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arXiv · 2505.17755

A graph-based approach for modification site assignment in proteomics

Dafni Skiadopoulou·Lukas Käll·Harald Barsnes·Veit Schwämmle·Marc Vaudel
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Abstract

Background In proteomics, the most probable localizations of post-translational modifications are assessed by localization scores evaluating the likelihood of a given modification to occupy a site on a peptide sequence. When identifying highly modified peptides, localization scores for different modifications can return conflicting results, stacking modifications on the same amino acid. Here, we propose a graph-based approach that assigns modifications to sites in a way that maximizes localization scores while avoiding conflicting assignments. Results The algorithm is implemented as both a standalone Python program and in the compomics-utilities Java library. Our graph-based approach showed the ability to match complex combinations of modifications and acceptor sites, allowing the processing of thousands of peptides in a few seconds. Conclusions Our graph-based approach to modification site assignment allows distributing multiple modifications in a way that maximizes individual localization scores. Having an optimal modification site assignment is important for spectrum annotation and biological interpretation.

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Dafni Skiadopoulou, Lukas Käll, Harald Barsnes, Veit Schwämmle, Marc Vaudel. 2025-05-23. A graph-based approach for modification site assignment in proteomics. https://arxiv.org/abs/2505.17755

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