Workflow to process tandem MS files and build MassBank records

Documentation for package ‘RMassBank’ version 3.15.1

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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.