In recent editorials, we have discussed how we select papers for publication in Nature Chemical Biology (Nat. Chem. Biol. 4, 715, 2008) and looked forward to some of the new content and features that are appearing in the journal in 2009 (Nat. Chem. Biol. 5, 1, 2009). This month, we look back at the first steps toward publication and answer some common questions about our manuscript submission processes.

Do you actually read cover letters? Yes. Your cover letter is the first thing we read, and so it is an ideal place to present your manuscript to the editorial team. Effective cover letters are concise and clear. Because the editors will read your paper, there is no need to reiterate the technical details of your manuscript. Instead, in a more conversational way, you should highlight the motivation for your study, frame your work in the context of current knowledge in the field and briefly summarize the key scientific advances and conclusions reported in your manuscript. Summary statements should focus on the immediate importance and utility of your work to the chemical biology community rather than emphasizing more distant objectives. Finally, cover letters are the appropriate place to recommend potential reviewers and request that we exclude certain individuals as referees.

Should I submit a Brief Communication or an Article? You should choose the article type that best reflects the scope of your study at the time of submission (http://www.nature.com/nchembio/authors/article_types). Independent of which article type you choose, you should ensure that the submitted manuscript and its accompanying Supplementary Information contain all of the information and data necessary for editors and referees to evaluate the manuscript. For example, experimental procedures and primary data (such as chemical characterization and crystallographic data) must be available for review. You should also make certain that copies of any related manuscripts that are under consideration elsewhere are included as Supplementary Information. Please keep in mind that manuscripts evolve as they undergo peer review and revision, and so the final decision about whether the manuscript will be published as a Brief Communication or an Article will be made later when a paper moves toward acceptance.

What do I need to submit? The team seeks to make the submission process for new manuscripts as straightforward as possible. All that is required at our online manuscript tracking system (http://mts-nchemb.nature.com) are three manuscript files: (1) your cover letter, (2) a single file that includes the manuscript text along with your display items (schemes, figures and tables) and (3) a file containing your Supplementary Information. If your paper is eventually accepted, we will provide you with further instructions on how to upload production-quality files.

Must my manuscript be perfectly formatted? Ideally, yes, but more importantly, your manuscript should be well organized and clearly written. Though we have established manuscript guidelines for authors (http://www.nature.com/nchembio/authors/submit/), we realize that formatting a manuscript to fit the particular style of the journal can be unnecessarily time intensive at initial submission, particularly since it may not be considered further for external review. Because manuscripts can undergo significant revisions on their way to publication, we generally feel that detailed manuscript formatting is most appropriately handled as the paper approaches acceptance. However, we encourage authors to consult our Guide to Authors as they prepare manuscripts to ensure that they include materials that are vital to the editorial assessment and peer review processes.

Are presubmission inquiries useful? Sometimes. Presubmission inquiries, an informal way for scientists to gauge editorial interest in a potential manuscript, are most useful in two cases. First, if you are unsure whether the paper falls within the scope of the journal, presubmission inquiries offer a quick way for you to get some editorial feedback. Second, if you are in the early stages of preparing a manuscript, presubmission inquiries provide an opportunity to discuss what we might be looking for in a particular area. The most productive presubmission inquiries contain a well-written abstract as well as the general information that you would place in a cover letter: the main objectives, key advances and immediate implications of the study (http://www.nature.com/nchembio/authors/ed_process). However, in most other circumstances, and particularly if you have already written the paper, we recommend that you bypass the presubmission inquiry step and submit the full manuscript. In general, we are best able to make informed decisions—and also provide appropriate feedback and save time for our authors—when we have the complete manuscript in hand during the assessment process.

How are papers assigned to editors? New manuscripts are assigned to a primary editor based on the principal scientific area of the paper. The primary editor, who will be your contact at the journal during all stages of manuscript evaluation, has developed expertise in handling manuscripts in a cross-section of chemical biology research areas. You can read the biographies of each editor and view the scientific areas that each editor handles at the journal by visiting our 'About the editors' section of our web site (http://www.nature.com/nchembio/about/about_eds/index.html). Because of the breadth of chemical biology research, our list of editorial areas is not exhaustive. However, if you have any questions about which editor handles papers in your area, please contact us at chembio@boston.nature.com.

We encourage potential authors to discuss their developing manuscripts with us, in confidence, prior to submission. Presubmission inquiries using our online system offer one way, but over the past four years, we have found that more informal discussions (via e-mail, by phone or at conferences) provide another alternative for authors to gauge our interest and receive feedback on a potential manuscript. In turn, these conversations are an opportunity for us to keep apprised of your most exciting science, to communicate our editorial criteria and to offer suggestions that we hope will lead to more significant manuscripts for the chemical biology community.