We recently submitted a paper to a fancy journal, and one thing that impressed me was how the journal made sure you carefully structure the cover letter to help the editorial team make the best possible decisions. When I first got started in this business, when submitting a paper I would basically just slap the cover letter on as an afterthought before hitting submit on a journal’s website. Something along the lines of:
“Dear Editor, Check out our new paper. Hope you like it, let us know if ya’ wanna publish it. K’thx."
And while that does convey the basics, over the years my letter has become more refined. Because really you want the letter not just to convey the title of your paper, but you want the editor to know what question you are addressing, why your findings are cool, and who would care to know about it. In this way they can quickly grasp the merits of your brilliant paper, begin to think about appropriate reviewers to send it off too, and more important to get excited about it. In some of the fancier journals this letter can mean whether your paper goes off for review or gets a desk reject.
So what should a cover letter contain? I think the best guidance you can get on this matter is from our friends over on eLife:
• How will your work make others in the field think differently and move the field forward?
• How does your work relate to the current literature on the topic?
• Who do you consider to be the most relevant audience for this work?
• Have you made clear in the letter what the work has and has not achieved?
And the key here is not expound for pages upon pages on this. Just a couple of concise sentences about each point will more than do. Don’t go nuts, don’t be pompous and overpraise yourself, don't write fucking War and Peace, just be helpful and guide the editor to the key points. In fact, it is always good to keep those points in mind while writing your manuscript and developing its narrative arc. It’s no guarantee your paper will be accepted or even reviewed, but at least it’ll improve your chances.