RMassBank: Workflow to process tandem MS files and build MassBank records
Version 2.4.0

Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Browse man pages Browse package API and functions Browse package files

AuthorMichael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze
Bioconductor views Bioinformatics MassSpectrometry Metabolomics Software
Date of publicationNone
MaintainerRMassBank at Eawag <massbank@eawag.ch>
LicenseArtistic-2.0
Version2.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RMassBank")

Man pages

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
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
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
dbe: Calculate Double Bond Equivalents
deprofile: 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...
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
findMsMsHRperxcms: Read in mz-files using XCMS
findMsMsHR.ticms2: Extract an MS/MS spectrum from MS2 TIC
findMz: Find compound information
findMz.formula: Find the exact mass +/- a given margin for a given formula or...
findProgress: Determine processed steps
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
gatherDataBabel: Retrieve annotation data
gatherDataUnknown: Retrieve annotation data
gatherPubChem: Retrieve supplemental annotation data from Pubchem
getCactus: Retrieve information from Cactus
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
getMolecule: Create Rcdk molecule from SMILES
getPcId: Search Pubchem CID
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
msmsRead: Extracts and processes spectra from a specified file list,...
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...
order.formula: Order a chemical formula correctly
parseMassBank: 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.
reanalyzeFailpeaks: Reanalyze unmatched peaks
recalibrate: Predefined recalibration functions.
recalibrate.addMS1data: Return MS1 peaks to be used for recalibration
RmbDefaultSettings: RMassBank settings
RmbSettings: RMassBank settings
selectPeaks: Select peaks from aggregate table
selectSpectra: Select a subset of spectra matching properties
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
updateSettings: Update settings to current version
validate: Validate MassBank records with a set of Unit tests

Functions

.msmsWorkspace Man page
CTS.externalIdSubset Man page Source code
CTS.externalIdTypes Man page Source code
RmbDefaultSettings Man page Source code
RmbSettings Man page
RmbSettingsTemplate Man page Source code
add.formula Man page Source code
addMB Man page Source code
addPeaks Man page Source code
addPeaksManually Man page Source code
addProperty Man page
addProperty,data.frame,character,character-method Man page
aggregateSpectra Man page Source code
analyzeMsMs Man page Source code
analyzeMsMs.formula Man page Source code
analyzeMsMs.formula.optimized Source code
analyzeMsMs.intensity Man page Source code
analyzeMsMs.optimized Source code
annotateFormulaToEnviPatTable Source code
annotator.default Man page Source code
archiveResults Man page Source code
checkForPsiMs Source code
checkIsotopes Man page Source code
checkMbSettings Source code
checkSpectra Man page
checkSpectra,RmbSpectraSet,character-method Man page
cleanElnoise Man page Source code
combineMultiplicities Man page Source code
compileRecord Man page Source code
createMolfile Man page Source code
createSpecsFromPeaklists Source code
dbe Man page Source code
decimalavoidance Source code
deprofile Man page Source code
deprofile.fwhm Man page Source code
deprofile.localMax Man page Source code
deprofile.scan Man page Source code
deprofile.spline Man page Source code
downloadPsiObo Source code
exportMassbank Man page Source code
filterLowaccResults Man page Source code
filterMultiplicity Man page Source code
filterPeakSatellites Man page Source code
filterPeaksMultiplicity Man page Source code
findCAS Man page Source code
findEIC Man page Source code
findFormula Man page Source code
findLevel Man page Source code
findMass Man page Source code
findMatchingPeaks Source code
findMsMsHR Man page Source code
findMsMsHR.direct Man page Source code
findMsMsHR.mass Man page Source code
findMsMsHR.ticMS2 Man page
findMsMsHR.ticms2 Man page Source code
findMsMsHR.ticms2.d Source code
findMsMsHR.ticms2.file Source code
findMsMsHRperxcms Man page Source code
findMsMsHRperxcms.direct Man page Source code
findMz Man page Source code
findMz.formula Man page Source code
findName Man page Source code
findPattern Source code
findPeaksInFracData Source code
findProgress Man page Source code
findProgress.v1 Source code
findRt Man page Source code
findSmiles Man page Source code
flatten Man page Source code
formulastring.to.list Man page Source code
fragDataIndexing Source code
gatherCompound Man page Source code
gatherData Man page Source code
gatherDataBabel Man page Source code
gatherDataUnknown Man page Source code
gatherPubChem Man page Source code
gatherSpectrum Man page Source code
get.mol2formula Source code
getBlockHash Source code
getBlockHist Source code
getCSID Man page Source code
getCactus Man page Source code
getCtsKey Man page Source code
getCtsRecord Man page Source code
getData Man page
getData,RmbSpectrum2-method Man page
getInstruments Source code
getMolecule Man page Source code
getPcCHEBI Source code
getPcIUPAC Source code
getPcId Man page Source code
getPcInchiKey Source code
getPcSDF Source code
getPcSynonym Source code
getSplash Source code
integer2base36 Source code
is.sub.formula Source code
is.valid.formula Man page Source code
list.to.formula Man page Source code
loadInfolist Man page Source code
loadInfolists Man page Source code
loadList Man page Source code
loadMsmsWorkspace Man page Source code
loadRmbSettings Man page Source code
loadRmbSettingsFromEnv Man page Source code
locb Source code
locf Source code
makeMollist Man page Source code
makePeaksCache Man page Source code
makeRecalibration Man page Source code
mbWorkflow Man page Source code
mbWorkspace-class Man page
msmsRead Man page Source code
msmsRead.RAW Man page Source code
msmsRead.ticms2 Source code
msmsWorkflow Man page Source code
msmsWorkspace-class Man page
multiply.formula Man page Source code
newMbWorkspace Man page Source code
newMsmsWorkspace Man page Source code
newStep2WorkFlow Source code
onLoad Source code
order.formula Man page Source code
parseMassBank Man page Source code
parseTitleString Source code
peakReasoner Source code
peaksMatched Man page
peaksMatched,data.frame-method Man page
peaksMatched,msmsWorkspace-method Man page
peaksUnmatched Man page
peaksUnmatched,data.frame-method Man page
peaksUnmatched,msmsWorkspace-method Man page
plotMbWorkspaces Man page Source code
plotRecalibration Man page Source code
plotRecalibration.direct Man page Source code
ppm Man page Source code
problematicPeaks Man page Source code
processProblematicPeaks Man page Source code
progressBarHook Man page Source code
pubChemOnline Source code
readMbdata Man page Source code
reanalyzeFailpeak Man page Source code
reanalyzeFailpeaks Man page Source code
recalibrate Man page Source code
recalibrate.addMS1data Man page Source code
recalibrate.identity Man page Source code
recalibrate.linear Man page Source code
recalibrate.loess Man page Source code
recalibrate.mean Man page Source code
recalibrateSingleSpec Man page Source code
recalibrateSpectra Man page Source code
resetInfolists Man page Source code
resetList Man page Source code
sOboReadable Source code
selectPeaks Man page
selectPeaks,data.frame-method Man page
selectPeaks,msmsWorkspace-method Man page
selectSpectra Man page
selectSpectra,RmbSpectraSetList,character-method Man page
selectSpectra,msmsWorkspace,character-method Man page
setData Man page
setData,RmbSpectrum2,data.frame-method Man page
show,mbWorkspace-method Man page
show,msmsWorkspace-method Man page
smiles2mass Man page Source code
spectraCount Man page
spectraCount,RmbSpectraSet-method Man page
spectraCount,RmbSpectraSetList-method Man page
spectraCount,msmsWorkspace-method Man page
split.formula.posneg Source code
to.limits.rcdk Man page Source code
toMassbank Man page Source code
toRMB Man page Source code
translateLevel Source code
unitTestRMB2 Source code
unitTestmzR Source code
updateObject.aggregated Source code
updateObject.refiltered Source code
updateObject.spectra Source code
updateSettings Man page Source code
validate Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AggregateMethods.R
R/Isotopic_Annotation.R
R/RmbWorkspace.R
R/RmbWorkspaceUpdate.R
R/SpectraSetMethods.R
R/SpectrumClasses.R
R/SpectrumMethods.R
R/alternateAnalyze.R
R/createMassBank.R
R/deprofile.R
R/formulaCalculator.R
R/getSplash.R
R/leCsvAccess.R
R/leMsMs.r
R/leMsmsRaw.R
R/msmsRawExtensions.r
R/msmsRead.R
R/parseMassBank.R
R/settings_example.R
R/tools.R
R/validateMassBank.R
R/webAccess.R
R/zzz.R
build
build/vignette.rds
inst
inst/CITATION
inst/RMB_options.ini
inst/doc
inst/doc/RMassBank.R
inst/doc/RMassBank.Rnw
inst/doc/RMassBank.pdf
inst/doc/RMassBankNonstandard.R
inst/doc/RMassBankNonstandard.Rnw
inst/doc/RMassBankNonstandard.pdf
inst/doc/RMassBankXCMS.R
inst/doc/RMassBankXCMS.Rnw
inst/doc/RMassBankXCMS.pdf
inst/psi-ms.obo
inst/unitTests
inst/unitTests/runTests.R
inst/unitTests/test_ElecNoise_FormulaCalc.R
inst/unitTests/test_NOPEAKS.R
inst/unitTests/test_mzR.R
inst/validationTests
inst/validationTests/runit.MS2.instruments.R-disabled
inst/validationTests/runit.MS2.test.R
inst/validationTests/runit.MSn.test.slashes.R
man
man/CTS.externalIdSubset.Rd
man/CTS.externalIdTypes.Rd
man/RmbDefaultSettings.Rd
man/RmbSettings.Rd
man/add.formula.Rd
man/addMB.Rd
man/addPeaks.Rd
man/addPeaksManually.Rd
man/addProperty.Rd
man/aggregateSpectra.Rd
man/analyzeMsMs.Rd
man/annotator.default.Rd
man/archiveResults.Rd
man/checkIsotopes.Rd
man/checkSpectra.Rd
man/cleanElnoise.Rd
man/combineMultiplicities.Rd
man/compileRecord.Rd
man/createMolfile.Rd
man/dbe.Rd
man/deprofile.Rd
man/exportMassbank.Rd
man/filterLowaccResults.Rd
man/filterMultiplicity.Rd
man/filterPeakSatellites.Rd
man/filterPeaksMultiplicity.Rd
man/findEIC.Rd
man/findMass.Rd
man/findMsMsHR.Rd
man/findMsMsHR.direct.Rd
man/findMsMsHR.ticms2.Rd
man/findMsMsHRperxcms.Rd
man/findMz.Rd
man/findMz.formula.Rd
man/findProgress.Rd
man/flatten.Rd
man/formulastring.to.list.Rd
man/gatherCompound.Rd
man/gatherData.Rd
man/gatherDataBabel.Rd
man/gatherDataUnknown.Rd
man/gatherPubChem.Rd
man/getCSID.Rd
man/getCactus.Rd
man/getCtsKey.Rd
man/getCtsRecord.Rd
man/getData.Rd
man/getMolecule.Rd
man/getPcId.Rd
man/is.valid.formula.Rd
man/loadInfolists.Rd
man/loadList.Rd
man/makeMollist.Rd
man/makePeaksCache.Rd
man/makeRecalibration.Rd
man/mbWorkflow.Rd
man/mbWorkspace-class.Rd
man/msmsRead.RAW.Rd
man/msmsRead.Rd
man/msmsWorkflow.Rd
man/msmsWorkspace-class.Rd
man/newMbWorkspace.Rd
man/newMsmsWorkspace.Rd
man/order.formula.Rd
man/parseMassBank.Rd
man/peaksMatched.Rd
man/peaksUnmatched.Rd
man/plotMbWorkspaces.Rd
man/plotRecalibration.Rd
man/ppm.Rd
man/problematicPeaks.Rd
man/processProblematicPeaks.Rd
man/progressBarHook.Rd
man/reanalyzeFailpeaks.Rd
man/recalibrate.Rd
man/recalibrate.addMS1data.Rd
man/selectPeaks.Rd
man/selectSpectra.Rd
man/setData.Rd
man/smiles2mass.Rd
man/spectraCount.Rd
man/to.limits.rcdk.Rd
man/toMassbank.Rd
man/toRMB.Rd
man/updateSettings.Rd
man/validate.Rd
tests
tests/doRUnit.R
vignettes
vignettes/RMassBank.Rnw
vignettes/RMassBankNonstandard.Rnw
vignettes/RMassBankXCMS.Rnw
vignettes/RMassBankXCMS.Rnw-disabled
vignettes/graphics
vignettes/graphics/proteowiz.PNG
RMassBank documentation built on May 20, 2017, 9:31 p.m.