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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)

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

is.valid.formula

Check validity of formula

Load compound list for RMassBank

recalibrate.addMS1data

Return MS1 peaks to be used for recalibration

Generate peaks cache

reanalyzeFailpeaks

Reanalyze unmatched peaks

Compile MassBank records

combineMultiplicities

Combine workspaces for multiplicity filtering

Create Rcdk molecule from SMILES

filterMultiplicity

filterMultiplicity

Update settings to current version

processProblematicPeaks

Generate list of problematic peaks

plotMbWorkspaces

Plots mbWorkspaces

Extract MS/MS spectra for specified precursor

gatherDataUnknown

Retrieve annotation data

Create new workspace for mbWorkflow

Extracts and processes spectra from a list of xcms-Objects

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

Calculations on molecular formulas

Retrieve the Chemspider ID for a given compound

Get data frame with all present peak data

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

RMassBank settings

MassBank-record Addition

Convert formula to Rcdk limits

aggregateSpectra

Aggregate analyzed spectra

Backup msmsWorkflow results

Add and initialize dataframe column

Convert a single ID to another using CTS.

Retrieve information from Cactus

Export internally stored MassBank data to files

filterLowaccResults

Filter peaks with low accuracy

findMsMsHR.direct

Discontinued: find MS/MS spectrum from open raw file

Select matching/unmatching peaks from aggregate table

Check if a spectra set is found, complete, empty

Write MassBank record into character array

gatherDataBabel

Retrieve annotation data

Flatten, or re-read, MassBank header blocks

annotator.default

Generate peak annotation from peaklist

Calculate exact mass

findMsMsHRperxcms

Read in mz-files using XCMS

Determine processed steps

Compose data block of MassBank record

msmsWorkspace-class

Workspace for msmsWorkflow data

Count MS2 spectra per compound

Conversion of XCMS-pseudospectra into RMassBank-spectra

filterPeaksMultiplicity

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

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

Find compound information

findMsMsHR.ticms2

Extract an MS/MS spectrum from MS2 TIC

Order a chemical formula correctly

problematicPeaks

Identify intense peaks (in a list of unmatched peaks)

plotRecalibration

Plot the recalibration graph.

MassBank-record Parser

Calculate the mass from a SMILES-String

Calculate ppm values

addPeaksManually

Addition of manual peaklists

Add additional peaks to spectra

Remove electronic noise

formulastring.to.list

Interconvert molecular formula representations

Search Pubchem CID

Retrieve information from CTS

MassBank record creation workflow

Select matching/unmatching peaks from aggregate table

progressBarHook

Standard progress bar hook.

Retrieve supplemental annotation data from Pubchem

Create MOL file for a chemical structure

RmbDefaultSettings

RMassBank settings

Write list.tsv file

Select a subset of spectra matching properties

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

Analyze MSMS spectra

Checks for isotopes in a msmsWorkspace

Calculate Double Bond Equivalents

filterPeakSatellites

Filter satellite peaks

Retrieve annotation data

Select peaks from aggregate table

RMassBank mass spectrometry pipeline

Predefined recalibration functions.

Set RmbSpectrum2 data from data.frame