The Annals of Proteomics and Bioinformatics (APB) upholds the highest editorial and ethical standards to ensure integrity, transparency, and fairness throughout the publication process. These editorial policies are designed to maintain scientific rigor, respect authorship rights, and provide equal opportunity for all contributors regardless of institutional or geographic background.

All editorial decisions at APB are independent, unbiased, and grounded in the principles of scholarly merit and ethical conduct as outlined by COPE (Committee on Publication Ethics), ICMJE (International Committee of Medical Journal Editors), and WAME (World Association of Medical Editors).

Editorial Independence

The Editor-in-Chief and Editorial Board operate independently of the publisher to guarantee impartial editorial decisions. Decisions on manuscript acceptance are based solely on scientific quality, originality, relevance, and clarity, without influence from advertising or institutional relationships.

Editors are required to disclose any potential conflicts of interest and recuse themselves from handling manuscripts where such conflicts may exist. Editorial staff are prohibited from exploiting unpublished material for personal gain.

Manuscript Assessment and Peer Review

APB employs a rigorous, double-blind peer-review process. Each submission is initially screened by the editorial office for scope and format compliance before being sent to at least two independent reviewers with subject expertise. Reviewers evaluate the manuscript for originality, scientific validity, methodology, and clarity of presentation.

Editors ensure reviewers provide constructive and respectful feedback.
All communications between editors, reviewers, and authors are confidential.
Revised manuscripts are re-evaluated prior to final decision.

The Editor-in-Chief makes the final publication decision after receiving reviewer recommendations. Authors may appeal editorial decisions by providing detailed justifications, which are reviewed by a senior editor or independent advisor.

Authorship and Contributorship

Authorship should reflect substantial intellectual contributions in line with ICMJE recommendations. Authors must clearly specify individual roles such as conceptualization, data curation, analysis, and manuscript preparation.

All authors must approve the final version before submission.
Changes to authorship after submission require written consent from all co-authors.
Contributors not meeting authorship criteria should be acknowledged appropriately.

Conflict of Interest Disclosure

Authors, reviewers, and editors are required to declare all potential conflicts of interest, whether financial, institutional, or personal. Conflicts must be disclosed at the time of submission or review acceptance. The journal publishes such declarations alongside accepted papers when relevant.

Data Availability and Reproducibility

APB mandates data transparency and encourages authors to deposit raw data, scripts, and code in public repositories to ensure reproducibility. Datasets related to proteomics (e.g., PRIDE, ProteomeXchange) and computational tools (e.g., GitHub, Zenodo) should be cited in the reference list with persistent identifiers.

Studies involving computational pipelines or machine-learning algorithms must include validation datasets or code availability statements for reviewer verification.

Handling of Allegations and Misconduct

Allegations of misconduct, including plagiarism, data fabrication, image manipulation, duplicate publication, or unethical research practices, are handled according to COPE guidelines. Investigations are confidential and impartial. Confirmed misconduct may lead to correction, retraction, or article withdrawal, depending on severity.

Editors maintain the right to contact authors’ institutions or funding bodies if ethical violations are substantiated.

Editorial Board Responsibilities

Uphold the principles of editorial independence and fairness.
Ensure transparent peer review and uphold confidentiality.
Promote diversity and inclusion within the reviewer pool and editorial appointments.
Encourage innovations that enhance the efficiency and integrity of scholarly publishing.

Editorial members may periodically be rotated to ensure inclusion of diverse expertise and perspectives across global proteomics and bioinformatics communities.

Corrections, Retractions, and Updates

If a published article contains errors that affect its scientific validity or integrity, the journal will issue a correction notice or retraction in line with COPE Retraction Guidelines. Minor typographical or metadata errors may be corrected without issuing a separate notice.

Corrigendum: Submitted by authors for minor factual corrections.
Erratum: Issued by the publisher for production-related errors.
Retraction: Applied when data or ethical breaches invalidate the findings.

All corrections and retractions remain permanently linked to the original publication record.

Editorial Decision Transparency

Editors document all decision rationales for internal accountability. Where feasible, anonymized review histories may be shared to improve transparency. The journal also supports optional open-peer review models for special issues or collaborative studies.

Confidentiality and Privacy

Editorial and review communications are confidential. Reviewers must not share or cite unpublished material under review. Personal data collected during submission or review is handled in accordance with the journal’s Privacy Statement and GDPR compliance framework.

Ethical Oversight and Compliance

The editorial team oversees compliance with ethical research requirements for studies involving human participants, animals, or environmental data. Authors must provide ethical approval statements, informed consent declarations, and relevant institutional review board (IRB) approvals.

Human and animal studies must comply with the Declaration of Helsinki or equivalent standards.
Genomic and proteomic data must respect participant confidentiality and consent.

Appeals and Complaints

Authors may appeal editorial decisions by submitting a formal written justification within 30 days. Appeals are independently reviewed by a senior editorial committee or advisory board member uninvolved in the original decision. Complaints regarding editorial conduct are handled transparently and according to COPE’s Code of Conduct for Journal Editors.

Advertising and Sponsorship Policy

APB does not allow commercial advertising that may influence editorial content. Sponsored supplements or thematic issues are subjected to independent editorial oversight, and sponsorship relationships are disclosed to readers to maintain transparency.

Editorial Accountability

The Editor-in-Chief bears overall responsibility for the integrity of the journal’s editorial process. Annual performance reviews assess peer-review timeliness, decision quality, and adherence to best practices. Feedback from authors, reviewers, and readers is used to improve editorial workflows continuously.

Commitment to Diversity and Inclusion

APB values diversity across gender, geography, and discipline. The editorial team seeks balanced representation among editors, reviewers, and contributors to foster equitable participation in global science.

Editorial Policies