Identification of Ultramodified Proteins Using Top-Down Spectra

Post-translational modifications (PTMs) play an important role in various biological processes through changing protein structure and function. Some

ultramodified

proteins (like histones) have multiple PTMs forming

PTM patterns

that define the functionality of a protein. While bottom-up mass spectrometry (MS) has been successful in identifying

individual

PTMs within short peptides, it is unable to identify PTM patterns spread along entire proteins in a coordinated fashion. In contrast, top-down MS analyzes intact proteins and reveals PTM patterns along the entire proteins. However, while recent advances in instrumentation have made top-down MS accessible to many laboratories, most computational tools for top-down MS focus on proteins with few PTMs and are unable to identify complex PTM patterns. We propose a new algorithm, MS-Align-E, that identifies both expected and unexpected PTMs in ultramodified proteins. We demonstrate that MS-Align-E identifies many protein forms of histone H4 and benchmark it against the currently accepted software tools.