problematicPeaks: Identify intense peaks (in a list of unmatched peaks)

In sneumann/RMassBank: Workflow to process tandem MS files and build MassBank records

Description

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.

Usage

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

Arguments

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.)

Value

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

Author(s)

Michael Stravs

See Also

msmsWorkflow

Examples

## 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)

sneumann/RMassBank documentation built on Oct. 20, 2020, 3:19 p.m.