Discussion at metaRbolomics, these two functions are a bit of a misnoma:

https://github.com/rformassspectrometry/Spectra/blob/master/R/Spectra.R#L401
"removePeaks" is rather "markPeaks" or something (it doesn't actually remove peaks)

`#' - `removePeaks`: *removes* peaks lower or equal to a threshold intensity
#'   value `threshold` by setting their intensity to `0`. With the default
#'   `threshold = "min"` all peaks with an intensity smaller or equal to the
#'   minimal non-zero intensity is set to `0`. If the spectrum is in
#'   profile mode, ranges of successive non-0 peaks <= `threshold` are set to 0.
#'   If the spectrum is centroided, then individual peaks <= `threshold` are set
#'   to 0. Note that the number of peaks is not changed unless `clean` is
#'   called after `removePeaks`.`

Whereas "clean" is not really clean but more analogous to trim

https://github.com/rformassspectrometry/Spectra/blob/master/R/Spectra.R#L412

`#' @param all for `clean`: `logical(1)` whether all 0 intensity peaks should be
#'     removed (`TRUE`) or whether 0-intensity peaks directly adjacent to a
#'     non-zero intensity peak should be kept (`FALSE`).`