MetaMorpheus is a software tool that identifies peptides, proteins, and proteoforms from mass spectrometry fragmentation (MS/MS) data. It is capable of searching both bottom-up (peptide) and top-down (intact proteoform) data. Currently, five graduate students and several undergraduates work on improving MetaMorpheus, making it one of our most collaborative and dynamic projects. Often, the motivation for adding a feature to MetaMorpheus is the need to analyze new types of data that existing software simply cannot handle. We use computer programming as a tool to solve these problems, much like traditional chemical biology uses organic chemistry to probe biological systems. MetaMorpheus was specifically designed to identify the “dark matter” of proteomics; where most search programs attempt to identify mostly unmodified peptides, we provide the capability of identifying peptides with a wide range of post-translational modifications. Recently, we have added the ability to identify proteoforms, chemically crosslinked peptides, and isotopically-labeled peptides. We also focus on providing this tool to the proteomics community as a free, open-source, easy-to-use tool. We have a community of over 200 users, which grows every day. We are constantly adding new features to the software, and release new versions of MetaMorpheus every few weeks.