rm.sat: Removal of satellite peaks from FT-MS peak lists

Description

Brute force method to remove satellite peak from a FT-HRMS peak list.

Usage

rm.sat(peaklist, dmz = 0.3, drt = 0.3, intrat = 0.01, spar = 0.8, 
corcut = 0.8, plotit = TRUE)

Arguments

peaklist

Dataframe of HRMS peaks with three numeric columns for (a) m/z, (b) intensity and (c) retention time, such as peaklist.

dmz

m/z window around a parent peak within which satellite peaks are searched for.

drt

Retention time window around a parent peak within which satellite peaks are searched for.

intrat

Intensity ratio between satellite peak/associated parent peak below which the former are removed.

spar

spar argument used in R-function smooth spline. See details and ?smooth.spline.

corcut

Correlation coefficient above which symmetrical peaks are marked as satellite peaks. To disable, set to -1000 See details.

plotit

Plot results?

Value

A dataframe with four columns. The first three columns are identical to those of argument peaklist. The fourth columns marks potential satellite peaks with FALSE, the other peaks with TRUE (see example).

Details

"Parent" peak refers to a peak having associated satellite peaks as artifacts from FT calculations.

rm.sat screens, along decreasing intensity, peaks for having other peaks within ranges set by arguments dmz, drt and intrat. If present, the latter are marked as satellite peaks and are subsequently excluded from further screening within rm.sat.

In addition, arguments spar and corcut evaluate the symmetry of satellite peaks around the parent peak (i.e. below and above the parent peak m/z), if enough peaks around a parent peak within ranges set by arguments dmz, drt and intrat are found (here: at least 8 peaks, 4 above and 4 below the parent peak m/z). Two splines are fitted by R function smooth.spline, one to those peaks above and one to those peaks below the parent peak m/z. If the splines are symmetric (i.e. correlated with each other, see argument corcut), the associated peaks are termed satellites. This approach has not yet faced validation and is highly dependent on the peak-picking algorithm.

Examples

Run this code


data(peaklist);
peaklist<-rm.sat(peaklist,dmz=0.3,drt=0.1,intrat=0.015,spar=0.8,corcut=-1000,plotit=TRUE);
peaklist<-peaklist[peaklist[,4],1:3];