most data-handling programs (e.g. Kaleidagraph, GraphPad Prism, etc.) will have a smoothing function to treat the raw data.
However, if possible I'd recommend trying to improve the quality of the raw data by modifying the acquisition parameters. In any case, you should detail in the paper whatever manipulation done to the data .
Hi, I know it's been some time since you posted this but I think the only proper way how to smooth your data is to measure your spectra multiple times and then do average. Each data point is an independent variable, you should not just assume it will be connected to several previous and following data point.Averaging just takes into account the random error which occurs due to measurement.