Your Zotero desktop library contains everything you need to read and annotate PDFs. You can:
When Full-text PDFs are added to your Zotero library, they will be "nested" under the main item entry in your library. You can tell an item has nested content by the small > arrow that appears beside the item. Click the item to find the PDF. (The Zotero Connector will automatically grab full-text PDFs during citation extraction whenever they're available. See Collecting material for more information.)
When you double-click a PDF in your Zotero library, it automatically opens in the library in a new tab. You can have multiple PDFs open and switch back and forth between the PDFs and your standard library view.
Within the PDF viewer, you can highlight text...
... and add "sticky note" comments:
Now, here's the really cool part!
You can extract all those highlights and notes you just created into a separate file in Zotero:
You can create notes associated with any item in your Zotero library. To do so:
You can add as many notes as you want to the same item. Notes you've created will appear "nested " under the relevant item.
You may want to extract your notes from Zotero to a word processing program. You can do this using the same Word/LibreOffice/Google plug-in you use to create citations and bibliographies (more on setting that up here).
These instructions are for Word. The process for the other programs is very similar, but contact us if you get stuck.
Pro tip: If you think you will be extracting notes from Zotero, consider giving your notes a descriptive name, or at least including the title of the associated article/item within the body of the note. If you call all your notes "My notes", it can get quite confusing to track a specific one down!