{
  "id": 5027350,
  "title": "dnoise: Fast Native Data Reduction for Bruker timsTOF",
  "url": "https://urgent.news/2026/09/01/dnoise-fast-native-data-reduction-for-bruker-timstof",
  "topic": "science",
  "section": "Science",
  "published": "2026-09-01T00:00:00.000Z",
  "source": {
    "name": "bioRxiv",
    "slug": "biorxiv",
    "url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747603v1?rss=1"
  },
  "original_language": "en",
  "account": "The Bruker timsTOF system generates large .d files during data acquisition, which can be challenging to store, transfer, and archive. To address this issue, a new open-source Rust tool called dnoise has been developed. This tool efficiently removes points directly from timsTOF frames while retaining the crucial information needed for analysis. By applying acquisition-aware gates, dnoise ensures that ions forming coherent streaks across the ion-mobility dimension are preserved. Additionally, it allows for the retention of signal that cannot be selected for fragmentation.\n\nIn a benchmark study involving three species, dnoise was tested on both ddaPASEF and diaPASEF modes at 5- and 15-minute gradients. The results showed that default MS1-only denoising reduced the frame binary size by 35 to 53% without compromising label-free quantification accuracy. Importantly, the peptide-spectrum-match, peptide, and protein-group counts remained unchanged, indicating that the MS/MS spectra were left untouched. When it came to diaPASEF, only slight changes were observed in the precursor and protein-group counts.\n\nThe processing time for each run completed within 69 seconds on the benchmark workstation, even with the optional MS/MS denoising enabled. However, this optional denoising option did result in a slight decrease in identifications. Overall, the dnoise tool successfully removes a significant portion of the native timsTOF frame data while maintaining the analytical integrity of the samples.",
  "summary": "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…",
  "key_points": [],
  "editors_take": null,
  "illustration": null,
  "coverage": {
    "outlets": 1,
    "also_reported_by": []
  },
  "ai_generated": true,
  "disclaimer": "Summaries, key points and the editor’s take are written by software from other outlets’ reporting and may contain errors — always check the linked original."
}