I need to use those highlights for papers that I’m writing, so when I highlight some in a text I need to be able to use that for something otherwise it’s pointless to do it. Thanks I’ll take a look at that 
Hi,
The ultimate pdf annotation software I recommend is MAXQDA. No exaggeration, it can beat all kinds of pdf readers. Although the software is mainly used to do qualitative data analysis (QDA), the logic behind QDA (coding system) is very suitable for bibliography annotation and management. With it, you no longer need to search for that very sentence you read several months ago in a mountain of references, no need to transfer your highlights. The software is commercial and not cheap, but I never regret to buy it. One hundred percent recommended!
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Thanks ygjose! And welcome to the forum 
I’m PDF Expert user for years originally on the Mac and now exclusively on the iPad. While their app, and their other apps, are distinct and need some getting used to. It’s also really powerful for many things
hmm! I never considered applying those “heavy equipment” research apps to my day-to-day, but it’s a good idea. You’re right: the power behind them should translate well to using lots of highlights and annotations.
Sadly, it seems that MAXQDA’s iOS app is in disrepair, and Nvivo doesn’t offer anything on iOS. Do you (or anyone else) know of iPad-friendly options for these qualitative data apps?
Hi @andreasl,
I’m also a super fan of PDF Expert. Basically use it to read papers on a daily basis. But the reason I highly recommend MAXQDA is that, as I mentioned earlier, the logic of reading and annotating is totally different!
When you use PDF Expert to read and highlight papers, you do it one at a time. So when papers piles up and time goes by (this is especially true for a long project like dissertation), you probably start forgetting some contents you already read several months or even years algo. Of course, you can export your notes from PDF Expert and search for them.
But imagine one day you read a new paper, some thoughts of that paper remind you of a similar point that you read in another paper. These can be interconnected and together can be used to support your argument. PDF Expert in this case may not help you relate these two papers or two paragraphs of these two papers. But MAXQDA can come in handy: use the same code to highlight the two paragraphs of those two papers, and then they will be grouped under that code. Next time when you want to see all paragraphs under that code to support your very argument. Just double-click that code, it will show you all the marked paragraphs in all papers you read. Isn’t it amazing?
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Hi @ryanjamurphy,
I never use iPad version of MAXQDA to read papers because of the small screen size. Even MacBook Pro for me is too small. In the main interface of MAXQDA, three parts are essential: document group, code system, and document reader. Since the first two sections already occupy part of the screen, the screen left for doc reader wouldn’t be that big. To tell the truth, those small letters in the doc reader really hurt my eyes. That’s why I use PDF Expert to read papers (truly sad…) and when I read something interesting or important, I will let MAXQDA help me save those interesting points.
If you really want to use MAXQDA on iPad, you can also have a look at ATLAS.ti. MAXQDA, ATLAS.ti, and Nvivo are all qualitative data analysis softwares. Since I only use MAXQDA, I can’t give a subjective evaluation on them. Maybe you can google search some relevant testing on these softwares?
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The QDA software has always been intriguing and possibly useful for my personal research, but the pricing of the three majors has always shocked me. It’s almost as though they coordinate pricing with one another. Anyway, better to eat than blow the budget on QDA software, unfortunately.
You’re probably right 
They are competitors but maybe somehow they agreed to set a really high price. As a student, I got a 50% discount, but still the price is outrageous!
Price for single user in educational section (annual subscription)
Ah, right, Atlas.ti!
It does offer an iPad app, but the app looks poorly developed:
Surprising that no major player has provided apps for this on iOS.
Sorry, I have no idea how their iPad apps are. I suppose they are really bad at designing good iPad apps…
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You should be aware, though, that MaxQDA uses a proprietary PDF handler (Foxit I think), not the native Mac handler, which means you can’t start annotating in another app then move into MaxQDA and keep your annotations. This and a lot of other UI quirks related to its cross-platform model have kept me from getting into it for all but the absolutely necessary QDA purposes, despite shelling out (from institutional funds, not my own pocket) for 12 and 18.
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Ah yes. That is a deal-breaker for me… though I’d already given up because of the lack of iOS support.
Aside: Highlights’ latest update on iOS is getting some love:
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Does anyone use Marginnote to read papers? I once used it and found out that it was very useful to do in-depth reading and understand the structure of the paper (the mindmapping feature). And I think it is also really good for those who want to memorize some details (the flashcard feature).
But later I gave it up because I think this e-reader like others focuses on a single paper. I want softwares like MAXQDA to help me link different papers and different annotations (from a bird-eye view). But I noticed that Marginnote now seemed to support organization of “multi-book reading notes all in ONE map”. Haven’t testes it out yet.
Anyone has some thoughts on this software? Appreciate your input 
MarginNote user, here. Haven’t used it as much I originally thought I would, but I very much appreciate the idea of MarginNote’s highlighting, annotation and export options. For a while I used to export notes from documents to iThoughts, which was useful at the time. My workflow at the moment is based on pushing notes from reading materials in Readdle Documents into a Zettlekasten inspired system in Drafts, but if/when I ever need to do anything more involved, MarginNote is my “go to” for that kind of work.
Also, hat tip to LiquidText. I prefer MarginNote, personally, but they have similar feature sets.
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I use it every day, both in legal and academic capacities.
It does not seem to be as powerful as MaxQDA, but it is awesome for tying up together different paragraphs from distinct PDFs.
The macOS version is its main advantage over Liquid Text.
Sync is not stellar, but definitely workable. And macOS app sometimes feels a bit slow to my taste, but works ok most of the time. iPadOS flies…
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Thank @ldebritto @jsamlarose for your input. Never tried LiquidText before. Just headed over to its website and checked some video tutorials. It seems interesting and supports interlinking different papers. Awesome!
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I’m currently developing an app that’s meant to improve on such a workflow. The app (Keypoints) is a plain-text focussed note-taking & PDF annotation app for the Mac. It stores each PDF highlight annotation as a separate plaintext (MultiMarkdown) note. These notes are self-contained, i.e., they each contain all relevant info (e.g., the PDF file & annotation info as well as the citation info which can be fetched from your reference manager).
Having individual, self-contained plaintext notes is crucial IMO – not only for reasons of maximum portability & long-term stability. This also enables you to sort/filter and organize them (e.g. via tags, color labels or ratings), mix & arrange them with other notes from other PDFs (via structure/overview notes), and link them together (via drag & drop or autocompletion). This allows you to create a network of semantically rich and linked notes, and to build your very own knowledge database.
Unfortunately, the app isn’t yet available as a public (alpha/beta) release, but the latest status report in the forums has some more screenshots and a 1-minute screencast that shows it in action.
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Incidentally this book on MaxQDA has just been released for free:
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That sounds really interesting. Please keep us updated.
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IAnnotate will export as plain text. Liquid text will export into a word document, without the hexadecimal colour coding.