Recently, I have submitted a manuscript for publication consideration into a journal (impact factor: 2). However, I realized that in the final PDF proof the cover letter is missing.

I think I have forgotten to include it.

Does this mean that the article would be rejected or will not be processed?

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    I don't know what discipline you're in; in my discipline, cover letters are completely pro forma, and I can't remember the last time I've read one. – Greg Martin May 25 at 2:26
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    Can't the cover letter be sent now, as you realized it was forgotten, as soon as possible? Why wait with it? – vsz May 25 at 4:19
  • Not sure about this case but the answers give you some possibilities. I just wanted to say something a bit OT. For well reputed journal a missing cover letter should imply no publication. Unless the work is so important and the person who first get it recognize that. In practice: the cover letter for Science or Nature is likely more important than the paper itself. – Alchimista May 25 at 11:18
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    Just send the cover letter now and apologize. – einpoklum May 25 at 12:58
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    You said, "I realized that in the final PDF proof the cover letter is missing". Are you absolutely certain that you forgot to submit the cover letter? Cover letters are not part of the PDF proof in the journal systems that I submit to. – Tripartio May 25 at 16:47

It is doubtful that they would reject it out of hand, but possible they won't process it as an incomplete submission. If the submission was through an online system, see if you can update your submission. You might also contact the editor directly and ask for advice, providing you can get contact information.

But, failing that, I suspect that it will be noted and you might be contacted.

If it is rejected (desk rejected), it would probably be done quickly and then you can take further action. You might be told why it was rejected and you might then be able to resubmit.

I suspect that such things happen frequently enough that the journal has procedures for dealing with it. You may learn something quite soon, perhaps directly and perhaps via the submission system itself.

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It is very unlikely for the paper to be rejected solely for the reason of the missing cover letter.

It is highly likely that you are going to be contacted (using an automated system or personal email) about an incomplete submission or the submission process itself will continue without the cover letter at all.

I would say, missing a cover letter might have an impact on the following:

  1. The potential delay between the journal realizing that the submission is incomplete, communicating that to you, and you resubmitting.

  2. The cover letter can help to assign the associate editor/track editor and, to some extent, select the reviewers. If the cover letter is not present in the submission, it might either take slightly longer or lead to some time/choice inefficiencies that could potentially be avoided.

  3. Sometimes, the cover letter contains substantial necessary information. Say, there was a previous submission to this or another journal some time ago, and you want to inform the editor about that and point out some crucial details that are new in this submission. Or explain why the presence of additional/supplementary materials for your paper is necessary for the review.

    In that case, leaving out the cover letter simply does not help to build your case in the best possible way.

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