The article details the development and application of precisION, an interactive, open-source software package for analyzing data from native top-down mass spectrometry (nTDMS). This new computational framework uses a data-driven fragment-level open search to overcome the limitations of current nTDMS methods, which often fail to detect uncharacterized or low-abundance protein modifications (PTMs) within intact protein complexes. The authors successfully applied precisION to therapeutically relevant targets—including PDE6, ACE2, osteopontin (SPP1), and a GABA transporter (GAT1)—to discover previously undocumented modifications such as phosphorylation, glycosylation, and lipidation, often resolving molecular complexity hidden beneath layers of heterogeneity. Importantly, the tool's ability to analyze internal fragments and recalibrate spectra significantly enhances sequence coverage and the localization and quantification of PTMs, improving structural insights for complex biomolecular systems like membrane proteins. The goal of precisION is to advance structural biology and drug development by providing an intuitive platform for interpreting complex protein fragmentation data.

References:

• Bennett J L, El-Baba T J, Zouboulis K C, et al. Uncovering hidden protein modifications with native top-down mass spectrometry[J]. Nature Methods, 2025: 1-11.