{
  "abstract": "Background\n\nProteoforms are the critical functional species that drive biological processes. However, conventional proteogenomic (\"shotgun\") analyses discard relevant proteoform-level information through bulk protein digestion. This study presents a proof-of-principle integrative Top-Down Proteomics workflow designed to identify and characterise proteoforms across the breadth of a proteome.Methods\n\nThis workflow combined two-dimensional electrophoresis, a custom grid-cutting lattice for reproducible gel sectioning, in-gel digestion, liquid chromatography-tandem mass spectrometry, and open-search algorithms. Gel-grid locations, isoelectric points, and molecular weights were integrated with mass-spectrometry results to further characterise identified proteoforms.Results\n\nThe approach enabled identification of a broad range of proteoforms and their inherent post-translational modifications, including phosphorylation, acetylation, methylation, and glycosylation. Notably, substantial numbers of proteoforms were identified in visually \"blank regions\" of replicate two-dimensional gels. This eliminated bias associated with assessing only visually detectable protein spots and substantially expanded proteome-level proteoform detection and characterisation.Conclusions\n\nThis integrative workflow provides a reproducible and comprehensive strategy for addressing the often-overlooked complexity of proteomes at the proteoform level. By extending analysis beyond visually detectable gel spots, it enables deeper characterisation of proteoform diversity and associated post-translational modifications.",
  "abstract_shown": true,
  "affiliations": [
    "School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW 2007, Australia.",
    "Institute for Globally Distributed Open Research and Education (IGDORE), St. Catharines, ON L2N 4X2, Canada."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 6,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Luke A Farrell",
      "orcid": "0009-0004-6953-8877"
    },
    {
      "affs": [
        0
      ],
      "name": "Breyer Woodland",
      "orcid": "0009-0004-7390-0189"
    },
    {
      "affs": [
        0
      ],
      "name": "Aiden Brennan"
    },
    {
      "affs": [
        1
      ],
      "name": "Jens R Coorssen",
      "orcid": "0000-0001-8048-7370"
    },
    {
      "affs": [
        0
      ],
      "name": "Matthew B O'Rourke",
      "orcid": "0000-0002-0552-2962"
    },
    {
      "affs": [
        0
      ],
      "name": "Matthew P Padula",
      "orcid": "0000-0002-8283-0643"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f4q2v6s23xqp5.bib",
  "cited_by": 0,
  "doi": "10.3390/proteomes14040053",
  "fulltext_url": "https://europepmc.org/articles/PMC13692341",
  "id": "f4q2v6s23xqp5",
  "issns": [
    "2227-7382"
  ],
  "landing_url": "https://europepmc.org/article/MED/42924751",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1607|Advanced Proteomics Techniques and Applications"
    ]
  ],
  "openalex": "W7221080231",
  "pdf_url": "https://europepmc.org/articles/PMC13692341?pdf=render",
  "pmcid": "PMC13692341",
  "pmid": "42924751",
  "published": "2026-10-09",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/f4q2v6s23xqp5.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:20:33Z",
      "native_id": "MED:42924751",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42924751"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "openalex:1607|Advanced Proteomics Techniques and Applications",
      "subfield": "physical"
    }
  ],
  "title": "Integrated Top-Down Proteomics for Comprehensive Proteome Analysis at the Proteoform Level.",
  "title_text": "Integrated Top-Down Proteomics for Comprehensive Proteome Analysis at the Proteoform Level.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:20:33Z",
  "url": "https://research.draconitic.com/paper/f4q2v6s23xqp5",
  "venue": "Proteomes",
  "versions": []
}