After a lot of consideration, it seemed that PNAS was our best shot because our protein is of general interest and our work reaches across more than one discipline. Papers like ours have appeared in PNAS in recent years on less important proteins and without validation of the importance or in vivo relevance of the data. So this is where we submitted 38 days ago.
The reason I decided to write this post is that the review process at PNAS is not like other journals and, based purely on anecdotal evidence (my own experience and that of two other junior PIs), my feeling is that a new PI should not even bother submitting to PNAS unless they have a strong network of NAS members interested in their work, a pre-arranged editor, or perhaps have a Nature-level paper that they want to get out fast.
First the paper goes to an editorial board member for initial review. You have to choose three editorial board members from a list of NAS members that is actually quite limited, and hope that whichever one is assigned is interested in your paper. This person can reject the paper or send it on to an editor (you suggest five NAS members to be possible editors). The editor can also reject the paper, or choose to send it for review.
These two steps are where the problems arise if you are not famous. Both of these editors are NAS members and if you are not famous or one of their buddies, they are not going to give your paper priority in their busy lives.
In case you haven't guessed, my paper was desk rejected after the 38 days, without going for review. Though, I will say that I did get a few sentences of justification from the editor that were perfectly reasonable and showed an understanding of the paper. But, this is a process that usually takes two days at a normal journal. Either they send it for review or they don't.
Moral of the story - don't submit to PNAS if there's any question of whether or not it will go to review. Chances are, they will waste your precious time on the tenure clock. Someone alerted me to the fact that just this week PNAS was tweeting that you don't have to be associated with an NAS member to submit to PNAS. My feeling is that this statement is disingenuous.
The status updates on the PNAS submission website are a little cryptic if you don't understand their process, so I'm going to end by copying and pasting my status updates along with my understanding of what they mean.
|Review Complete; E-Mail Notification Sent||2014-06-23 You have been rejected. You should have received a generic form letter.|
|Pending Final Recommendation||2014-06-20 Rejection is imminent, but even though the decision has been made, don't expect to hear anything for a few days. This would say "Under Review" otherwise.|
|Under Editor Review||2014-06-16 Your paper may be sent for review, or maybe not.|
|Under Editorial Board Review||2014-05-16 This is initial screening by one of the super famous editorial board members. It is possible that if they don't act within a month, then the journal staff automatically does something, because that seems to be what happened with my paper.|
|Quality Control Review Completed||2014-05-16 Everything below this is just standard administrative stuff that happens with every paper.|
|Quality Control Review Started||2014-05-15|
|Author Approved Submission||2014-05-15|
|Waiting for Author Approval of Converted Files||2014-05-15|
|File Conversion Complete||2014-05-15|
|Waiting for File Conversion||2014-05-15|
|Preliminary Manuscript Information Submitted||2014-05-15|