There is More to a Journal Submission Than Uploading Your Manuscript

You have invested great time and energy into your research and worked diligently, perhaps with co-authors, to write a well-organized and thoughtful manuscript. At this point, you are ready to submit the completed manuscript to a high-quality journal. But have you considered the additional steps required ahead of submission? 

Beyond the manuscript itself, multiple documents and steps are required at the time of submission. Many authors consider these requirements hastily only at the time of submission, leading to errors or omissions that can delay publication and impact their co-researchers.

These requirements can be intrinsic to the manuscript such as the target journal, format, acknowledgments, and figures. Alternatively, many important requirements are extrinsic to the manuscript such as the cover letter, agreements, statements, choice of editors and reviewers, publication charges, and article promotion. You should consider these important items before journal submission to ensure successful submission and review. 

Check your manuscript for important details

Make sure your acknowledgments are fully inclusive 

The metric for success in science is acknowledgment through publication. The Acknowledgements section is as crucial as the list of authors because it recognizes contributions to your research success. Despite its importance, this section is often written hastily to finish the manuscript. Being unacknowledged can be hurtful not only to individuals but can affect the success and funding of organizations that contributed to your research. 

1. Individuals. This recognition includes students, technicians, informal manuscript reviewers, graphic artists, and others who do not rise to the level of authorship. It is easy to neglect these contributions when hurriedly preparing this section. You should keep in mind that you will rarely be faulted for being too inclusive in your acknowledgments. 
2. Organizations. This recognition should include organizations even if they are service providers in some cases. For example, if a company provides invaluable expertise beyond basic services, it may warrant acknowledgment. Another example is academic core facilities that are fee-based but provide technical expertise and advice akin to collaborators. For many core laboratories, acknowledgments, methods citations, and co-authorships are critical metrics to evaluate their success and funding.
3. Funding sources. It is essential to cite grants supporting laboratories, core facilities, and individuals. Granting agencies typically recognize only publications citing specific grant numbers towards success which can impact future funding opportunities.

It is critical to check for plagiarism and figure errors

Prior to submission, search the manuscript for plagiarism. While often unintentional, journals routinely search for plagiarism, which is grounds for revision or rejection. MS Word add-on tools such as Grammarly can search for text duplicated in the literature. Sophisticated AI tools to identify duplicate or manipulated images, such as Proofig, are available to publishers. So, all authors should carefully examine all figures independently to identify any potential instances of incorrect images or duplications.

Essential steps before you submit the manuscript

Think carefully about the target journal

Although your manuscript format is flexible, contemplate your target journal in advance because of page limits and figure formats. For example, some journals permit extensive text and numerous figures (i.e., Cell), whereas others require limited concise text with fewer but typically more complex figures (i.e., Nature journals). In selecting appropriate journals, remember that some journals permit longer text for articles published exclusively online (i.e., Proceedings of the National Academy of Sciences, USA).

Is your manuscript appropriately formatted for submission?

Authors may write their manuscripts in a generic format that does not conform to a specific journal. For example, authors may prefer to embed citations in the text (i.e., Smith et al., 2010) rather than numbered citations for ease of reference during writing. For many journals, initial submissions do not require a specific format for peer review. However, you should consult the instructions for authors because formatting to assist reviewers, such as line numbers, double-spacing, and word counts for each section may be required.

Is there a final manuscript format?

Upon acceptance, you must convert your manuscript to the proper format for publication. Journals provide formatting instructions or templates to assist you with manuscript writing or conversion. For example, Proceedings of the National Academy of Sciences USA provides a style template. Along with style conversions, you should adapt your headings and figure legends to the proper style. When creating your figures, consider the final published sizes of numbers and letters. Enlarged figures submitted for peer review may contain illegible text when reduced to print proportions. To avoid late-stage edits, you should think ahead and create figures in their final proportions (one or two-column format). Consider submitting your manuscript with figures at the final size to ensure that the results are clear to peer reviewers and other readers.

Understand publication charges before you submit

Don’t be surprised by publication fees. Before submission, be sure you understand all publication charges, including page charges and charges for color figures. If the journal is not open access, there is a fee for this option which permits wider readership and posting to sites such as ResearchGate to promote your research. 

Increase your impact by promoting the article

Before submission, several steps can promote your manuscript in anticipation of acceptance.

1. Make sure your article will be easily searchable by using a descriptive title and as many relevant keywords and phrases as possible.
2. Consider posting your manuscript to a preprint server such as bioRxiv. Confirm this in the author directions of your target journal, but most journals will not consider such postings as previously published work. A preprint posting will promote your research and solicit feedback that can improve your manuscript and anticipate peer reviewer comments.

Information you must submit with your manuscript

Your cover letter is critical to evaluate your submission

This letter communicates to journal editors and peer reviewers why they should consider your manuscript. You may refer to the Abstract section of your manuscript, but the letter should also emphasize the significance of the research and its appropriateness for the journal. Your cover letter should include these elements.

1. A brief background of the research field (a paragraph or less).
2. The major questions or overall hypotheses of the research (several sentences).
3. A brief overview of the findings (no more than two paragraphs). Here you can utilize aspects of your Abstract.
4. The significance of the research scientifically and its impacts on society, if any. For example, a scientific finding could be a new form of gene editing, whereas its impact on society could be a new approach to gene therapies.
5. A statement explaining why the manuscript is within the scope of the journal. If the journal has a readership across disciplines, then emphasize why your manuscript would be interesting to a broad scientific audience rather than to specialists.
6. A concise and compact letter. Editors and reviewers are busy, so verbose cover letters are viewed negatively. A length of one page is optimal, but no more than two pages.

 You should think carefully about editors and reviewers

1. Preferred editors. If permissible, consider which editor will handle your manuscript. Using the example of Proceedings of the National Academy of Sciences again, editors from many fields are available. Submit to an editor who understands the scope of your research and can assign appropriate peer reviewers.
2. Preferred reviewers. Prepare a list of preferred reviewers (up to five) who you feel understand your field of research and can provide an objective peer review. Editors are not required to choose your preferred reviewers but may include one of your choices as well as an independent reviewer.
3. Excluded reviewers. Carefully consider any potential peer reviewers you wish to exclude from reviewing your manuscript. Professional reasons for exclusion may include reviewers who are biased due to competition for discoveries or research funding, among other reasons. 

Be aware that you must complete and upload numerous statements and agreements during submission

Statements and agreements communicate the meaning of your research to editors and assure that authors adhere to publication standards and ethics.

1. Significance statement. Journals may require a statement communicating the scientific and societal significance of the research to editors and non-experts.
2. Competing interest statement. For transparency, state potential conflicts of interest that could affect the objectivity of any author or influence the content of the article. Examples include research funding by a commercial source, direct financial interests by authors such as equity, salary, patent royalties, future employment, or other compensation that affects the perception of objectivity.
3. Licensing agreements. Such agreements grant the journal rights to distribute the content while retaining author copyright for noncommercial reasons such as personal use and education.
4. Ethics statements. Such statements confirm that research involving humans and animals was done in accordance with ethical guidelines and with the approval of appropriate institutional committees.
5. Use of recombinant DNA. This statement confirms that research involving recombinant DNA was done according to established guidelines with the approval of appropriate institutional committees.
6. Data sharing plan. This statement outlines your plan for sharing data such as DNA sequence, mass spec profiles, databases, computer code, and other information necessary for access and independent replication. Journals have specific requirements for posting data.
7. Diversity statement. Some journals have diversity statements indicating how the research supports inclusion and diversity in science. See, for example, Cell.

After submission and peer review

You should be prepared for revisions

Manuscripts are rarely accepted without addressing peer reviewer comments either as text corrections (e.g., misstated or overstated conclusions) or additional experiments (e.g., insufficient experimental proof). For minor corrections (Provisional Acceptance), journals will provide a deadline, typically 30 to 90 days, to complete your revisions. For corrections requiring more experimentation (Rejections with Encouragement to Resubmit), a new submission and peer review will be required. There is no deadline to resubmit, but be prompt because the initial peer reviewers will probably evaluate your manuscript a second time. If you delay significantly, the reviewers may forget the details of your manuscript or be unavailable to review it again. 

Upon acceptance, you should be prepared for page proofs

After revisions following peer review and acceptance, be prepared for page proofs that need to be reviewed and accepted by all authors, then resubmitted in less than one week typically. With multiple authors each required to accept the proofs, you should initiate this immediately to avoid publication delays.

Successful publication requires more than your well-crafted manuscript. Awareness of these additional elements will result in a complete and professional journal submission that contributes to efficient review and, hopefully, acceptance for publication. Good luck!