I had a student successfully do this using Minitab. It is not fundamentally different from doing PCA on other data sets except NMR spectra tend to be quite large. If you need a free resource, R seems to have PCA packages, but I do not have experience of using these (I have used other R packages). R isn't as user friendly but can do just about any statistical task.

I would suggest binning the data and then you can either do a PCA in AMIX directly or in R using, e.g., the function prcomp.