# How to cite dnoise. Read by GitHub (the "Cite this repository" button) and by
# Zenodo, which uses it to populate the metadata of the archived release rather
# than guessing from the repository name.
#
# Two things to update at release time:
# - `version` and `date-released` must match the tag being archived.
# - once Zenodo has minted a DOI, add it under `identifiers` so the record is
# self-describing; and once the paper is published, fill in `preferred-citation`
# with its DOI so citing the software points readers at the paper.
cff-version: 1.2.0
message: "If you use this software, please cite it using the metadata below."
title: dnoise
abstract: >-
Fast, in-place denoising of Bruker timsTOF .d files. Real ions form streaks
along the ion-mobility axis whereas chemical and electronic noise is short,
isolated, or scattered; dnoise exploits that structural prior to remove noise
from MS1 (and optionally MS/MS) frames, writing cleaned .d folders that stay
drop-in compatible with existing tools. No per-dataset calibration is required.
type: software
authors:
- given-names: Patrick
family-names: Garrett
email: pgarrett@scripps.edu
orcid: "https://orcid.org/0000-0002-8434-9693"
affiliation: >-
Department of Chemical Physiology, The Scripps Research Institute,
La Jolla, CA, USA
- given-names: Jolene K.
family-names: Diedrich
orcid: "https://orcid.org/0000-0001-6489-4558"
affiliation: >-
Multi-Omics Core, The Scripps Research Institute, La Jolla, CA, USA
- given-names: John R.
name-suffix: III
family-names: Yates
orcid: "https://orcid.org/0000-0001-5267-1672"
affiliation: >-
Department of Chemical Physiology, The Scripps Research Institute,
La Jolla, CA, USA
repository-code: "https://github.com/pgarrett-scripps/dnoise"
url: "https://github.com/pgarrett-scripps/dnoise"
license: MIT
version: 0.1.0
date-released: "2026-08-14"
keywords:
- mass spectrometry
- proteomics
- timsTOF
- ion mobility
- denoising
- PASEF
- Bruker