Here are some tips to help you navigate this process:
- First, take a deep breath! Remember the goal of peer review is to improve the final manuscript (and research shows that papers that have been through several rounds of peer review get cited more than those that were more immediately accepted!). Keep your reader in mind and work to make the changes that will make the text more accurate, clear and valuable for them. As a baseline, assume that editors and reviewers also share this goal and try to take their comments in that spirit.
- Read through the reviews carefully, paying special attention to the Editor's instructions - this should guide your prioritization for revision. Look for common themes across reviewers- areas of agreement are important to clarify in the manuscript. Consider the type of comment- does it relate to the overall argument/soundness of the work in supporting claims with evidence, is it more about the structure of the writing, or a small detail to clarify in wording? Getting the big picture helps you get an idea about where to focus your revisions.
- As first author, you have primary responsibility for leading revisions to address reviewer's comments, and for keeping all of your coauthors informed- including asking for their help with revisions where needed, and getting input and consent from all coauthors on your suggested response to reviews and the revised manuscript before resubmitting it to the journal. It is important to share the reviews received with your coauthors right away and keep them informed of due dates and progress. You should suggest a timeline for making the revisions needed, that will give all coauthors time to read and respond to your suggested revisions. Be sure to ask for what you need in terms of support- i.e., do you want a brainstorming Skype session to help formulate your overall response strategy? Are you unclear what certain reviewers' comments mean, or what they are looking for? Are there parts of reanalysis or writing that you need coauthors to lead?
- Save a new draft of the manuscript where you'll work in Track Changes to share with your coauthors. Consider annotating this with some of the key, overarching comments from reviewers (i.e., "Insert Comment" in Word at the relevant section where the reviewer's comment applies- see example above left from a recently accepted paper led by Klara Winkler). This can help the manuscript read more coherently and coauthors will understand your motivation for the changes you've made, and help assess if these changes have fully addressed the reviewer's concern.
- Make a table with the Editor's and Reviewer's responses in the left column, labeling the source of each comment (e.g., first all comments from the Editor, then from Reviewer 1, etc.). Give each main idea its own row. Be sure to include any in-text comments that were received here as well. In the right column, you will write your response to address this comment (see example above right from Winkler et al., accepted). The final version will answer the reviewer's question (e.g., "Yes you're right and we did this on line X," quoting the relevant manuscript text here if needed). For a first draft, this column can contain notes to your coauthors, e.g., "I don't understand what the reviewer means here" or "Kim, can you please answer this one?", or some initial bullet points about your planned response ("Rewrite this para to make link with research question 2 explicit").
For more in depth tips, I suggest the excellent article "How to reply to referees' comments when submitting manuscripts for publication." Peer review would go so much more quickly and smoothly if everyone followed Hywel Williams' three Golden Rules: Answer completely, answer politely, answer with evidence. See also his phrasings for suggested responses to reviewers, and tips for how to deal with common scenarios like reviewers who disagree, or who are rude.
Another good source is "10 simple rules for writing a response to reviewers," by William Stafford Noble in PLOS.