Looking to move away from Endnote to something cross-platform

Hi MPU, I’ve been using EndNote for awhile now on Windows, Mac, and iOS and my online subscription is coming up for renewal (I think this means I won’t be able to sync documents anymore). I know Endnote has a long history of being ignored on Mac and the iOS app is terrible. It looks like the new Endnote 20 is only for windows, although they say a Mac version will be released soon. It will probably take years for a native apple silicon support though as the app only got 64-bit support in the last year. Not encouraging.

I was wondering if there is a better solution that works on windows and mac (and ideally iOS too) that is better than Endnote? Here’s what my current research tells me and I’m open to input from others.

Endnote - cross platform, but buggy on all platforms; ugly UI
Bookends - nice app but no windows support.
Zotero - free, but electron; no iPad app for reading
Papers - this seems like the closest thing to a cross platform solution. I tried v3 a couple of years ago but it was horribly buggy to the point of being unusable. Has it improved since then? Not ideal that it’s a subscription-only app, but you can’t have everything right?

Are there other solutions that I might be missing that I haven’t considered? Thanks for any advice.

ReadCube has released a successor to Papers 3. I haven’t used it, but it has feature for feature comparisons with Papers 3 and other ref managers, as well as a 30 day trial.

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If you qualify for the educational subscription its pretty cheap

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I am in a state of constant dissatisfaction with reference managers. Every single one of them is crap, in it’s own way.

Papers3: can’t add BibTex records from the clipboard. (or did anyone find a workaround for this?). This drove me insane yesterday.
Zotero: had to drive to the office to refresh the bibliography because the Word plug-in on the Mac was not willing to format it…


I used BibDesk yesterday to look at a .bib file, and it was refreshing in its minimalism.

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I always have BibDesk installed. But I like the look-up feature of Papers3, it’s PDF features…

None of the reference applications makes me really happy.


I continue to use Mendeley, though it’s not a super-popular reference manager with many. It’s cross platform and extremely versatile, and they’ve put in a lot of work recently on cloud sync capabilities. The iPad app isn’t half bad either. The only downside is that you have to manually make sure to save and sync your files and make it a habit, I’d love it they had a decent auto-syncing feature.

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Do you mean the $5/month price or is there another discount I’m not aware of? I do have an edu e-mail so hopefully that is sufficient for the discount.

I had been using Mendeley for years before switching to Endnote 2 years ago. The switch to an encrypted database really put me off and It was a struggle to get my citations out of Mendeley into endnote. I can’t see myself ever going back to Mendeley.

In case of Papers3, just copy your BibTeX record, then choose “File > New Paper > From Clipboard”. This should import all of your copied BibTeX record(s).

Alternatively, Papers3 does (or did at least as long as it was supported):

  • allow you to copy just a DOI (e.g. 10.1002/2016GB005569) and choose “File > New Paper > From Clipboard” to import the article’s corresponding metadata.

  • Create a new (empty) paper, then paste any identifier (like its DOI, PMID, PMCID or URL) into its corresponding field. Papers3 will then attempt to fetch the publication metadata.

  • Choose “File > New Paper > From Reference…” and paste one or more formatted references, or just a few descriptive words from the citation (like first author last name, year, plus some words from the title). (*)

In all cases, Papers3 would also attempt to fetch the article’s fulltext PDF (if available).

(*) I just tried it again using Papers 3.4.10 and I couldn’t get import from formatted references to work anymore. The automatic PDF download also seems to work much less often. Sigh, this all worked nicely when I coded it :slight_smile: but someone has to maintain it. I’d love to do so, but it’s not in my hands anymore. And Readcube has clearly moved on.

My mistake: I was referring to the newest version “Papers” (Readcube), the successor of Papers 3.

That’s exacly the feature I loved to use and now it’s gone.

Can you explain a bit more about this? I am sending all my files to my iPad for reading and then bringing them back into Zotero all the time. It’s now a major part of my scientific paper workflow.

And I’ll probably post elsewhere about electron.

As noted elsewhere, their Papers3 successor is in reality a rewrite of their previous ReadCube product (and not of Papers3), based instead on cross-platform web technologies and styled to look like Papers 3. But these are actually completely different products which happen to share the same name & target user group.

It has some very nice features. But I think I will move back to Papers 3. Which I despised for other reasons… :smiley:

I’d be interested in hearing more about your Zotero > iPad > Zotero workflow. Do you manually export the pdfs to a reader like Goodreader or PDF expert or have you automated the process more? I did find Papership, a third party app which integrates with a synced Zotero library, but haven’t investigated further. It hasn’t been updated in over a year which also gives me pause. Is this what you use?

I think you can just store your zotero library in any cloud storage and sync it to GoodReader for reading. But you can’t access the metadata except on web.

I’m working on writing it all up. I’ll move that to the top of the longer post writing section of my forum time and try to get it up here by the end of the week.

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Im using bookends but its not on windows. Works great otherwise on mac and ipad.

I used Zotero when doing my dissertation, but that was several years ago. At the time it worked for me, especially for APA formatting. The Word plugin worked at that time. But, it’s been several years now…and I haven’t touched Zotero since and I hope to never have to again! That’s one thing about writing a dissertation, when you are done, you are very happy to be done!


That is the one ( academic), however there is a further 40% off that if you used the previous papers app