Highlights v. MarginNote v. LiquidText v

There looks to be a sudden wave of PDF note taking apps, and I am wondering if anyone has taken the opportunity to play around with them/add them to their workflow/have other alternatives… really liking LiquidText right now, but always open to ideas, suggestions and the like…

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Hmmm, MarginNote, LiquidText, Highlights are not suddenly new – they’ve all been around for several years. I have them all, and prefer MarginNote - though it has some weird and frustrating interface issues.

Backing up to the beginning though – the question is what’s your use case? Are you taking notes for academic research? For personal records? Something else? If you are taking notes on a corpus of PDFs that are related to one-another, and want to bring in web-resources into the notes then MarginNote is very good for this.

Personally, I have large corpuses of dual-language source texts comprising thousands of pages of text in deeply intertwined (cross-referenced) documents. For me, MarginNote is unique in its ability to handle that.

If you want to focus on one-off PDFs that do not need to be managed as a group, then Highlights is OK for this. I like Highlights, but unfortunately do not trust it. As a product, it seemed to be abandoned for a long time, then came back to life. Some macOS-version bugs were fixed, and an iOS/iPadOS app came to market. I do not like the latter – it’s clunky.

LiquidText is very interesting – export is better than the other two apps, IMO.

Don’t forget the other annotation options for PDFs – there are dozens.


Unfortunately, there does not seem to be a killer-app in this space even though the space deserves one. I have tried each of these, but each has frustrating shortcomings. Highlights is nice, but does not even have tabs for multiple files. Youch. Yet Highlights seems to have the smoothest UI. How is that possible (good UI in one place, and massive oversight in another)? Weird, but each seems to have similar guffaws (IMO).

I’m just curious since I see this phrase here and there. What the heck is a “killer-app”? If it merely means “something I don’t like” then fine, but if it means “the best app ever created” or something superlative like that, I don’t see how such a thing can exist in the PDF annotation category – or most software categories for that matter. (Related to “game-changer” – another term that seems to have no meaning at all.)

In How to Read a Book , Mortimer J. Adler and Charles Van Doren classified four levels of reading: Elementary Reading, Inspectional reading, Analytical reading, Syntopical reading.

Here is a blogpost summarizes it:

I think MarginNote and Highlights are suitable for the third level reading. With them, you can chew and digest papers or books, i.e. a more in-depth reading.

LiquidText for me is more suitable for the fourth level reading, whose focus is comparison. So you need a software to help you compare or contrast ideas & arguments of a specific subject matter from different papers/books. Based on this, you develop our own ideas and theories.


@anon41602260 The “killer app” usage I am most familiar with is an app that is so useful that it all but defines a space or… a computer platform. Desktop publishing is (I believe) recognized as the “killer app” which put Apple Macintosh on the map (back in the day) even in the face of MS/PC monopoly.

My suggestion is that the PDF reader space exists but the killer-app does not. In other words, an ironic and sad (and frustrating) state of affairs (IMO).

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I shall take another peek at LiquidText. I don’t remember what turned me off about it earlier. (It was my previous contender before Highlights, but now I’m getting frustrated with Highlights.) I do recall that LiquidText is very nice for combining Notes across sources. And I need to check out that exporting… which I was not doing earlier (but am using now from Highlights which seems pretty good at it).

Highlights doesn’t seem support different source checking in one window, especially when you want to check one specific subject matter that appears in various sources. LiquidText has sort of “magic” that combines that subject matter from different sources in one window. But LiquidText only has iPadOS version, which is pretty cool with Apple pencil. The website says the Mac and Windows versions are coming soon.

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@ygjose Are you able to get Auto-Excerpt to work from Apple Pencil (double-tap)? I cannot.
I just tried LiquidText again and found the i/f cumbersome. It crashed on me as well. And the export did not seem to provide the excerpts or other features as requested. The potential is high, but the execution (in my experience) is poor. Perhaps I’m using it ‘wrong’ ;-).

Makes me wonder… How are people using LiquidText that it’s featureful and performant?

It’s embarrassing to say, I don’t have Apple pencil. My iPad is very old, so I don’t plan to use it to take notes. I saw a couple of video tutorials of LiquidText. I’m very interested in its features. I’m waiting its Mac version.

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As I’m also building a (plain-text focussed) note-taking & PDF annotation app for the Mac, I’d be very interested if you (or others) could specify in more detail what features/aspects you’d consider as most essential or must haves. Thank you!

@msteffens I’ll know it when I see it! Just kidding.

1st order of business: reliability and universal (iPad + MacOS).
I’d suggest cherrypicking the best features off the apps mentioned here, adding reliabilty where necessary.

I’d like to see highlighting by pen without necessity of tapping a menu choice (e.g., for color) and with auto-excerpt to notes and with auto citation of source document with page number.

It should export to Drafts (text) with full text (note + citation).
Ditto mindmap programs - iThoughtsX (and many like MindNode).
Then add support for (e.g.) hypothes.is for notes aggregation and reminders.
Then add support for RoamResearch.com - the new hotness in notes mgmt.

What I’ve just described are several useful (or one complex) workflow where these tools fall down. If you make these workflow(s) seamless, then that’s a great step forward. Perhaps that’s more complex than the app itself, but it’s a very pragmatic goal (IMO).

Good luck!

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@occam, thank you!

While I think that it’s impossible for an app to please everyone (as everyone has slightly different needs & priorities), I very much believe that app’s should strive for good interoperability (e.g., via sound import/export options & ideally support for scripting/automation). This will also allow users to create a personal workflow by combining multiple special-purpose tools (instead of one universal tool that tries to fit all).

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I sometimes get the sense that most PDF annotation products are built from the perspective of the PDF – rather than from the perspective of a user, annotating that PDF.

By way is example, 99% of them see too many taps to change highlight colours, or tools, or don’t treat a single highlight as a separate event from other highlights on the same page – or don’t easily present a way to remember most used colours or tools.

I suspect the point above is why so many of them look virtually the same. PDF front and centre, some form of toolbar on the side(s), or appearing at cursor point, with the standard fare of options in terms of interacting with the PDF. I’d love to see something examining the most typical requirements/approaches regarding annotating (doctor, researcher, teacher, academic, lawyer, student etc.), and having profiles and toolsets presented accordingly… in other words, switching up the paradigm, and starting with the user.

My 2 cents.


Very astute take on the purpose of these apps, in my opinion. Also, thanks for posting the link to that blog post — I always enjoy reading about reading. :slight_smile:


Good points. TY for response.

Yes to automation: Shortcuts!

Yes, thanks for that reference, @ygjose. It’s an excellent framework for this kind of “processing written ideas” work.

I agree with your take that LiquidText fits “level 4” the most. However, I think that’s because it does more than help you read. It’s about excerption, ordering, memo-writing, etc… Grounded Theory sorta stuff. In that sense, there are also a lot of other tools that fill in that gap, from index cards to Scrivener and Ulysses’s notes and reference material features to Curio, Tinderbox, all the way to Zettelkasten-type systems and Roam-like systems.

Since everything’s a stack, it might be a good idea for knowledge workers to conceptualize their writing tools as a stack, too. The framework summarized on Farnam Street is a decent template for what “full stack” reading looks like. So, we’re challenged to find the tools and processes that fit us the best on each of those levels.



Perhaps @BradG PDF annotation seems incomplete or “from the perspective of the PDF” because for many of us the annotation process is step on a road going elsewhere – leading outside of the annotation process to a book, or an article, or private essay consolidating excerpts and notes. PDFs are flat and linear, and annotations are, in essence, snippets or a reduction of the overall PDF. Personally, when I can get those snippets / notes out of the PDF and begin to work with them in relation to other things I’m reading, or other media, that the notes enter a broader context. Then, the annotation process broadens out and informs knowledge. Escapes the software, so to speak, to become something better.


I completely agree with you! And yes, I think LiquidText does more than comparisons. Although I haven’t tried it personally, from what I saw in the video tutorials provided by the website, it seems that LiquidText can do memo-writing and stuff like that.

I’m glad you mentioned Grounded Theory, which is one of the key theories in qualitative research. I don’t know if someone has ever talked about the similar thing before: I think when we do reading, especially scientific reading, we are actually doing something pretty similar to Grounded Theory. That is, at the first step, we collect relevant papers/data; then we constantly compare concepts from the papers/data; we sensitize concepts, write memos, reflect, etc. until our own provisional theory is saturated; finally, the ultimate theory is established.

Since doing scientific reading and notetaking is a qualitative process, I think a computer-assisted qualitative data analysis software (CAQDAS) would reach at its finest. If you remember what I posted in another thread, I recommended a QDA software called MAXQDA. This software certainly fits the fourth level reading. That’s why I’m using it for my whole literature reading, quotation, ordering, memo-writing, etc.

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I consider LiquidText and MarginNote to be comparable in that they both offer the ability to play with the annotations directly within the app itself. Highlights is not in this same league. In my testing on an iPad Pro with an Apple Pencil 2, I found that LiquidText does not consistently import annotations from other PDF annotation apps and MarginNote does not reliably sync. I preferred MarginNote because I could tag annotations, I could write hand notes to annotations, and hand-written annotations were kept as one group.

In truth, I never took the time to play much with the annotations in LiquidText or MarginNote (e.g. mind mapping). But from my first tests, LiquidText seems to have the cleaner UI setup to start the process while MarginNote seems to have the deeper toolset to analyze and compare annotations (e.g. flashcards).

At the end of the day, I realized that consistency and reliability are more important that the ability to play with annotations inside a PDF annotation app. Since MarginNote could not export its annotations (the PDF is flattened), I went back to a stable PDF editor (PDF Expert) and hope to explore the options to sync with external apps some day soon.


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