wfondrie/depthcharge

Built on PyTorch, Depthcharge provides reusable modules and Transformer architectures specifically designed for mass spectrometry analysis, eliminating the need to rebuild common components. It offers domain-specific building blocks for peptide identification, molecular characterization, and spectral analysis while maintaining flexibility for custom model assembly. The toolkit targets researchers building deep learning pipelines around mass spectrometry data without reimplementing standard preprocessing, encoding, and model layers.