Substance Indexing SPL files can convey information on a wide variety of substances, such as therapeutic proteins including modified proteins. Chemical modifications of proteins affect their biological activity and sometimes constitute the entirety of their biological activity. This includes modifications that occur as the result of natural biochemical processes, i.e posttranslational modifications. Substance Indexing SPL files describe such posttranslationally modified proteins with atomic precision even if one is dealing with a large protein . We take advantage of these Substance Indexing SPL capabilities for Reaction SPL.