We use the regular C18 materials also used for analysis of linear peptides in e.g. standard digests, however have optimized gradients as peptide/peptide cross-links tend to be more hydrophobic. E.g. a cross-link gradient should go up to 50% ACN, not 35% as for regular proteome analysis.

If you have a lot of material, you should perform an upfront prefractionation using a peptide SEC column.