RmbSettings {RMassBank} | R Documentation

## RMassBank settings

### Description

Describes all settings for the RMassBank settings file.

### Details

- `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- `use_version` Which MassBank record format to use; version 2 is strongly advised, version 1 is considered outdated and should be used only if for some reason you are running old servers and an upgrade is not feasible.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!

### Author(s)

Michael Stravs, Emma Schymanski

### See Also

`loadRmbSettings`

[Package RMassBank version 3.0.0 Index]