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.

AuthorMichael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze
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

Files in this package

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

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