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

Description Details Author(s) See Also

Describes all settings for the RMassBank settings file.

deprofile Whether and how to deprofile input raw files. Leave the setting empty if your raw files are already in "centroid" mode. If your input files are in profile mode, you have the choice between algorithms deprofile.spline, deprofile.fwhm, deprofile.localMax; refer to the individual manpages for more information.
rtMargin, rtShift The allowed retention time deviation relative to the values specified in your compound list (see loadList), and the systematic shift (due to the use of, e.g., pre-columns or other special equipment.
babeldir Directory to OpenBabel. Required for creating molfiles for MassBank export. If no OpenBabel directory is given, RMassBank will attempt to use the CACTUS webservice for SDF generation. It is strongly advised to install OpenBabel; the CACTUS structures have explicit hydrogen atoms. The path should point to the directory where babel.exe (or the Linux "babel" equivalent) lies.
use_version Which MassBank record format to use; version 2 is strongly advised, version 1 is considered outdated and should be used only if for some reason you are running old servers and an upgrade is not feasible.
use_rean_peaks Whether to include peaks from reanalysis (see reanalyzeFailpeaks) in the MassBank records. Boolean, TRUE or FALSE.
annotations A list of constant annotations to use in the MassBank records. The entries authors, copyright, license, instrument, instrument_type, compound_class correspond to the MassBank entries AUTHORS, COPYRIGHT, PUBLICATION, LICENSE, AC$INSTRUMENT, AC$INSTRUMENT_TYPE, CH$COMPOUND_CLASS. The entry confidence_comment is added as COMMENT: CONFIDENCE entry.

The entry internal_id_fieldname is used to name the MassBank entry which will keep a reference to the internal compound ID used in the workflow: for internal_id_fieldname = MYID and e.g. compound 1234, an entry will be added to the MassBank record with COMMENT: MYID 1234. The internal fieldname should not be left empty!

The entries lc_gradient, lc_flow, lc_solvent_a, lc_solvent_b, lc_column correspond to the MassBank entries AC$CHROMATOGRAPHY: FLOW_GRADIENT, FLOW_RATE, SOLVENT A, SOLVENT B, COLUMN_NAME.

ms_type, ionization correspond to AC$MASS_SPECTROMETRY: MS_TYPE, IONIZATION.

entry_prefix is the two-letter prefix used when building MassBank accession codes.

Entries under ms_dataprocessing are added as MS$DATA_PROCESSING: entries, in addition to the default WHOLE: RMassBank.
annotator For advanced users: option to select your own custom annotator. Check annotator.default and the source code for details.
spectraList This setting describes the experimental annotations for the single data-dependent scans. For every data-dependent scan event, a spectraList entry with mode, ces, ce, res denoting collision mode, collision energy in short and verbose notation, and FT resolution.
accessionNumberShifts This denotes the starting points for accession numbers for different ion types. For example, pH: 0, mH: 50 means that [M+H]+ spectra will start at XX123401 (XX being the entry_prefix and 1234 the compound id) and [M-H]- will start at XX123451.
electronicNoise, electronicNoiseWidth Known electronic noise peaks and the window to be used by cleanElnoise
recalibrateBy dppm or dmz to recalibrate either by delta ppm or by delta mz.
recalibrateMS1 common or separate to recalibrate MS1 data points together or separately from MS2 data points.
recalibrator: MS1, MS2 The functions to use for recalibration of MS1 and MS2 data points. Note that the MS1 setting is only meaningful if recalibrateMS1: separate, otherwise the MS2 setting is used for a common recalibration curve. See recalibrate.loess for details.
multiplicityFilter Define the multiplicity filtering level. Default is 2, a value of 1 is off (no filtering) and >2 is harsher filtering.
titleFormat The title of MassBank records is a mini-summary of the record, for example "Dinotefuran; LC-ESI-QFT; MS2; CE: 35 By default, the first compound name CH$NAME, instrument type AC$INSTRUMENT_TYPE, MS/MS type AC$MASS_SPECTROMETRY: MS_TYPE, collision energy RECORD_TITLE_CE, resolution AC$MASS_SPECTROMETRY: RESOLUTION and precursor MS$FOCUSED_ION: PRECURSOR_TYPE are used. If alternative information is relevant to differentiate acquired spectra, the title should be adjusted. For example, many TOFs do not have a resolution setting. See MassBank documentation for more.
filterSettings A list of settings that affect the MS/MS processing. The entries ppmHighMass, ppmLowMass, massRangeDivision set values for pre-processing, prior to recalibration. ppmHighMass defines the ppm error for the high mass range (default 10 ppm for Orbitraps), ppmLowMass is the error for the low mass range (default 15 ppm for Orbitraps) and massRangeDivision is the m/z value defining the split between the high and low mass range (default m/z = 120).

The entry ppmFine defines the ppm cut-off post recalibration. The default value of 5 ppm is recommended for Orbitraps. For other instruments this can be interpreted from the recalibration plot. All ppm limits are one-sided (e.g. this includes values to +5 ppm or -5 ppm deviation from the exact mass).

The entries prelimCut, prelimCutRatio define the intensity cut-off and cut-off ratio (in the peak selection for the recalibration only. Careful: the default value 1e4 for Orbitrap LTQ positive mode could remove all peaks for TOF data and will remove too many peaks for Orbitrap LTQ negative mode spectra!

The entry specOKLimit defines the intensity limit to include MS/MS spectra. MS/MS spectra must have at least one peak above this limit to proceed through the workflow.

dbeMinLimit defines the minimum allowable ring and double bond equivalents (DBE) allowed for assigned formulas. This assumes maximum valuences for elements with multiple valence states. The default is -0.5 (accounting for fragments being ions).

The entries satelliteMzLimit, satelliteIntLimit define the cut-off m/z and intensity values for satellite peak removal (an artefact of Fourier Transform processing). All peaks within the m/z limit (default 0.5) and intensity ratio (default 0.05 or 5 Fourier Transform instruments only (e.g. Orbitrap).
filterSettings Parameters for adjusting the raw data retrieval. The entry ppmFine defines the ppm error to look for the precursor in the MS1 (parent) spectrum. Default is 10 ppm for Orbitrap.

mzCoarse defines the error to search for the precursor specification in the MS2 spectrum. This is often only saved to 2 decimal places and thus can be quite inaccurate. The accuracy also depends on the isolation window used. The default settings (for e.g. Orbitrap) is 0.5 (Da, or Th for m/z).

The entry fillPrecursorScan is largely untested. The default value (FALSE) assumes all necessary precursor information is available in the mzML file. A setting ot TRUE tries to fill in the precursor data scan number if it is missing. Only tested on one case study so far - feedback welcome!