Zotero: managing papers across devices

Near the end of the first year of my MSc, during the CENG promotion days in summer 2024, a research assistant colleague introduced me to Zotero. Until then, I had changed my paper-management method several times, but the parts of the system did not really work together.

I began with printed papers. For digital copies, I kept papers in folders on my Drive and computer and synchronized them manually. After I bought an iPad, I started sending papers to Goodnotes 6 and organizing them in folders there. At the same time, I was still keeping copies in Drive and on my computer. My annotated versions remained in Goodnotes and its cloud storage, which I accessed through the Apple ecosystem at that time. As a result, the same paper and its annotations could be spread across several places.

Zotero gave me a more unified workflow. I started with the desktop application on my Lenovo computer, the Zotero Connector for Chrome, and the Zotero app for iOS and iPadOS. Later, I also began using the official Zotero app for Android on my Samsung phone. I now have one library for collecting papers, organizing them, reading and annotating PDFs, and accessing the same research material from different devices.

Syncing and storage

Zotero separates library data from attachment files. According to Zotero’s sync documentation, synchronization of library items, notes, links, and tags is free and unlimited. PDF and other attachment files use a separate file-syncing option. Zotero Storage includes 300 MB free, with larger paid plans. I currently pay for Zotero Storage because it is the most direct option for my workflow.

There is also a free alternative for personal-library attachments: Zotero can use a compatible WebDAV service. This does not necessarily mean operating your own server; an institution or a third-party provider may offer WebDAV storage. WebDAV does not support files in Zotero group libraries, and Zotero provides only limited support for third-party servers. Zotero also warns against putting its database directory directly in a cloud-synced folder such as Google Drive, Dropbox, or OneDrive because that can corrupt the database.

For me, Zotero’s main benefit is not simply storing PDFs. It reduces the number of separate places I have to manage and keeps the paper, its bibliographic information, and my annotations within the same research workflow. It is the first program I recommend in this MSc thesis recommendations series.