biostudies-literatureSchulte DExacte en NatuurwetenschappenEuropean Research Council23120-23130https://www.ebi.ac.uk/biostudies/studies/S-EPMC12573231biostudies-literatureUnknown97(42)Accurate and comprehensive peptide spectrum annotation is a crucial step to interpreting mass spectrometry-based proteomics data. While peak assignment in peptide fragmentation spectra is central to a broad range of proteomics applications, current tools tend to be specialized to a specific task. Here, we present a more comprehensive interactive graphical tool (Annotator), along with the underlying codebase written in Rust (rustyms). Annotator enables unified spectrum annotation for bottom-up, middle-down, top-down, cross-linked, and glycopeptide fragmentation mass spectra from all fragmentation methods, including all ion types: a/b/c, x/y/z, d/v/w, and immonium ions. The Annotator integrates all known post-translational modifications from common databases and additionally allows for the dAnalytical chemistryA Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.PMC12573231024.002.009101077640Leuvenink RWHeck AJRSnijder JJager SSchulte DfalseA Universal Spectrum Annotator for Complex Peptidoforms in Mass Spectrometry-Based Proteomics.Accurate and comprehensive peptide spectrum annotation is a crucial step to interpreting mass spectrometry-based proteomics data. While peak assignment in peptide fragmentation spectra is central to a broad range of proteomics applications, current tools tend to be specialized to a specific task. Here, we present a more comprehensive interactive graphical tool (Annotator), along with the underlying codebase written in Rust (rustyms). Annotator enables unified spectrum annotation for bottom-up, middle-down, top-down, cross-linked, and glycopeptide fragmentation mass spectra from all fragmentation methods, including all ion types: a/b/c, x/y/z, d/v/w, and immonium ions. The Annotator integrates all known post-translational modifications from common databases and additionally allows for the d2025-01-01T00:00:00Z2025 Oct2026-06-05T10:32:31.084Z2026-05-16T03:07:53.263ZS-EPMC125732314108541110.1021/acs.analchem.5c02832