## load package
library("MALDIquant")
## load example data
data("fiedler2009subset", package="MALDIquant")
## choose only the first mass spectrum
s <- fiedler2009subset[[1]]
## transform intensities
s <- transformIntensity(s, method="sqrt")
## smoothing spectrum
s <- smoothIntensity(s, method="MovingAverage")
## remove baseline
s <- removeBaseline(s)
## plot spectrum
plot(s)
## call peak detection
p <- detectPeaks(s)
## draw peaks on the plot
points(p)
## label 10 highest peaks
top10 <- intensity(p) %in% sort(intensity(p), decreasing=TRUE)[1:10]
labelPeaks(p, index=top10)
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