{
  "abstract": "De novo peptide sequencing detects peptides directly from tandem mass spectra without a protein sequence database, and deep learning has substantially advanced its performance. Casanovo, one such widely used model, is distributed as a Python command-line program. Consequently, installation, GPU and dependency configuration, and manual parameterization can be challenging for many bench scientists and are a recurring source of errors. Interpreting and validating the resulting predictions poses a further challenge. We present CasanovoGUI, an open-source Java-based desktop application that makes all of Casanovo's main analysis functions available through a point-and-click interface on Windows, macOS, and Linux. On first use, CasanovoGUI automatically installs a private Python environment and Casanovo with a GPU-matched build, requiring no prior software setup. The GUI provides access to Casanovo's analysis functions and configuration parameters, streams live progress, and integrates results interpretation: annotated spectra with per-residue confidence scores in the PDV viewer, and mismatch-tolerant mapping of de novo peptides back to a reference proteome. CasanovoGUI is available at https://github.com/Noble-Lab/CasanovoGUI.",
  "abstract_shown": true,
  "affiliations": [
    "University of Washington"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "name": "B. Wen"
    },
    {
      "name": "K. Li"
    },
    {
      "name": "M. Riffle"
    },
    {
      "name": "M. J. MacCoss"
    },
    {
      "name": "W. Bittremieux"
    },
    {
      "affs": [
        0
      ],
      "name": "W. S. Noble"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bzwmbjtjvm8yh.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.07.11.737889",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.07.11.737889v2.full",
  "id": "bzwmbjtjvm8yh",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.07.11.737889v2",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioinformatics"
    ],
    [
      "openalex",
      "1607|Advanced Proteomics Techniques and Applications"
    ]
  ],
  "openalex": "W7169511116",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.07.11.737889v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-07-11",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/bzwmbjtjvm8yh.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:21:41Z",
      "native_id": "10.64898/2026.07.11.737889",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.07.11.737889v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo",
  "title_text": "CasanovoGUI: a cross-platform desktop application for deep learning-based de novo peptide sequencing with Casanovo",
  "type": "preprint",
  "updated_at": "2026-10-30T12:21:41Z",
  "url": "https://research.draconitic.com/paper/bzwmbjtjvm8yh",
  "venue": "bioRxiv",
  "versions": []
}