Workflow to process tandem MS files and build MassBank records


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Documentation for package ‘RMassBank’ version 1.0.0

Help Pages

add.formula Calculations on molecular formulas
addPeaks Add additional peaks to spectra
aggregateSpectra Aggregate analyzed spectra
analyzeMsMs Analyze MSMS spectra
archiveResults Backup 'msmsWorkflow' results
cleanElnoise Remove electronic noise
compileRecord Compile MassBank records
createMolfile Create MOL file for a chemical structure
dbe Calculate Double Bond Equivalents
deprofile De-profile a high-resolution MS scan in profile mode.
deprofile.fwhm De-profile a high-resolution MS scan in profile mode.
deprofile.localMax De-profile a high-resolution MS scan in profile mode.
deprofile.scan De-profile a high-resolution MS scan in profile mode.
deprofile.spline De-profile a high-resolution MS scan in profile mode.
exportMassbank Export internally stored MassBank data to files
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.
findCAS Find compound information
findEIC Extract EICs
findFormula Find compound information
findMass Calculate exact mass
findMsMsHR Extract MS/MS spectra for specified precursor
findMsMsHR.direct Extract MS/MS spectra for specified precursor
findMsMsHR.mass Extract MS/MS spectra for specified precursor
findMz Find compound information
findMz.formula Find the exact mass +/- a given margin for a given formula or its ions and adducts.
findName Find compound information
findRt Find compound information
findSmiles Find compound information
flatten Flatten, or re-read, MassBank header blocks
formulastring.to.list Interconvert molecular formula representations
gatherCompound Compose data block of MassBank record
gatherData Retrieve annotation data
gatherSpectrum Compose data block of MassBank record
getCactus Retrieve information from Cactus
getCtsRecord Retrieve information from CTS
getMolecule Create Rcdk molecule from SMILES
getPcId Search Pubchem CID
is.valid.formula Check validity of formula
list.to.formula Interconvert molecular formula representations
loadInfolist Load MassBank compound information lists
loadInfolists Load MassBank compound information lists
loadList Load compound list for RMassBank
loadMsmsWorkspace Create new empty workspace or load saved data for 'msmsWorkflow'
loadRmbSettings RMassBank settings
loadRmbSettingsFromEnv RMassBank settings
makeMollist Write list.tsv file
makeRecalibration Recalibrate MS/MS spectra
mbWorkflow MassBank record creation workflow
mbWorkspace-class Workspace for 'mbWorkflow' data
msmsWorkflow RMassBank mass spectrometry pipeline
msmsWorkspace-class Workspace for 'msmsWorkflow' data
multiply.formula Calculations on molecular formulas
newMbWorkspace Create new workspace for 'mbWorkflow'
newMsmsWorkspace Create new empty workspace or load saved data for 'msmsWorkflow'
order.formula Order a chemical formula correctly
ppm Calculate ppm values
problematicPeaks Identify intense peaks (in a list of unmatched peaks)
readMbdata Flatten, or re-read, MassBank header blocks
reanalyzeFailpeak Reanalyze unmatched peaks
reanalyzeFailpeaks Reanalyze unmatched peaks
recalibrate Predefined recalibration functions.
recalibrate.addMS1data Return MS1 peaks to be used for recalibration
recalibrate.loess Predefined recalibration functions.
recalibrateSingleSpec Recalibrate MS/MS spectra
recalibrateSpectra Recalibrate MS/MS spectra
resetInfolists Load MassBank compound information lists
resetList Load compound list for RMassBank
RmbDefaultSettings RMassBank settings
RmbSettings RMassBank settings
RmbSettingsTemplate RMassBank settings
show-method Workspace for 'mbWorkflow' data
show-method Workspace for 'msmsWorkflow' data
to.limits.rcdk Convert formula to Rcdk limits
toMassbank Write MassBank record into character array