{
  "abstract": "Bruker timsTOF acquisitions produce dense native .d files whose storage, transfer, and archival become substantial at high throughput. We present dnoise, an open-source Rust tool that removes points directly from timsTOF frames and writes a native-compatible .d directory. dnoise retains ions that form coherent streaks across the ion-mobility dimension and applies acquisition-aware gates to signal that cannot be selected for fragmentation. On a three-species benchmark spanning ddaPASEF and diaPASEF at 5- and 15-minute gradients, default MS1-only denoising reduced the frame binary by 35 to 53%. Label-free quantification accuracy was preserved in both modes. ddaPASEF peptide-spectrum-match, peptide, and protein-group counts were unchanged, as expected with the searched MS/MS spectra untouched, and diaPASEF precursor and protein-group counts changed only slightly. Every tested processing run completed in 69 seconds or less on the benchmark workstation. Optional MS/MS denoising produced greater reduction but sacrificed several percent of identifications. Thus, a substantial fraction of native timsTOF frame data can be removed with little analytical change.",
  "abstract_shown": true,
  "affiliations": [
    "The Scripps Research Institute"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "name": "P. T. Garrett"
    },
    {
      "name": "J. K. Diedrich"
    },
    {
      "affs": [
        0
      ],
      "name": "J. R. Yates"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/a4m8k5wkqwkby.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.27.747603",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747603v1.full",
  "id": "a4m8k5wkqwkby",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747603v1",
  "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": "W7205017242",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747603v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/a4m8k5wkqwkby.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:18:29Z",
      "native_id": "10.64898/2026.08.27.747603",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747603v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioinformatics",
      "subfield": "bioinformatics"
    }
  ],
  "title": "dnoise: Fast Native Data Reduction for Bruker timsTOF",
  "title_text": "dnoise: Fast Native Data Reduction for Bruker timsTOF",
  "type": "preprint",
  "updated_at": "2026-10-30T12:18:29Z",
  "url": "https://research.draconitic.com/paper/a4m8k5wkqwkby",
  "venue": "bioRxiv",
  "versions": []
}