In this report we summarize our experiences with the reaction products of N-hydroxysuccinimide (NHS) esters, which are widely used for chemical cross-linking of lysine residues in proteins. We describe the products, which should be scrutinized during data analysis using customized software when NHS esters are employed for chemical cross-linking. Reaction products of NHS esters were observed not only with lysines, but also with serines, tyrosines, and threonines. This report is intended to be a practical guide for those working in the field of chemical cross-linking and mass spectrometry.