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

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RMassBank")
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
Version2.2.1

View on Bioconductor

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

add.formula Man page
addMB Man page
addPeaks Man page
addPeaksManually Man page
addProperty Man page
addProperty,data.frame,character,character-method Man page
aggregateSpectra Man page
analyzeMsMs Man page
analyzeMsMs.formula Man page
analyzeMsMs.intensity Man page
annotator.default Man page
archiveResults Man page
checkIsotopes Man page
checkSpectra Man page
checkSpectra,RmbSpectraSet,character-method Man page
cleanElnoise Man page
combineMultiplicities Man page
compileRecord Man page
createMolfile Man page
CTS.externalIdSubset Man page
CTS.externalIdTypes Man page
dbe Man page
deprofile Man page
deprofile.fwhm Man page
deprofile.localMax Man page
deprofile.scan Man page
deprofile.spline Man page
exportMassbank Man page
filterLowaccResults Man page
filterMultiplicity Man page
filterPeakSatellites Man page
filterPeaksMultiplicity Man page
findCAS Man page
findEIC Man page
findFormula Man page
findLevel Man page
findMass Man page
findMsMsHR Man page
findMsMsHR.direct Man page
findMsMsHR.mass Man page
findMsMsHRperxcms Man page
findMsMsHRperxcms.direct Man page
findMsMsHR.ticms2 Man page
findMsMsHR.ticMS2 Man page
findMz Man page
findMz.formula Man page
findName Man page
findProgress Man page
findRt Man page
findSmiles Man page
flatten Man page
formulastring.to.list Man page
gatherCompound Man page
gatherData Man page
gatherDataBabel Man page
gatherDataUnknown Man page
gatherPubChem Man page
gatherSpectrum Man page
getCactus Man page
getCSID Man page
getCtsKey Man page
getCtsRecord Man page
getData Man page
getData,RmbSpectrum2-method Man page
getMolecule Man page
getPcId Man page
is.valid.formula Man page
list.to.formula Man page
loadInfolist Man page
loadInfolists Man page
loadList Man page
loadMsmsWorkspace Man page
loadRmbSettings Man page
loadRmbSettingsFromEnv Man page
makeMollist Man page
makePeaksCache Man page
makeRecalibration Man page
mbWorkflow Man page
mbWorkspace-class Man page
msmsRead Man page
msmsRead.RAW Man page
msmsWorkflow Man page
.msmsWorkspace Man page
msmsWorkspace-class Man page
multiply.formula Man page
newMbWorkspace Man page
newMsmsWorkspace Man page
order.formula Man page
parseMassBank Man page
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
plotRecalibration Man page
plotRecalibration.direct Man page
ppm Man page
problematicPeaks Man page
processProblematicPeaks Man page
progressBarHook Man page
readMbdata Man page
reanalyzeFailpeak Man page
reanalyzeFailpeaks Man page
recalibrate Man page
recalibrate.addMS1data Man page
recalibrate.identity Man page
recalibrate.linear Man page
recalibrate.loess Man page
recalibrate.mean Man page
recalibrateSingleSpec Man page
recalibrateSpectra Man page
resetInfolists Man page
resetList Man page
RmbDefaultSettings Man page
RmbSettings Man page
RmbSettingsTemplate Man page
selectPeaks Man page
selectPeaks,data.frame-method Man page
selectPeaks,msmsWorkspace-method Man page
selectSpectra Man page
selectSpectra,msmsWorkspace,character-method Man page
selectSpectra,RmbSpectraSetList,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
spectraCount Man page
spectraCount,msmsWorkspace-method Man page
spectraCount,RmbSpectraSetList-method Man page
spectraCount,RmbSpectraSet-method Man page
to.limits.rcdk Man page
toMassbank Man page
toRMB Man page
updateSettings Man page
validate Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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