Ethics

Ethics & Compliance Reviewer

SCORE: 5 CONFIDENCE: 5

Summary

This manuscript presents no ethics or compliance concerns. The work is a purely computational analysis of publicly deposited, commercially available multi-species proteomic standards with no human subjects, animal research, clinical applications, or restricted data involved. Funding sources are disclosed and competing interests are explicitly declared as none. The work is in scope and compliant.

Compliance checklist

Human subjects or identifiable data: Not applicable. The benchmark dataset (PXD070049) is a commercial three-species digest standard (human/yeast/E. coli mixture) with no human biological samples, no patient data, and no identifiable information.

Clinical trials: Not applicable. No clinical trial data or patient outcomes are involved.

Animal research: Not applicable. The manuscript explicitly states "involved no human subjects or animal procedures."

Dual-use or biosafety risk: Not applicable. The work is a data-reduction algorithm for mass spectrometry; no pathogenic organisms, gain-of-function research, or dual-use materials are involved.

Restricted-consent data: Not applicable. The benchmark data are publicly available with no access restrictions or consent limitations.

Funding disclosure: Present and adequate. The manuscript names specific NIH grants (R01 HL165168, R01 AG077046, R01 MH100175, R01 AG075862, R01 MH132570, U01 AG088679) and acknowledges the Skaggs Graduate School.

Competing interests: Declared as none: "The authors declare no competing financial interest."

Data and code availability: Fully compliant. Raw data are public (PRIDE PXD070049), dnoise is open-source (MIT licensed, github.com/pgarrett-scripps/dnoise, crates.io, Zenodo doi.org/10.5281/zenodo.21959649), and all parameters and configurations are provided in the manuscript and Supporting Information.

No ethics or compliance issues identified.