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In part 1 of this Perspective, I discussed general principles of scientific peer review in the biomedical sciences aimed at earlystage investigators (i.e., graduate students, postdoctoral fellows, and junior faculty). Here in part 2, I share my thoughts specifically on the topic of peer review of manuscripts. I begin by defining manuscript peer review and discussing the goals and importance of the concept. I then describe the organizational structure of the process, including the two distinct stages involved. Next, I emphasize several important considerations for manuscript reviewers, both general points and key considerations when evaluating specific types of papers, including original research manuscripts, reviews, methods articles, and opinion pieces. I then advance some practical suggestions for developing the written critique document, offer advice for making an overall recommendation to the editor (i.e., accept, revise, reject), and describe the unique issues involved when assessing a revised manuscript. Finally, I comment on how best to gain experience in the essential academic research skill of manuscript peer review. In part 3 of the series, I will discuss the topic of reviewing grant applications submitted to research funding agencies. [ABSTRACT FROM AUTHOR]