To smooth your raw data call one of the available NoiseFilters via the Tools-menu, (Tools > Apply TOPP tool), then select NoiseFilterSGolay or NoiseFilterGaussian as TOPPtool (green rectangle). The parameters for the filter type can be adapted (blue rectangle). For the Savitzky-Golay filter you can set the frame length and the order of the polynomial that is fitted. For the Gaussian filter the gaussian width and the ppm tolerance for a flexible gaussian width depending on the m/z value can be adapted. Press Ok to run the selected NoiseFilter.

The following image shows a part of the spectrum after smoothing as red line with the un-smoothed data in green.