Dave discusses the prospect for a manuscript with a CPTAC working group

Shepherding a paper with many authors to publication

Twice in my career, I have been asked to take the lead in creating a manuscript to represent the labor of a large working group.  Both times, the effort has posed a considerable challenge and chewed through a significant amount of time.  I wanted to share the strategies that led to my eventual success in publishing a paper for a working group.  Hopefully they will let me succeed in my current manuscript, as well!

My first paper of this type was “Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry” on behalf of the National Cancer Institute’s Clinical Proteomic Technology Assessment for Cancer (CPTAC) program.  A network of five lead institutions, their partner institutions, along with NCI and National Institute of Standards and Technology, had conducted a variety of multi-site experiments to evaluate the stability of technologies in proteomics.  Our group was intended as a response (technology assessment) to many challenges that had been raised about proteomics; funding agencies needed to know that if they made grants in the area of proteomics, they weren’t simply throwing their money away.  My second manuscript of this type is in its final stages of preparation for the successor to CPTAC, now renamed the “Clinical Proteomic Tumor Analysis Consortium.”

Large grant programs face a lot of pressure within the National Institutes of Health.  A single CPTAC network may cost ten times as much as an individual R01 grant, and so expectations are quite high for productivity.  The working group papers, then, have special significance; they are perceived as “points on the board” for these teams, and generating the most impact possible from the data is the order of the day.  These are the guidelines that helped me navigate through to a published paper.

Choose a purpose important to your group
The energy people apply to supporting you in your manuscript goal reflects their individual interest in seeing its key question answered. It also reflects the support they will receive from their own leaders to get it done. At several points during the authorship of the repeatability paper, I felt that others did not have the sense that this topic was worth a publication of its own. In fact, at one low point in its preparation (after rejection by the initial target journal), other authors sought to move some analysis from my manuscript to others in preparation. The manuscript might have sundered altogether if I and some senior investigators in the program hadn’t been able to hold the line.
Accept that the paper critically depends upon you
The paper may, in the end, list upwards of thirty authors, but almost every successful group paper effort I have ever seen depended critically upon one person who championed the publication effort from start to finish. I am not referring solely to the effort of writing the text, although my experience suggests that 80% of the words on the page come from one person. Nor am I talking about the data analysis or other experiments, though I’ve never seen a case where the lead author didn’t perform a serious amount of that work, too. The task of the paper champion is to build and maintain the momentum in contributing authors toward the common goal of publication. If you don’t feel enthusiastic about the effort and convey that enthusiasm to others in your teleconferences and in-person meetings, your paper will probably sink in a mire of ho-hum.  The appreciation you lavish on your contributors privately and publicly will help to set a tone for the project.
Know when to fold ’em
This line from Kenny Roger’s “The Gambler” is very good advice! There are certainly times when the data simply aren’t good enough or the analysis you have constructed does not tell the story you sought to relate. There will be times when your flagship manuscript needs serious reformulation before its time will come. Don’t force it. It’s far better for you and your co-authors to decide to mothball your work while additional data or analyses can be assembled than it is for the journal’s peer-reviewers to tell you to start over. I know from personal experience that a bad peer-review (whether or not you think it is unfair) may threaten to scuttle a manuscript effort altogether.
Pick a target journal appropriate to your reach
Many large consortia take the perspective that multi-lab experiments must obviously be published in high-impact journals. Some researchers even take the perspective that a field-specific publication (like Journal of Proteome Research) would be a failure or a disappointment. If you throw all your effort into high publication, be aware that you are rolling the dice. You may throw your manuscript to peer-reviewers who are peeved because they didn’t receive funding from the program that is sponsoring your paper. You are nearly certain to meet serious restrictions in figures and word counts to format your manuscript for the journal, leading to more material in supporting information than in the manuscript itself.  High-profile publications must also meet political criteria outside your control; acceptance will not be based on the science alone. For my part, I know that I can write a really solid manuscript for a journal like JPR above, but my skills at formulating research for Nature Biotechnology have not been as good. I also know that I generally afford more credibility to a paper that explains its methods well, and that causes me to look at the “lower-impact” journals first for something I can trust. In the end, if your project has produced results that the whole world needs to see, you will have to target the big journals, and best of luck to you.
Work, work, and work some more
The heads of the program have called upon you to take on this project. You know how to tackle a fair bit of the analysis, and you identify a core group of other researchers who can fill in for the parts you do not know how to do. Some of them even provide a couple of pages of text to explain their work! Now you will shove aside other tasks that are begging for your attention to give your time and effort to the analysis and the write-up. You will sail the dangerous waters of framing a full author list! You will seek approvals from leadership for including that bit of data or for limiting your scope to one of several lines of analysis. In the end, you cast your manuscript upon the waters, letting all the authors see a nearly-finished manuscript, and after a week or two of begging, the comments will begin to trickle back. Some of them will be useful. With those objectives satisfied, you can seek final approval from program leadership for submission.

Remember, it is an honor to be asked to write a manuscript on behalf of a group.  Smile!


One thought on “Shepherding a paper with many authors to publication

  1. Pingback: China: Proteomics at Phoenix Center and the National Institute of Biological Sciences | Picking Up The Tabb

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