# Workflow to process tandem MS files and build MassBank records

## Documentation for package ‘RMassBank’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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

## -- A --

add.formula | Calculations on molecular formulas
addMB | MassBank-record Addition
addPeaks | Add additional peaks to spectra
addPeaksManually | Addition of manual peaklists
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

## -- C --

c.msmsWSspecs | Concatenation of raw spectra in msmsWorkspace
cleanElnoise | Remove electronic noise
combineMultiplicities | Combine workspaces for multiplicity filtering
compileRecord | Compile MassBank records
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 --

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
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 --

gatherCompound | Compose data block of MassBank record
gatherData | Retrieve annotation data
gatherDataBabel | Retrieve annotation data
gatherPubChem | Retrieve supplemental annotation data from Pubchem
gatherSpectrum | Compose data block of MassBank record
getCactus | Retrieve information from Cactus
getCtsKey | Convert a single ID to another using CTS.
getCtsRecord | Retrieve information from CTS
getMolecule | Create Rcdk molecule from SMILES
getPcId | Search Pubchem CID

## -- 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
makeRecalibration | Recalibrate MS/MS spectra
mbWorkflow | MassBank record creation workflow
mbWorkspace-class | Workspace for 'mbWorkflow' data
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'

## -- O --

order.formula | Order a chemical formula correctly

## -- P --

parseMassBank | MassBank-record Parser
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)
progressBarHook | Standard progress bar hook.

## -- 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

## -- S --

show-method | Workspace for 'mbWorkflow' data
show-method | Workspace for 'msmsWorkflow' data
smiles2mass | Calculate the mass from a SMILES-String

## -- T --

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

## -- U --

updateSettings | Update settings to current version

## -- V --

validate | Validate MassBank records with a set of Unit tests