The intensity of peaks varies with their mobility. Sections of the protein in secondary structure will be fairly rigid. They should all show similar, reasonably strong, peak intensities. Slightly mobile regions, such as loop regions tend to show reduced peak intensities and in the worst case scenario are simply not visible at all. Very highly flexible regions, such as the C-terminus show very high peak intensities. Peak intensities will tend to go in waves along the backbone with neighbouring residues tending to have similar peak intensities.

The C-terminus can usually be identified fairly easily due to its strong peak in a very characteristic part of the HSQC spectrum (see here for a figure).

Serine peaks are often rather weak.