Author Overview

Journal of Proteomics and Genomics Research publishes rigorous research across proteomics, genomics, and systems biology. Authors should ensure their manuscripts are methodologically robust, clearly written, and aligned with JPGR scope.

Follow these guidelines to streamline review and improve your manuscript readiness.

Article Types

• Original research articles
• Systematic reviews and meta analysis
• Method and technology reports
• Short communications
• Data resources with reuse guidance
• Perspectives or commentaries by invitation

Manuscript Structure

• Title page with author affiliations and corresponding author contact
• Structured abstract with objectives, methods, results, and conclusions
• Introduction describing the research question and context
• Methods with experimental design, datasets, and analytical steps
• Results with clear figures, tables, and statistical reporting
• Discussion highlighting biological meaning and limitations
• Data availability, ethics, and funding statements
• References in Vancouver style

Title Page and Abstract

Include a concise title, running title, author names, affiliations, and contact information for the corresponding author. Provide three to six keywords using proteomics and genomics terminology for discovery.

Structured abstracts should summarize objectives, methods, results, and conclusions. Mention data repositories and platforms when relevant.

Data and Methods Transparency

JPGR requires transparent methods and data availability. Provide repository accession numbers and describe analytical pipelines in detail so results are reproducible.

Include software versions, parameter settings, and quality control criteria for proteomics or sequencing workflows.

• Proteomics data: raw spectra, search parameters, and FDR thresholds
• Genomics data: FASTQ or VCF files, reference genome, and filtering criteria
• Multi-omics: integration methods and normalization strategies
• Code and workflow: scripts, containers, or notebooks when possible

Data Availability Statement

Every submission must include a data availability statement describing where data are stored, how to access them, and any restrictions. Provide accession numbers and DOIs whenever possible.

If data are under embargo or controlled access, explain the reason and describe how qualified researchers can request access.

Repository Guidance

Use recognized repositories for long term preservation and reuse. Provide clear metadata and sample information to support discovery and validation.

• Proteomics: PRIDE, ProteomeXchange, MassIVE
• Genomics: GEO, SRA, ENA
• General data: Zenodo, Figshare, Dryad

Formatting and File Preparation

• Use clear section headings and consistent numbering
• Ensure tables are editable and not embedded images
• Name files clearly (e.g., MainManuscript, Figure1, Table2)
• Provide figure files separately in high resolution format
• Confirm all abbreviations are defined on first use
• Check that units and symbols follow SI conventions

Authorship and Contributions

List authors who made substantive contributions to the work and confirm that all authors approve the final submission. Contribution statements improve transparency and protect the integrity of the record.

Any changes to the author list after submission must be approved by all authors and reviewed by the editorial office.

• Describe each author contribution clearly
• Identify the guarantor responsible for data integrity
• Disclose medical writers or editorial assistance
• Confirm that all authors meet authorship criteria

Ethics and Consent

Human studies require ethics approval and informed consent. Animal studies must follow institutional welfare guidelines. Clinical trials should include registration identifiers.

• Include ethics committee approvals
• Disclose conflicts of interest and funding sources
• Describe consent procedures for human participants

Conflicts of Interest and Funding

Declare all financial or non financial conflicts of interest. Provide funding sources and grant identifiers to support transparency and compliance.

Figures, Tables, and Supplementary Files

• Provide high resolution figures with clear legends
• Ensure tables are editable and include units
• Cite all figures and tables in the text
• Include supplementary data files with descriptions

Image Integrity

Images must accurately represent the original data. Avoid excessive manipulation and disclose any adjustments applied to images or spectra.

If composite images are used, clearly label boundaries and describe the composition in the figure legend.

Supplementary Materials

Supplementary files should include protocols, extended methods, and large datasets that support the main results. Provide clear titles and descriptions so readers can interpret the materials quickly.

Reporting Standards

• CONSORT for randomized trials
• STROBE for observational studies
• PRISMA for systematic reviews
• CARE for case reports when applicable

Clinical Trial Registration

Clinical trials should include a registration identifier and describe protocol adherence. If a protocol was amended after registration, explain the changes and timing in the methods section.

Statistical Reporting

• Describe sample size calculations and power where relevant
• Report confidence intervals alongside p values
• Explain handling of missing data and outliers
• Specify statistical software and version

Preprints and Prior Dissemination

Preprints are allowed when disclosed in the cover letter and cited in the manuscript. Prior conference presentations should also be noted for transparency.

Cover Letter and Declarations

• Explain scope fit and clinical relevance
• Summarize the manuscript contribution and novelty
• List suggested reviewers with affiliations and emails
• Disclose related submissions or preprints
• Confirm funding and conflicts of interest

Submission Steps

Submit through ManuscriptZone and provide all required files and declarations. A complete submission helps reduce delays and improves review efficiency.

• Register or log in at https://oap.manuscriptzone.net
• Enter title, abstract, keywords, and author details
• Upload manuscript, figures, and supplementary files
• Complete ethics, funding, and conflict disclosures
• Submit and track your manuscript in the dashboard

Peer Review and Decision

JPGR uses single blind peer review. Reviewers evaluate methodological rigor, data quality, and relevance to proteomics or genomics. Editors issue decisions based on scientific merit.

Authors should respond to reviewer comments point by point and highlight revisions clearly.

Revision Guidance

Address reviewer comments in a structured response letter and highlight changes in the manuscript. Clear responses help accelerate decisions and improve review efficiency.

Revision Checklist

• Point by point response to reviewer comments
• Revised manuscript with highlighted changes
• Updated data availability statement if needed
• Revised figures, tables, or supplementary files

After Acceptance

Accepted manuscripts proceed to production for copyediting, proof review, and DOI registration. APCs are invoiced after acceptance and payment within 48 hours helps avoid delays.

Authors should verify metadata, affiliations, and funding details during proof review to support accurate indexing.

Proof Review Tips

• Verify author names, affiliations, and funding statements
• Check tables, figures, and captions for accuracy
• Confirm that references and DOI links are complete
• Ensure supplementary files are final and referenced

Indexing and Metadata Readiness

Accurate metadata improves discoverability. Confirm author details, keywords, and funding statements during proof review so indexing services can capture your article correctly.

Reliable metadata also supports funder reporting and institutional dashboards.

APC and Waivers

The standard APC is $2100 and applies after acceptance. Affordable APC waivers are available for eligible authors. Membership options may reduce APCs for active contributors.

Post Publication Updates

If errors are identified after publication, contact the editorial office promptly. JPGR supports transparent corrections that maintain the integrity of the scientific record.

Data Citation and Reuse

When referencing datasets, include DOIs or accession numbers in the reference list. Clear data citation supports credit for data generation and improves dataset tracking across platforms.

If you reuse external datasets, cite the original source and describe how the data were integrated into the analysis.

Consistent dataset citation improves transparency and supports reproducibility across studies.

Post Publication Visibility

After publication, share your article using the DOI link to support discoverability. Consistent metadata and repository links improve indexing and citation tracking.

Language and Formatting Support

Clear writing improves review efficiency and reader comprehension. If you need language editing support, contact the editorial office before submission.

Early support helps avoid delays during peer review.

Author Checklist

• Scope fit confirmed for proteomics or genomics
• Methods and data availability statements complete
• Repository accession numbers provided
• Ethics approvals and consent documented
• Figures, tables, and supplementary files prepared
• Cover letter prepared with scope fit summary

JPGR Commitment

JPGR is committed to rigorous, transparent publishing in proteomics and genomics. We emphasize reproducible methods, complete data statements, and ethical compliance across all article types.

The editorial office supports authors, editors, and reviewers with clear guidance and responsive communication. For questions about scope or workflow, contact [email protected].

We encourage continuous improvement in reporting practices and share updates that help the community maintain high standards in molecular publishing.