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

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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.

Author
Michael Stravs, Emma Schymanski, Steffen Neumann, Erik Mueller, with contributions from Tobias Schulze
Date of publication
None
Maintainer
RMassBank at Eawag <massbank@eawag.ch>
License
Artistic-2.0
Version
2.2.0

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