I'm planning a project using MALDI-TOF MS where I'll try to differentiate two series of spectra coming from experiments using cells. In the experiments one parameter influencing the cell growth will be changed, what I need is a software that I can use to differentiate MS spectra before and after the treatments. I expect fairly complex spectra as result, if this could be of help.

If the software is free, open or in alternative low cost it will be appreciated.