Ethics

Ethics & Compliance Reviewer

SCORE: 5 CONFIDENCE: 4

Summary

This manuscript describes RIPUP, a streamlined multi-protease workflow for histone post-translational modification (PTM) analysis that reduces sample preparation time to ~3 hours while improving detection of acidic acylations through TMT labeling. The work is methodologically sound, the claims are well-supported by the evidence presented, and the ethical and compliance framework is transparent and complete. No ethics or compliance concerns are identified.

Compliance Assessment

Human subjects and animal research: The manuscript involves two animal studies (rat hippocampal tissue) and one cell culture study (HEK293T). The rat work is explicitly approved by the Scripps Research Institute IACUC (protocol #09-0006) and follows ARRIVE guidelines; this statement is present and adequate. The HEK293T cell line work requires no animal or human subject approval. No identifiable human data are presented.

Funding and competing interests: Funding sources are fully disclosed (NIAAA grants listed with specific numbers: T32 AA007456, AA013498, P60 AA006420, AA017447, AA029841, AA021491). No competing interests are declared; this is appropriate for a methods paper with no commercial product endorsement or financial stake beyond standard institutional affiliation.

Data availability: Raw MS data, annotations, and search results are deposited in ProteomeXchange (PXD073683, PRIDE repository); custom R scripts are available on GitHub. This meets current standards for reproducibility in proteomics.

Dual-use or biosafety risk: None identified. The work is analytical methodology applied to standard cell culture and tissue samples with no pathogenic, synthetic, or dual-use components.

Secondary or restricted-consent data: Not applicable. All samples are de novo extractions from standard sources (HEK293T cells, rat tissue from a controlled breeding colony).

No compliance gaps are present. All required statements are in place with appropriate specificity.