1. CHECKING YOUR MANUSCRIPT
Before submitting your manuscript, review the instructions to authors from the journal. If the journal provides a manuscript-submission checklist, remember to use it. Make sure you have followed all instructions. If a manuscript deviates substantially from what is required, it may be returned for correction of the problems before it undergoes review.
Unless the journal (or the style manual that it says to use) instructs otherwise, follow these guidelines: 
Grammar-checking and spell-checking functions can help but should not be relied on too heavily. Grammar checkers associated with word-processing programs can alert you to possible problems in grammar and style. But given their limitations, you should accept their suggestions only if you confirm that they are correct. Almost all spell-checkers provide for the creation of custom dictionaries—for example, for scientific terms and unusual words; also, some specialized spell-checkers are commercially available. Spell-checkers recognize definite misspellings but not those typographical errors that result in the wrong word (for example, as occurs embarrassingly often, “pubic” instead of “public”). Thus, proofreading still is necessary, to make sure the correct word has appeared and to detect errors such as missing words. In addition to proofreading the manuscript yourself, try to have someone do so who has not seen the manuscript before and therefore may notice probl ems that you miss. Consider also reading the manuscript aloud, as doing so can aid in noticing difficulties.
2. SUBMITTING YOUR MANUSCRIPT
For most of the history of scientific publication, researchers submitted their papers by mail. Yes, physical mail. Yes, the postal service, not email. In fact, earlier editions of this book advised readers on how to package a manuscript for mailing and what class of mail to use. Today, if a journal asks you to submit a hard copy of your manuscript by post, take a clue: The journal probably still is still stuck in the last century—which presumably is not where you want the output of your new research to be.
Today, journals commonly have online submission systems through which authors must submit their manuscripts. Journals that are small or are not associated with major publishers sometimes request manuscripts simply as email attachments. Over the years, online systems for electronic submission have become relatively easy to use. And conveniently, they can allow authors to track the progress of their papers toward publication. For guidance on how to submit your manuscript, consult the journal’s instructions to authors and look at the journal’s website.
3. THE COVER LETTER
Finally, you should submit a cover letter with the manuscript (or provide equivalent information if an online submission system prompts you to do so). This letter, which is from the corresponding author, provides context for considering your paper. Most basically, it identifies the title of the article, the authors, and the journal to which the paper is being submitted. It may also identify the type of submission (for example, scientific paper or review article) and, if applicable, indicate the intended subject-matter section of the journal. Commonly, the letter must attest that the work is original and that the manuscript is not being considered by other journals. (Whereas one may apply to multiple graduate schools for admission and accept the best offer, standard practice is to submit a paper to one journal at a time. If the paper is not accepted, it can then be submitted to another journal.)
The letter also may attest that all the listed authors qualify to be listed and that no one meeting the criteria for authors was excluded. In addition, it may indicate whether the authors have conflicts of interest and, if so, what these conflicts are. If some content of the paper has appeared previously, for example in a conference abstract, the cover letter typically should state so. The letter also may do other items, such as mention a photograph or other image in the paper that may be well suited to appear on the cover of the journal.
Sometimes cover letters also suggest potential peer reviewers of the paper— or identify individuals whom the authors do not want as peer reviewers. Suggested reviewers should be scientists who can review the paper knowledgeably and without bias. They should not be people with conflicts of interest (for example, colleagues at the authors’ institution or mentors, close friends, or family members of the authors). They can, however—as may be inevitable in small fields—be people whom the authors have met at conferences or otherwise know casually. Only if serious reason exists to believe that someone will be biased or otherwise unsuitable should a request be made to exclude a potential reviewer. Such a request may be made if, for example, someone in the authors’ research area has had a major professional conflict with an author, is suspected of unscrupulous behavior, or is a spouse—or former spouse—of an author. Suggestions regarding reviewers are simply that: suggestions. The journal may follow them or not; commonly, they may use some reviewers suggested by authors plus some other reviewers. Journals often appreciate, and sometimes request or require, names and contact information of potential reviewers.
Explaining why the paper is believed to merit publication in the journal can also be useful in the cover letter. Doing so may be especially helpful if the relevance of the subject matter to the journal or the novelty or value of the research may not be immediately apparent. It also may be especially valuable if the journal is of broad scope, in which case the editor who first sees the paper might not be very familiar with the research topic and so might not readily recognize the importance of the contribution.
Some journals’ instructions to authors include guidance on what to include in the cover letter. If so, of course proceed accordingly.
4. SAMPLE COVER LETTER
Dear Dr._________ :
Accompanying this letter is a manuscript by Mary Q. Smith and Adam B. Appiah titled “Fatty Acid Metabolism in Cedecia neteri” which is being submitted for possible publication in the Physiology and Metabolism section of the Journal of Bacteriology.
This manuscript is new, is not being considered elsewhere, and reports new findings that extend results we reported earlier in the Journal of
Biological Chemistry (284:112-117, 2014). An abstract of this manuscript was presented earlier (Abstr. Annu. Meet. Am. Soc. Microbiol., p. 406, 2015).
Mary Q. Smith
The above is a model of a brief, simple cover letter. A more extensive example appears at journals . lww . com / greenjournal / Documents / SampleCoverLetter . pdf. You may find this letter, which introduces the (fictional) paper “Primary Cesarean Delivery Among Pandas,” both instructive and amusing.
5. ELECTRONIC COVER LETTERS
If you are submitting your manuscript electronically, the manuscript- submission website may supply a mechanism for providing your cover letter. Alternatively, it may prompt you for the information the journal wants to receive, thus automatically generating a cover letter or the equivalent. This electronic option saves you the trouble of composing a letter and helps ensure that the journal receives the information it requires.
6. CONFIRMATION OF RECEIPT
Most journals send out an “acknowledgment of receipt” by email or other means when the manuscript is received or have a mechanism by which authors check the journal website to see whether submission is complete. Ifyou do not receive acknowledgment within 2 weeks (or less for electronically submitted manuscripts), call or write to the editorial office to verify that your manuscript was indeed received. We know of one author whose manuscript was lost in transit, and not until 9 months later was the problem brought to light by his meek inquiry as to whether the reviewers had reached a decision about his manuscript. Do be sure that your manuscript was received.
Source: Gastel Barbara, Day Robert A. (2016), How to Write and Publish a Scientific Paper, Greenwood; 8th edition.