The scientific community increasingly recognizes that algorithms, while not software or tools themselves but rather the underlying steps and methodology, are becoming significant research outputs in their own right. Algorithms are no longer seen merely as tools but are valued as core research outputs, reflecting the critical steps and methodologies at the heart of scientific innovation. For example, the peptide spectrum scoring function HyperScore was originally implemented in the open-source search engine X!Tandem , later adopted by search engines including MSFragger , EncyclopeDIA , PepQuery and Sage .