Although usually unsuccessful, a strong appeal letter can be an important tool for authors.

Rejection is never easy. You’ve put long weeks, months, maybe even years of work into a project that you think is perfect to publish in Nature Methods, so your feelings of disappointment, anger, frustration or self-doubt are completely understandable. Your first instinct might be to hit “reply” and send an angry email to the editor. But your best bet is to take some time to cool off, then move on and submit the paper elsewhere. If you are convinced, however, that a serious error has been made or that you can fully address the specific criticisms raised by the editors or by referees, then you may send a constructive appeal letter to the editor.

Nature Methods has different types of rejections, with or without peer review. There are outright rejections (which represent the vast majority), and then there are those rejections where the editor indicates that a manuscript could be reconsidered if the authors can address specific shortcomings. The editorial decision process is of course a subjective and imperfect one. Appeals, however, are usually unsuccessful. Those that are successful are those where the authors make a strong case for reconsideration, typically by proposing to add new data that will strengthen the application or demonstrate how the work is a strong advance over existing methods.

Be aware that appeals are necessarily given a lower priority than manuscripts still under consideration. Decisions on appeals can therefore take a considerable amount of time and the majority of appeals are turned down. Decisions are usually only reversed if the editors can be convinced that the decision to reject was a serious mistake, if the authors can add a substantial amount of data to address certain shortcomings, or if a negative referee is found to have made serious errors or show specific evidence of bias.

An appeal letter is not the same as a rebuttal letter to referees (see the related post, “How to write a rebuttal letter”). An appeal letter is only read by the editors, so sensitive information not meant to be seen by the referees can be included.

Here are some things that do and don’t work when writing an appeal letter.

The DOs:

• Do consider whether you have a good case for appealing that is worth investing time in the process. By editorial policy, appeals must take second place to new submissions. This means that it can take as long as several weeks for the editors to discuss an appeal, possibly get input from referees, and reach a decision. Unless your case is very strong, it will save you precious time by accepting the editorial decision and submitting the manuscript elsewhere.
• Do clearly explain the reasons why you disagree with the decision to reject. In some successful cases, authors provide new information, not apparent from the original submission, explaining how the method will have a strong impact on a broad audience. Ideally such information would have been included in the cover letter with the original submission (see the post, “How to write a cover letter”), which can help avoid the need for a lengthy appeals process for a manuscript that is otherwise a good candidate for peer review.
• Do explain how you plan to rectify any major shortcomings pointed out by the editor or by the referees. If you are willing to add data to the paper to address the shortcomings, explain what this data is and what it shows. If you have figures or tables prepared, include them with your appeal letter. (However, don’t yet rewrite your manuscript – since most appeals are turned down, this is usually just a waste of your time.) If you have a valid reason for not including such data, explain why not. 
• Do include a separate point-by-point rebuttal letter to referees to assist the editors in reaching a decision (see the post on “How to write a rebuttal letter”). If the editors feel that a rebuttal letter is required to help them reach a decision, and one is not included, they will request one of you.
• Do provide evidence for any accusations of referee bias. Describe in specific terms why you believe a referee is biased or has made technical errors in their review. In our experience, it is extremely rare that ALL of the referees of a paper would be biased or misjudge its impact. Don’t try to guess who the referees were (you will most often be wrong). In cases where one set of negative referee comments is far out of line with others that are generally positive, we often will consult with the positive referees to determine whether the dissenting referees’ concerns are serious and how they should be addressed.

The DON’Ts:

• Don’t do anything in the heat of the moment but take some time to cool down and consider whether you would be better off resubmitting elsewhere.
• Don’t simply reaffirm the importance of the work, write “we think you are making a mistake” or urge us to send a manuscript out for peer review without providing any justification. Appeal letters lacking a good justification will not convince us to change our minds.
• Don’t try to bribe us with promises of high citations. While of course we hope for high citations for each research paper we publish, citation potential is far from being the most important editorial consideration (and it cannot be accurately predicted, anyway). Papers must first meet our standards of methodological novelty and potential community interest and impact.
• Don’t assume that the paper must be of interest to us because we have previously published a similar paper. Editorial standards are constantly evolving, and the methodological novelty may be compromised by our previous publication. Additionally, we strive to publish a variety of novel methods across fields, so we must consider what is currently in our pipeline.
• Don’t bash previous work. As editors, we want to know how a new method addresses certain shortcomings or significantly expands the applicability of a previously published method, but this discussion should be fair and balanced. Don’t simply say “the previous method doesn’t work,” explain why, and ideally provide experimental evidence. Providing a detailed comparison to previous methods in your paper in the first place can help avoid the need for a lengthy appeals process for a manuscript that is otherwise a good candidate for peer review at Nature Methods.
• Don’t expect us to be swayed by your scientific reputation. While it is informative to give some background of your expertise in a field, we make decisions based on the fit of a paper with our journal in terms of scope, novelty and potential impact, not simply because the work comes from a good lab. The fact that you have coauthored papers in high-impact journals will not lead us to reverse our decision.
•  Don’t rely on “celebrity endorsements”. It is good to hear that a leader in the field has read and likes your paper, or that 50 people came to view your poster at a conference. But if we feel that the paper is editorially not a good fit for Nature Methods, this is unlikely to make us change our minds about rejection.
•  Don’t insult the intelligence or competence of the editors or referees. We know that rejections are upsetting and can often seem unfair. But personal attacks and bullying could compromise your success in an otherwise promising appeal situation.
•  Don’t appeal every decision. Remember the old saying, “you’ve got to pick your battles.”

Don’t miss parts 1 and 2 of this series of posts covering cover letters and rebuttal letters. We encourage questions, comments and feedback below. The editors will do their best to answer any questions you have.