# Workflow to process tandem MS files and build MassBank records

## Documentation for package ‘RMassBank’ version 3.23.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I L M N O P R S T U V misc

## -- A --

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
addProperty-method | Add and initialize dataframe column
aggregateSpectra | Aggregate analyzed spectra
analyzeMsMs | Analyze MSMS spectra
analyzeMsMs.formula | Analyze MSMS spectra
analyzeMsMs.intensity | Analyze MSMS spectra
annotator.default | Generate peak annotation from peaklist
archiveResults | Backup 'msmsWorkflow' results

## -- B --

buildRecord | Build MassBank records
buildRecord-method | Build MassBank records

## -- C --

CAS2SMILES | Convert CAS to SMILES
checkIsotopes | Checks for isotopes in a 'msmsWorkspace'
checkSpectra | Check if a spectra set is found, complete, empty
checkSpectra-method | Check if a spectra set is found, complete, empty
cleanElnoise | Remove electronic noise
cleanElnoise-method | 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
CTS.externalIdSubset | Select a subset of external IDs from a CTS record.
CTS.externalIdTypes | Find all available databases for a CTS record

## -- D --

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.

## -- E --

exportMassbank | Export internally stored MassBank data to files

## -- F --

fillback | Fill back reanalyzed / refiltered peak info into spectra
fillback-method | 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.
findCAS | Find compound information
findEIC | Extract EICs
findFormula | Find compound information
findLevel | Find compound information
findMass | Calculate exact mass
findMsMsHR | Extract MS/MS spectra for specified precursor
findMsMsHR.direct | Discontinued: find MS/MS spectrum from open raw file
findMsMsHR.mass | Extract MS/MS spectra for specified precursor
findMsMsHR.ticMS2 | Extract an MS/MS spectrum from MS2 TIC
findMsMsHR.ticms2 | Extract an MS/MS spectrum from MS2 TIC
findMsMsHRperMsp | Retrieve spectra from msp files
findMsMsHRperMsp.direct | Retrieve spectra from msp files
findMsMsHRperxcms | Read in mz-files using XCMS
findMsMsHRperxcms.direct | 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.
findName | Find compound information
findProgress | Determine processed steps
findRt | Find compound information
findSmiles | Find compound information
flatten | Flatten, or re-read, MassBank header blocks
formulastring.to.list | Interconvert molecular formula representations

## -- G --

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
getCactus | Retrieve information from Cactus
getCASRN | Search CCTE CAS registration number
getCSID | Retrieve the Chemspider ID for a given compound
getCtsKey | Convert a single ID to another using CTS.
getCtsRecord | Retrieve information from CTS
getData | Get data frame with all present peak data
getData-method | Get data frame with all present peak data
getDTXCID | Search CCTE DTXCID
getDTXSID | Search CCTE DTXSID
getDTXSMILES | Search CCTE SMILES
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

## -- I --

is.valid.formula | Check validity of formula

## -- L --

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

## -- M --

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.
mergePeaks-method | Merge peaks for spectra merging, FT shoulder elimination etc.
mergeSpectra | Merge multiple spectra into one
mergeSpectra-method | 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
multiply.formula | Calculations on molecular formulas

## -- N --

newMbWorkspace | Create new workspace for 'mbWorkflow'
newMsmsWorkspace | Create new empty workspace or load saved data for 'msmsWorkflow'
normalize-method | Scale spectrum to specified intensity range
normalize-method | Normalize spectra

## -- O --

order.formula | Order a chemical formula correctly

## -- P --

parseMassBank | MassBank-record Parser
parseMbRecord | MassBank-record Parser
peaksMatched | Select matching/unmatching peaks from aggregate table
peaksMatched-method | Select matching/unmatching peaks from aggregate table
peaksUnmatched | Select matching/unmatching peaks from aggregate table
peaksUnmatched-method | Select matching/unmatching peaks from aggregate table
plotMbWorkspaces | Plots mbWorkspaces
plotRecalibration | Plot the recalibration graph.
plotRecalibration.direct | 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-method | Get a property of an RmbSpectrum2 object
property<- | Replacement function to set properties of an RmbSpectrum2 object
property<--method | Replacement function to set properties of an RmbSpectrum2 object

## -- R --

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.identity | Predefined recalibration functions.
recalibrate.linear | Predefined recalibration functions.
recalibrate.loess | Predefined recalibration functions.
recalibrate.mean | 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
RmbSpectraSet-class | Set of spectra pertaining to one compound
RmbSpectraSetList | SimpleList specializations
RmbSpectraSetList-class | SimpleList specializations
RmbSpectrum2-class | RMassBank Representation of an MSMS Spectrum
RmbSpectrum2List-class | SimpleList specializations
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

## -- S --

selectPeaks | Select peaks from aggregate table
selectPeaks-method | Select peaks from aggregate table
selectSpectra | Select a subset of spectra matching properties
selectSpectra-method | Select a subset of spectra matching properties
setAccessionBuilder | Define a programmatic or gluey ACCESSION builder
setData | Set 'RmbSpectrum2' data from data.frame
setData-method | Set 'RmbSpectrum2' data from data.frame
show-method | Workspace for 'mbWorkflow' data
show-method | Workspace for 'msmsWorkflow' data
smiles2mass | Calculate the mass from a SMILES-String
spectraCount | Count MS2 spectra per compound
spectraCount-method | Count MS2 spectra per compound

## -- T --

to.limits.rcdk | Convert formula to Rcdk limits
toMassbank | Write MassBank record into character array
toMassbank-method | Write MassBank record into character array
toRMB | Conversion of XCMS-pseudospectra into RMassBank-spectra

## -- U --

updateHeader | Add a header to a Multiblock JCAMP file
updateSettings | Update settings to current version

## -- V --

validate | Validate MassBank records with a set of Unit tests

## -- misc --

+-method | Add a mass shift to a list of spectra
+-method | Add a mass shift to a list of spectra
+-method | Add a mass shift to a spectrum
--method | Add a negative mass shift to a list of spectra
--method | Add a negative mass shift to a list of spectra
--method | Add a negative mass shift to a spectrum
.msmsWorkspace | Workspace for 'msmsWorkflow' data
.parseTitleString | Parse record title
.RmbSpectraSet | Set of spectra pertaining to one compound
.RmbSpectraSetList | SimpleList specializations
.RmbSpectrum2 | RMassBank Representation of an MSMS Spectrum
.RmbSpectrum2List | SimpleList specializations
.updateObject.RmbSpectrum2.formulaSource | Add formulaSource column to spectrum.