filterPeakSatellites: Filter satellite peaks

Description

Filters satellite peaks in FT spectra which arise from FT artifacts and from conversion to stick mode. A very simple rule is used which holds mostly true for MSMS spectra (and shouldn't be applied to MS1 spectra which contain isotope structures...)

Usage

filterPeakSatellites(peaks, filterSettings = getOption("RMassBank")$filterSettings)

Arguments

peaks

A peak dataframe with at least the columns mz, int. Note that mz is used even for the recalibrated spectra, i.e. the desatellited spectrum is identical for both the unrecalibrated and the recalibrated spectra.

filterSettings

The settings used for filtering. Refer to analyzeMsMs documentation for filter settings.

Value

Returns the peak table with satellite peaks removed.

Details

The function cuts off all peaks within 0.5 m/z from every peak, in decreasing intensity order, which are below 5 intensity. E.g. for peaks m/z=100, int=100; m/z=100.2, int=2, m/z=100.3, int=6, m/z 150, int=10: The most intense peak (m/z=100) is selected, all neighborhood peaks below 5 peak) and the next less intense peak is selected. Here this is the m/z=150 peak. All low-intensity neighborhood peaks are removed (nothing). The next less intense peak is selected (m/z=100.3) and again neighborhood peaks are cut away (nothing to cut here. Note that the m/z = 100.2 peak was alredy removed.)

Examples

Run this code


# From the workflow:
## Not run: 
#     # Filter out satellite peaks:
#     shot <- filterPeakSatellites(shot)
#     shot_satellite_n <- setdiff(row.names(shot_full), row.names(shot))
#     shot_satellite <- shot_full[shot_satellite_n,]
#     # shot_satellite contains the peaks which were eliminated as satellites.
# ## End(Not run)