About APB

Introduction to APB

The Annals of Proteomics and Bioinformatics (APB) is a peer-reviewed, open‐access academic journal dedicated to advancing research in the highly dynamic fields of proteomics, bioinformatics and integrative omics sciences. According to its previous site description, APB “publishes rigorously peer reviewed manuscripts encompassing versatile aspects of proteomics and bioinformatics science.” :contentReference[oaicite:0]{index=0}

APB serves as a global platform where authors, researchers and practitioners can share novel findings, methodological advances, and integrative analytics in the study of proteins and complex biological data. With the accelerating pace of high‐throughput proteomics technologies and computational bioinformatics pipelines, APB is committed to facilitating the dissemination of high-quality, reproducible and accessible research that addresses challenges across organisms, systems, disease and environmental contexts.

Why Choose APB?

• Rigorous peer review and editorial oversight – every manuscript undergoes structured review by experienced editors and external reviewers to ensure scientific integrity, novelty and relevance.
• Open access and global reach – APB’s content is freely available online to readers worldwide, accelerating dissemination and ensuring maximum visibility for authors.
• Interdisciplinary focus – spanning proteomics, bioinformatics, systems biology, network proteomics, post-translational modifications, protein‐drug interactions, biomarker discovery and more.
• Commitment to best practices – APB aligns with the principles of the Committee on Publication Ethics (COPE), International Committee of Medical Journal Editors (ICMJE), and World Association of Medical Editors (WAME) regarding publication ethics, access, transparency and data integrity.

Whether your work focuses on experimental proteomics, mass-spectrometry analytics, computational protein networks, or translational bioinformatics, APB offers a venue tailored for high‐impact dissemination and scholarly recognition.

Aims and Scope Overview

While a dedicated “Aims & Scope” page will follow elsewhere, here is a summary of APB’s scope of interest and mission:

The objective is to publish original research articles, reviews, commentaries and technical reports that significantly advance our understanding of proteome-driven biology and informatics workflows, and that are accessible to a wide range of readers—from bench scientists to computational biologists.

Ethos and Editorial Mission

APB is committed to fostering transparency, scientific rigour, and inclusivity. Its editorial mission emphasises:

• Promoting reproducible research and transparent data workflows.
• Encouraging the submission of negative results, method validation and replication studies, provided they meet high quality standards.
• Ensuring diversity and fairness in peer review and editorial decision-making, independent of author geography or institution.
• Recognising the importance of data availability, code sharing, and alignment with the FAIR (Findable, Accessible, Interoperable, Reusable) principles.

For example, authors are encouraged to deposit raw proteomics data in established repositories, submit metadata in standard formats, provide code for bioinformatics pipelines, and include transparent descriptions of materials and methods. Such practices help safeguard research integrity and reproducibility across the field.

The editorial board and reviewers adhere to high ethical standards, including declarations of conflict of interest, consent for human/animal studies where appropriate, and compliance with data protection regulations such as the General Data Protection Regulation (GDPR) for EU data submissions.

Audience and Community Engagement

The readership of APB includes academic researchers, industry scientists, clinical proteomics specialists, bioinformaticians, software developers, and data-science professionals engaged in omics workflows. To support community integration, the journal provides:

• Regular calls for special issues on emerging themes (e.g., spatial proteomics, AI-driven proteome discovery). :contentReference[oaicite:6]{index=6}
• Invited commentaries and thematic editorials to stimulate debate across sub-disciplines.
• Open peer discussion forums (where appropriate) to encourage methodological transparency and cross-discipline interaction.

Authors are welcome to engage the journal in outreach via conference tie-ins, webinars, and social media, supporting a wider impact of their published work beyond traditional citations.

History & Evolution

The old website states that APB has undergone several iterations to keep pace with evolving publishing standards and technological innovations in the proteomics/bioinformatics landscape. According to the archived content, APB began as an initiative publishing manuscripts aimed at professionals in sports medicine and therapy (though listing proteomics and bioinformatics) and later evolved to a full-blown multidisciplinary journal focusing on proteome and data sciences. :contentReference[oaicite:7]{index=7}

Over time, the journal has adopted:

• Assignment of Digital Object Identifiers (DOIs) to all published articles.
• Online publishing with continuous article releases rather than fixed issues.
• Indexing in major databases and implementation of archiving policies (to be detailed in other menu items).

This legacy indicates the journal’s responsiveness to change and commitment to maintaining relevance, transparency and integrity in scholarly publishing.

How to Get Involved

Whether you are an author, reviewer or reader, APB offers multiple avenues to participate:

• Submit your manuscript: Visit our “Submission Guidelines” section and follow the step-by-step instructions, including manuscript preparation, ethical compliance, and open access workflow.
• Join as a reviewer or editor: Experts in proteomics, bioinformatics, data science and related fields are invited to serve as peer reviewers or editorial board members. Guidelines and roles are detailed in the Reviewer Guidelines and Editor’s Guidelines sections.
• Engage with the community: Suggest special-issue themes, engage in research commentary, and propose collaborations or guest-editor roles to shape the journal’s future direction.

We value your contribution to advancing the frontiers of proteomics and bioinformatics, and look forward to working with you to deliver rigorous, impactful and open‐access scholarship.

Key Facts at a Glance

For further details of indexing, archiving, ethical policies, author charges and waiver information, please explore the relevant menu items in the journal navigation.

Examples of Published Content

To illustrate the breadth of APB’s published work, the journal typically includes:

• A computational workflow for shotgun proteomics quantification in human cancer cell lines.
• A network‐based bioinformatics analysis of microbial metaproteomes under environmental stress conditions.
• A methodological study validating a novel mass‐spectrometry platform for phosphoproteome profiling in plant systems.
• A translational paper on bioinformatics biomarker discovery from proteome data repositories with downstream clinical validation.

These represent the variety of content that authors may submit and that reviewers and readers expect when considering the journal’s contributions.

Frequently Asked Questions (FAQ)

What types of manuscripts do you accept?

APB accepts original research articles, state-of-the-art reviews, short communications, technical notes, and special-issue contributions. Manuscripts must align with the journal’s scope and demonstrate methodological rigor, clear data presentation, reproducibility and transparency.

Is open access mandatory?

Yes — all articles published in APB are open access under the selected Creative Commons licence (see “Copyright & Licensing” section for details). This ensures free permanent access for readers worldwide.

What is the peer-review process like?

Manuscripts are first assessed by the editorial office for scope and basic compliance. Then each paper undergoes at least two independent reviews (blind or double-blind, depending on article type) by experts. The editorial team makes the final decision—reviews may include revision rounds to address reviewer feedback.

How long does publication take?

The target time from submission to a first decision is often around 4–6 weeks (depending on reviewer availability and revision complexity). After acceptance, articles are published online promptly in “article in press” format and subsequently assigned a DOI and integrated into the archive.

Do you require data deposition?

Yes — authors are strongly encouraged (and in many cases required) to deposit raw and processed proteomics data into an appropriate public repository (e.g., PRIDE, ProteomeXchange) and to provide detailed data-availability statements. Bioinformatics code and pipelines should be shared where possible.