How does alignment work?

The algorithm attempts to line up an individual spectrum with a weighted average spectrum (based on the entire experiment). The spectra are compared using Fast Fourier Transforms to calculate how much they should shift to improve the match. The spectra are gradually cut into smaller and smaller pieces and they are aligned as well until it has converged. The search area gives the algorithm a maximum shift during each pass and the Iterative cycles parameter indicates a level of iteration before saying it is complete. If you set these parameters to high then the spectra can misalign and create artefacts (horizontal straight lines). If this happens reduce them to help get a better fit.