You're peer-reviewing a paper for a journal. The methodology has gaps, the citation in paragraph three is wrong, and the conclusion overstates the data. Your review needs to be specific, paragraph-by-paragraph, and clear enough for the author to act on.
Annotated PDF is the conventional format. Flint gives you the tools.
Use comments for paragraph-level critique
Open annotate PDF, drop the manuscript. Drop sticky notes next to each issue. Be specific: not 'this paragraph is unclear' but 'the leap from x to y assumes z, which isn't supported by the data in Table 3'. Anchored notes let the author find each point quickly.
Highlight quoted text
When you're responding to specific text, highlight it and attach the comment. The author sees exactly which sentence you're reacting to. Different colours for different feedback types: yellow=clarification needed, red=methodology issue, green=strong point worth keeping, blue=minor note.
Methodology and stats sections
These need detailed treatment. Use arrows to connect related parts of the analysis. Add detailed comments on assumptions, sample size, statistical choices. If you're recommending a different test, name it. If a figure misrepresents data, mark the figure and explain how.
Summary review separately
Detailed annotations on the PDF + a separate summary letter (the review report) is standard. The summary covers your overall judgment; the annotations are the supporting detail. Authors revise based on both. Don't try to put everything in annotations — some thoughts belong in the higher-level letter.
FAQ
What's the right tone for academic annotation?
Constructive, specific, focused on the work not the author. Even harsh critique should be actionable.
Can I annotate anonymously?
Yes — change the author name in PDF settings before annotating. Or use a generic name like 'Reviewer 2'.
Will references and cross-citations remain navigable?
Yes. Annotations sit on top; the source file's hyperlinks and references still work for both you and the author.
Should I attach my CV or contact info?
Usually not in annotations themselves. Identifying info goes in the review letter, separate from the annotated PDF.
Annotate rigorously, summarise separately. Review academic PDFs.