problematicPeaks: Identify intense peaks (in a list of unmatched peaks)
In RMassBank: Workflow to process tandem MS files and build MassBank records

Description Usage Arguments Value Author(s) See Also Examples

Finds a list of peaks in spectra with a high relative intensity (>10 1e4, or >1 checked. Peaks orbiting around the parent peak mass (calculated from the compound ID), which are very likely co-isolated substances, are ignored.

1	problematicPeaks(peaks_unmatched, peaks_matched, mode = "pH")

`peaks_unmatched`	Table of unmatched peaks, with at least `cpdID, scan, mzFound, int`.
`peaks_matched`	Table of matched peaks (used for base peak reference), with at least `cpdID, scan, int`.
`mode`	Processing mode (`"pH", "pNa"` etc.)

A filtered table with the potentially problematic peaks, including the precursor mass and MSMS base peak intensity (aMax) for reference.

Michael Stravs

msmsWorkflow

## Not run: 
# As used in the workflow: 
fp <- problematicPeaks(specs[!specs$filterOK & !specs$noise & 
						((specs$dppm == specs$dppmBest) | (is.na(specs$dppmBest)))
				,,drop=FALSE], peaksMatched(w), mode)

## End(Not run)