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RMassBank (version 2.0.0)

Workflow to process tandem MS files and build MassBank records

Description

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.

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Version

Version

2.0.0

License

Artistic-2.0

Maintainer

RMassBank at Eawag

Last Published

February 15th, 2017

Functions in RMassBank (2.0.0)

findMz.formula

Find the exact mass +/- a given margin for a given formula or its ions and adducts.
is.valid.formula

Check validity of formula
loadList

Load compound list for RMassBank
recalibrate.addMS1data

Return MS1 peaks to be used for recalibration
makePeaksCache

Generate peaks cache
reanalyzeFailpeaks

Reanalyze unmatched peaks
compileRecord

Compile MassBank records
combineMultiplicities

Combine workspaces for multiplicity filtering
getMolecule

Create Rcdk molecule from SMILES
filterMultiplicity

filterMultiplicity
updateSettings

Update settings to current version
processProblematicPeaks

Generate list of problematic peaks
plotMbWorkspaces

Plots mbWorkspaces
findMsMsHR

Extract MS/MS spectra for specified precursor
gatherDataUnknown

Retrieve annotation data
newMbWorkspace

Create new workspace for mbWorkflow
msmsRead.RAW

Extracts and processes spectra from a list of xcms-Objects
validate

Validate MassBank records with a set of Unit tests
CTS.externalIdSubset

Select a subset of external IDs from a CTS record.
CTS.externalIdTypes

Find all available databases for a CTS record
add.formula

Calculations on molecular formulas
getCSID

Retrieve the Chemspider ID for a given compound
getData

Get data frame with all present peak data
loadInfolists

Load MassBank compound information lists
mbWorkspace-class

Workspace for mbWorkflow data
makeRecalibration

Recalibrate MS/MS spectra
newMsmsWorkspace

Create new empty workspace or load saved data for msmsWorkflow
RmbSettings

RMassBank settings
addMB

MassBank-record Addition
to.limits.rcdk

Convert formula to Rcdk limits
aggregateSpectra

Aggregate analyzed spectra
archiveResults

Backup msmsWorkflow results
addProperty

Add and initialize dataframe column
getCtsKey

Convert a single ID to another using CTS.
getCactus

Retrieve information from Cactus
exportMassbank

Export internally stored MassBank data to files
filterLowaccResults

Filter peaks with low accuracy
findMsMsHR.direct

Discontinued: find MS/MS spectrum from open raw file
peaksUnmatched

Select matching/unmatching peaks from aggregate table
checkSpectra

Check if a spectra set is found, complete, empty
toMassbank

Write MassBank record into character array
gatherDataBabel

Retrieve annotation data
flatten

Flatten, or re-read, MassBank header blocks
annotator.default

Generate peak annotation from peaklist
findMass

Calculate exact mass
findMsMsHRperxcms

Read in mz-files using XCMS
findProgress

Determine processed steps
gatherCompound

Compose data block of MassBank record
msmsWorkspace-class

Workspace for msmsWorkflow data
spectraCount

Count MS2 spectra per compound
toRMB

Conversion of XCMS-pseudospectra into RMassBank-spectra
filterPeaksMultiplicity

Multiplicity filtering: Removes peaks which occur only once in a n-spectra set.
deprofile

De-profile a high-resolution MS scan in profile mode.
findEIC

Extract EICs
findMz

Find compound information
findMsMsHR.ticms2

Extract an MS/MS spectrum from MS2 TIC
order.formula

Order a chemical formula correctly
problematicPeaks

Identify intense peaks (in a list of unmatched peaks)
plotRecalibration

Plot the recalibration graph.
parseMassBank

MassBank-record Parser
smiles2mass

Calculate the mass from a SMILES-String
ppm

Calculate ppm values
addPeaksManually

Addition of manual peaklists
addPeaks

Add additional peaks to spectra
cleanElnoise

Remove electronic noise
formulastring.to.list

Interconvert molecular formula representations
getPcId

Search Pubchem CID
getCtsRecord

Retrieve information from CTS
mbWorkflow

MassBank record creation workflow
peaksMatched

Select matching/unmatching peaks from aggregate table
progressBarHook

Standard progress bar hook.
gatherPubChem

Retrieve supplemental annotation data from Pubchem
createMolfile

Create MOL file for a chemical structure
RmbDefaultSettings

RMassBank settings
makeMollist

Write list.tsv file
selectSpectra

Select a subset of spectra matching properties
msmsRead

Extracts and processes spectra from a specified file list, according to loaded options and given parameters.
analyzeMsMs

Analyze MSMS spectra
checkIsotopes

Checks for isotopes in a msmsWorkspace
dbe

Calculate Double Bond Equivalents
filterPeakSatellites

Filter satellite peaks
gatherData

Retrieve annotation data
selectPeaks

Select peaks from aggregate table
msmsWorkflow

RMassBank mass spectrometry pipeline
recalibrate

Predefined recalibration functions.
setData

Set RmbSpectrum2 data from data.frame