{
  "abstract": "Membrane trafficking determines the subcellular localization and compartment-residence time of receptors, channels, transporters and other transmembrane proteins and thereby influences where in the cell and how long these proteins function. Functional-enrichment computational approaches may predict the membrane-trafficking regulations but do not resolve the directionality of the transport between cellular compartments. We present Traffickome, a deterministic method organizing 754 trafficking proteins into 11 directed transitions across seven compartments and 1,837 signaling proteins across 22 pathways. Implemented as an interactive browser and open-source Python package, Traffickome infers compartment-to-compartment transport, cargo fate and signaling-pathway activity and enables in silico perturbation from a single proteomic comparison. Across 29 proteomic comparisons spanning 14 studies encompassing over 66,000 gene-level observations across over 10,000 genes, Traffickome ranked the expected trafficking transition first in 23 cases (79%), outperforming the best conventional enrichment methods (17 of 29, 59%). Mean accuracy fell to 18% after randomizing the protein-to-transition assignments. To illustrate the power of Traffickome, we performed time-resolved analysis of the phosphoproteome in EGF-stimulated cells with the goal to distinguish signaling by internalized versus plasma-membrane EGFR. In the resulting datasets, comprising over 18,000 phosphosite-level measurements, Traffickome revealed localization-dependent differences in EGF-induced phosphorylation and prioritized trafficking regulators for testing their effects on signaling processes.",
  "abstract_shown": true,
  "affiliations": [
    "University of Pittsburgh"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "R. H. Deshpande"
    },
    {
      "name": "I. Pinilla-Macua"
    },
    {
      "name": "J. A. Paulo"
    },
    {
      "name": "S. Gygi"
    },
    {
      "name": "A. Sorkin"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/3sftpp1pabwj9.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.20.753016",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753016v1.full",
  "id": "3sftpp1pabwj9",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753016v1",
  "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",
      "cell biology"
    ],
    [
      "openalex",
      "1307|Cellular transport and secretion"
    ]
  ],
  "openalex": "W7214330614",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753016v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-20",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/3sftpp1pabwj9.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:23:49Z",
      "native_id": "10.64898/2026.09.20.753016",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753016v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:cell biology",
      "subfield": "cell-biology"
    }
  ],
  "title": "Traffickome infers directed, compartment-resolved membrane trafficking from proteomic data",
  "title_text": "Traffickome infers directed, compartment-resolved membrane trafficking from proteomic data",
  "type": "preprint",
  "updated_at": "2026-10-30T12:23:49Z",
  "url": "https://research.draconitic.com/paper/3sftpp1pabwj9",
  "venue": "bioRxiv",
  "versions": []
}