Q: I would like to ask you how to protest against the rejection of a paper.

Thanks for your very detailed query. We absolutely understand the reason for writing such a long query. A rejection decision after 5½ months since submission, a major revision, a minor revision after a major revision, and comments by five reviewers can be very frustrating and even agonizing. Before we continue though, note that for reasons of brevity, we have removed the editor’s mail to you, and also because you have already shared in your query the basic content of that mail.

So, you actually have two main queries. Let’s take them one by one.

Do situations like this – multiple reviewers and a final decision based on a new reviewer – happen often?

To get straight to it, while this is not very common, it does happen. This typically happens when the Associate Editor (AE), the Editor-in-Chief (EIC), or both are not entirely sure of some aspects of the paper after the peer review (or even a revision), and especially a key aspect. So, they refer the paper to further reviewers. Some papers are even known to have been referred to eight or nine reviewers, and some papers have received rejection decisions three years after submission! That may possibly help you feel just a bit better. :-)

Anyway, while we are not entirely familiar with your field of study and do not have access to your paper, based on Reviewer 5’s comment (and their fairly balanced tone), we believe they may have a point that you may wish to consider. Reviewer 5 is probably a fairly experienced researcher in the field, which is why the AE/EIC must have finally referred the paper to them. Based on their comment, you may indeed wish to pull back a bit and see whether your paper does indeed add a great amount of novelty to the field of proteomics or not. We understand this may not be what you wish to hear now, but perhaps, you could take a bit of a break and then look at your study with new eyes. Perhaps then, you’ll also be able to work on it in a more holistic way.

Should you write a rebuttal/protest letter, and if so, how should you write it?

Firstly, please note that this would not be a rebuttal letter, but a protest letter. A rebuttal letter is written during a (major) revision, about changes you are not making and the reasons for (not) doing so.

Coming to your query, while you could go ahead and write a protest mail, note that it may not achieve much. At the most, you could talk about how it was a very long process that eventually resulted in nothing and that it was also frustrating to have multiple reviewers provide commentary at various points. However, again, we believe the journal would have included reviewers at later stages only for the good of research: they are no doubt keen to make sure only the soundest research is published, and presently, they believe, your paper may not be entirely at that level. However, this mail is not likely to go very far at the journal, or even be opened. To know more, you may go through this article by an AE on how they arrive at a decision on a paper after peer review and revisions: How a journal editor reaches a decision on a manuscript after peer review

So, we would recommend saving your energy, and rather, diverting it to your paper. As we just said, it would help to take a short break from the paper, and then come back to it with a fresh perspective.

Incidentally, you haven’t said whether you have had someone else look at the paper – a colleague or a supervisor. In case you haven’t, doing so now may help. They may help you with some critical elements that you need to add to it.

Once you have managed to make your paper more solid, you could submit it to some other journal. This time, as a pre-emptive measure, to save you time and effort, you may write a presubmission inquiry to other journals providing both an outline of your research (to see if it interests them) and a short history of the submission to the previous journal (so that there are no issues with submitting to another journal).

Now, you have already made one major revision to your paper. So, the present version of the paper is probably much better than what you started with. If you make the remaining key change(s), those may help take your paper toward publication. Additionally, while the experience was frustrating, it helped you gain valuable knowledge, both about the necessity of including multiple reviewers and possibly about how (some) international journals work.

Having said all that, we also sense that while you are quite despondent about the rejection, you are not absolutely dejected. So, that’s a great thing – and kudos for that!

We hope that addresses your questions and thoughts. Before we end though, we would like to talk about just a couple of things. We wanted to keep this at the end, to both address your query to the best way possible and also to not be too ‘pushy’ about the ways some of our services could help you avoid/minimize rejection.

Firstly, as you may know, we have a variety of review and editing services. Apart from editing your paper for an international audience, they also review the science to ensure the research is novel and interesting, thus helping to increase the chances of acceptance. You may learn more about our range of review and editing services here: Editage Editing Services

Additionally, we would also like to tell you about R Pubsure, a new platform that aims to help you minimize rejection. It does this in two ways. Firstly, its AI-powered check helps improve your manuscript, to make it submission-ready. Then, you get the chance to showcase your ready manuscript to multiple journal editors, one of whom may consider it for publishing with their journal (if of course they find it interesting and relevant). Even better, a part of R Pubsure’s services are free. If interested, you may learn more here: R Pubsure

Hope all this helps. Again, we would suggest taking a bit of a breather before coming back and working on your paper again, this time hopefully, with more positive results! All the best!