molecule from SMILES
getPcId                 Search Pubchem CID
getPrefName             Search CCTE Preferred Name
is.valid.formula        Check validity of formula
loadInfolists           Load MassBank compound information lists
loadList                Load compound list for RMassBank
makeMollist             Write list.tsv file
makePeaksCache          Generate peaks cache
makeRecalibration       Recalibrate MS/MS spectra
mbWorkflow              MassBank record creation workflow
mbWorkspace-class       Workspace for 'mbWorkflow' data
mergePeaks              Merge peaks for spectra merging, FT shoulder
                        elimination etc.
mergeSpectra            Merge multiple spectra into one
msmsRead                Extracts and processes spectra from a specified
                        file list, according to loaded options and
                        given parameters.
msmsRead.RAW            Extracts and processes spectra from a list of
                        xcms-Objects
msmsWorkflow            RMassBank mass spectrometry pipeline
msmsWorkspace-class     Workspace for 'msmsWorkflow' data
newMbWorkspace          Create new workspace for 'mbWorkflow'
newMsmsWorkspace        Create new empty workspace or load saved data
                        for 'msmsWorkflow'
normalize,RmbSpectrum2-method
                        Scale spectrum to specified intensity range
normalize,RmbSpectrum2List-method
                        Normalize spectra
order.formula           Order a chemical formula correctly
parseMassBank           MassBank-record Parser
parseMbRecord           MassBank-record Parser
peaksMatched            Select matching/unmatching peaks from aggregate
                        table
peaksUnmatched          Select matching/unmatching peaks from aggregate
                        table
plotMbWorkspaces        Plots mbWorkspaces
plotRecalibration       Plot the recalibration graph.
ppm                     Calculate ppm values
problematicPeaks        Identify intense peaks (in a list of unmatched
                        peaks)
processProblematicPeaks
                        Generate list of problematic peaks
progressBarHook         Standard progress bar hook.
property                Get a property of an RmbSpectrum2 object
property<-              Replacement function to set properties of an
                        RmbSpectrum2 object
reanalyzeFailpeaks      Reanalyze unmatched peaks
recalibrate             Predefined recalibration functions.
recalibrate.addMS1data
                        Return MS1 peaks to be used for recalibration
rmb_log_debug           Pass arguments to logger::log_debug using
                        custom RMassBank-logging settings
rmb_log_error           Pass arguments to logger::log_error using
                        custom RMassBank-logging settings
rmb_log_fatal           Pass arguments to logger::log_fatal using
                        custom RMassBank-logging settings
rmb_log_info            Pass arguments to logger::log_info using custom
                        RMassBank-logging settings
rmb_log_success         Pass arguments to logger::log_success using
                        custom RMassBank-logging settings
rmb_log_trace           Pass arguments to logger::log_trace using
                        custom RMassBank-logging settings
rmb_log_warn            Pass arguments to logger::log_warn using custom
                        RMassBank-logging settings
selectPeaks             Select peaks from aggregate table
selectSpectra           Select a subset of spectra matching properties
setAccessionBuilder     Define a programmatic or gluey ACCESSION
                        builder
setData                 Set 'RmbSpectrum2' data from data.frame
smiles2mass             Calculate the mass from a SMILES-String
spectraCount            Count MS2 spectra per compound
to.limits.rcdk          Convert formula to Rcdk limits
toMassbank              Write MassBank record into character array
toRMB                   Conversion of XCMS-pseudospectra into
                        RMassBank-spectra
updateHeader            Add a header to a Multiblock JCAMP file
updateSettings          Update settings to current version
validate                Validate MassBank records with a set of Unit
                        tests
