mergeMassPeaks(l, labels, method=c("mean", "median", "sum"), ignore.na=TRUE,
               ...)

## load package
library("MALDIquant")

## create four MassPeaks objects and add them to the list
p <- list(createMassPeaks(mass=1:2, intensity=1:2),
          createMassPeaks(mass=1:3, intensity=1:3),
          createMassPeaks(mass=1:4, intensity=1:4),
          createMassPeaks(mass=1:5, intensity=1:5))

## merge all four MassPeaks objects into a single new one
## by sum their intensities
## (no labels, returns only one new MassPeaks object)
mergedPeaks <- mergeMassPeaks(p, method="sum")

## only merge MassPeaks objects in a group
## (two different labels, returns a list of two new MassPeaks objects)
groups <- factor(c("a", "a", "b", "b"), levels=c("a", "b"))
mergedPeaks <- mergeMassPeaks(p, labels=groups, method="mean")

## the same, but treat NA as zero
mergedPeaks <- mergeMassPeaks(p, labels=groups, method="mean", ignore.na=FALSE)