The ultimate guide on how to annotate PDF files on the iPad

Ultimate guide on how to annotate PDF files on the iPadFor most people in university and college, the ability to annotate PDF files is one of the main reasons for buying an iPad. There are hundreds of apps out there that let you annotate PDFs: how do you know which one is the best one for you?

Rather than discussing one particular app in detail, this post presents the bigger picture by discussing three different user profiles whose needs are different with regards to PDF annotation and management. Once you know what type of user you are, you can check out the overview of 10 (plus 3) apps, my personal favorites, and some thoughts on using a stylus. With all this information, finding out what app you need to annotate PDF files “your style” becomes a piece of cake.

What type of reader are you?

Because everybody’s reading habits and PDF management requirements are unique, there is no such thing as “the best app to annotate PDF files on the iPad”. What works for you can be a nightmare for your colleague. However, one can make out three different user profiles with roughly similar needs: the Penny Pincher, the All-Around Reader, and the PDF Management Master.

You might fall in between two of these profiles. In this case, you can either decide what requirement is more important for your individual workflow, or you can use two apps for different workflows and different tasks. For example, I am currently using Sente to annotate journal articles and iAnnotate to annotate PDF files for committee work.


The Penny Pincher: Annotate PDF files for free

The Penny Pincher does not want to spend money to annotate PDF filesIf you don’t deal with PDFs very often, there is no big reason to spend money on PDF apps. iOS lets you read PDFs without any additional software needed; however, if you want to annotate PDF files you need an extra app. Luckily, Adobe Reader  and pdf-notes (iTunes links) are two free PDF annotation apps that are powerful enough to let you highlight PDFs and even add sticky notes. pdf-notes is particularly interesting because it lets you change annotation tools through gesture-based shortcuts. The only downturn is that the free version of pdf-notes displays advertisements, which you can get rid of by buying the paid version. Adobe Reader does not display ads.

In general these apps come pretty close to the apps listed in the second category, so you might want to check out these free options before you are investing money on paid All-Around Reader apps. However, these free apps do not substitute full-blown PDF management system apps that are described in the third category.


The All-Around Reader: Using the iPad as the main reading device

Annotate PDF files on your iPadThe serious reader uses the iPad frequently to annotate PDF files, and it might be even his or her main device for reading PDFs. If your PDF reading workflow has one of the two following requirements, your annotating needs are best served by apps for the all-around reader.

If you value flexibility, then the apps in this category are a good fit for you, because you will be able to view annotations you made on the iPad in every other standard PDF viewer on the Mac (e.g., Preview) or the PC (e.g., Adobe Reader).

Another reason why you need an app for the All-Around Reader is that you want to or need to make annotations in a free-drawing mode. For example, many of your PDFs could be just scanned-in images that don’t allow you to select lines of text as you would in a text-based PDF. Another reason might be that you want to make handwritten annotations in the margins of the PDF; however, I am not convinced that this is a good way to annotate PDFs (see below).

If you are serious about annotating PDFs and need to sync your files with a PC, your best bet is All-Around annotation app or Papers from mekentosj.

If one or more of these examples are must-haves for you, then you would fare well with apps like GoodReader for iPad ($5), PDF Reader Pro ($6), PDF Reader Pro Edition for iPad ($10; same name, different company), PDF Expert ($10), iAnnotate PDF ($10), or PDFpen for iPad ($10; iTunes links).

If, however, it is important for you to have your PDF not just lying around in folders but organized in a library, you probably will be more happy with an app targeted for the third user profile.


The PDF Management Master: Integrate the iPad in your read-write-cite workflow

This user profile is for the geeks. While the apps mentioned for the first and second user profile started out as apps to read and annotate PDF files, the apps in this category started out as reference management apps on the Mac and later added companion apps for the iPad that let you annotate PDF files.

This user profile is the best fit for you when you want to have a tightly integrated ecosystem that allows you to find, manage, read, annotate, and cite your PDFs in your academic workflow.

Typically, you would also own the Mac (or Windows) companion app that serves as your main tool to curate your library, to insert in-text citations in your write-ups, and to create bibliographies at the end of your paper. While the iPad apps in this category also allow you to add and manage papers, they lack the powerful citation functions of their respective Mac versions. However, they are great tools to access your library on the go, and it is much more convenient to read and annotate PDF files on the couch with your iPad than at the desk with your Mac.

The biggest benefit of this tight integration is that you can view and edit your highlights and notes regardless of whether you are working with you iPad or with your Mac. Also, storing your PDFs in a library (vs. a simple folder structure) lets you better organize your papers. You can assign one PDF file to multiple collections and you can add keywords, tags, status, and rankings to your PDFs.

In my opinion, if you annotate PDF files as part of your research workflow (maybe you even have some annotation strategies), then PDF management apps are a very good investment for you.

One of the best ways for academics to annotate PDF files is through dedicated PDF management systems.

If you are dealing with a lot of PDFs (and chances are good you do if you are in academia), then you should consider to invest some time and money into a PDF Management System.

However, the power of PDF management systems comes at a price: First, you will not easily see your annotations with apps that are outside your ecosystem (e.g., Preview, Adobe Reader). This is a lesser concern for you, since you sit comfortably in your ecosystem, but it might be a hurdle when you are working with a co-author who does not use a PDF management system.

Second, none of the apps that target this user profile allow you to annotate PDF files in a free-drawing mode. This is not a big concern either, as I find that handwritten annotations are overrated anyways (see below, you are almost there).

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Right now, the only two apps that let you annotate PDF files are Papers ($15) and Sente ($20; iTunes links). You can read a detailed comparison between Papers and Sente here, or even more detailed reviews of each individual app (both iPad and Mac versions) over there: Sente for iPad, Papers Touch for iPadSente for Mac, and Papers for Mac. The reviews for the iPad apps even have videos, so you can experience them (almost) first-hand without spending 15 or 20 bucks up front!

Also, there are three more apps that are targeted to this user profile, but that don’t have the ability to add annotations (yet): Sente Viewer (free), Mendeley (free), and Bookends on Tap ($10; iTunes links). The first two are simply viewers, but Mendely says that Mendely Pro (most likely with annotation support) is in the works. I also expect that Bookends on Tap will add annotation support some time in the future.


A few thoughts on writing margin notes with a stylus

Personally, I believed that the iPad would allow me to annotate PDF files exactly the same way as I was used to do it on paper copies: by squeezing handwritten notes into the margins.But upon reflection, this is actually not the best idea.

The problem with handwritten notes is that they are neither searchable nor easily editable. I therefore prefer nowadays to use sticky notes, and more advanced PDF management system apps such as Sente can display your notes in a separate space, which makes reviewing your papers really fast.

A stylus is useful for some applications on the iPad, but I don’t think that scribbling text into the margins of a PDF is one of them.

Of course, if you are a fan of expressing your thoughts not in pure text but through sketching out diagrams and images, an application that allows you to add free drawings is your best bet.

Read next: What stylus is optimized for handwriting and conceptualizing ideas?


Overview: 10 + 3 apps to annotate PDF files

Once you have identified what kind of user profile matches most closely your own requirements, you can check out what app might be the best fit for you. The table below gives you a first overview (Note: the * indicates that I was able to personally try out the application), but you can also check the button of this page for links to more detailed reviews on the web. (edit: iAnnotate also has a tagging function. Thanks Jojoba for pointing this out! I updated this post with Adobe Reader which is not shown in the table.)

Overview of 13 apps to annotate PDF files on the iPad

This table gives you an overview over the features of the best annotation apps that you can find for the iPad. Sorted by user profile.


What are my favorites?

I am a big fan of PDF management systems because of the ability to sync my entire library across different devices, the powerful organizing system (especially tags and smart folders), and the ability to handle in-text citations and bibliographies.

Another benefit of having a dedicated ecosystem for your PDF workflow has to do with cloud space. Since starting my PhD, my main library has already grown to 1.5 GB of disk space. While dropbox is awesome in helping you to stay in sync, the free account is only 4 GB. If I had all my papers in a dropbox folder, I would quickly run out of my free dropbox space!

Organize, read, and annotate PDF filesOrganize, read, and annotate PDF files

Right now I would say that Papers and Sente (iTunes links) are the leading PDF management systems (see my comparison article here). While they both let you annotate PDF files, their individual offerings are actually quite different from each other, so check out the in-depth reviews on academiPad (links are at the end of this post). UPDATE: Mekentosj has announced its Papers for Windows app.

In terms of more flexible, dedicated PDF readers, I use iAnnotate (iTunes link) to work with non-research related papers (e.g., committee work), and the main reason for this is that iAnnotate was one of the first apps that allowed me to annotate PDF files. I must say though that through writing this post I became interested in trying out two other PDF annotation apps that seem very promising:

The first one is PDFpen for iPad (iTunes link), which is a highly acclaimed newcomer to the field (it won the Macworld 2012 Best of Show Award and the Mac Observer Editors’ Choice 2012 Award). What I particularly like is that PDFpen offers an ecosystem by having established Mac applications next to the iPad app, while at the same time it offers the flexibility to freely draw annotations. Sounds like a winner to me!

PDFpen is the new kid in the gang of annotating apps on the iPad, but the developer Smile on my Mac has plenty of experience in PDF management and annotation on the Mac.

Another app that I was quite positively surprised about is pdf-notes (iTunes link). My first impression was very negative: the free app displays advertisements in its lower left corner, greeted me with bug warnings, and took a long time to load a PDF for the first time (it is much faster after that). But don’t let this discourage you: pdf-notes is clearly on to something with its focus on gesture-based interactions. In iAnnotate, for example, you need to tab a button to switch from annotating to navigating. pdf-notes, on the other hand, lets you annotate PDF files with one finger, navigate with two fingers, and switch your tool with three fingers. Given that the paid version ($10) is ad-free, you should include this one in the list of annotation apps for the serious reader.

Shameless plug: If you found this article useful, I would like to ask you for two things. First, please share this article with others in your social network. The sharing buttons at the left side make this super easy, and you can find more ideas on how to spread the word here. Second, if you want to use your iPad not only for reading but also for serious (academic) writing, please check out my other guide on how to pick a keyboard case that perfectly fits your writing style. Thanks, and enjoy reading and writing!


Appendix: academiPad reviews

Appendix: Other reviews

What app are you using to annotate PDF files? Please let us know in the comment section, and if you like, maybe you can share some thoughts on what makes the app you are using a great app?

Disclaimer: Panorama image, Yoda with iPad image, and overview table by academiPad. This article contains affiliate links.

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  1. Laurissa says:

    Great article and a good resource. I’m going to have to look into Papers and Sente. Thanks for the tips.

  2. Gareth Lock says:

    I am using Sente on the MBP and really like it. Looking to get an iPad2 very shortly (likely when iPad3 is announced and the subsequent drop in price) but have also been looking at Remarks and Ghostwriter Notes as a couple of apps to do quick and dirty scribbles on the pdf before entering it into Sente. The issue I can see with that is that I will need to keep 2 copies of the files otherwise the exported Sente files will have ‘scribbles’ on them.


    • Jo says:

      Hey Gareth, glad to hear that you are liking Sente for Mac (me too). I am personally hoping that Sente and Papers add scribbling support at some time, since for me scribbling is not so important to justify changing the workflow to include another app. I am too much a fan of PDF management systems. But everyone’s needs are different, so if you find your way of combining Sente with a scribbling app, please let us know!

      Quick note though about your iPad comment: I would make my decision on whether to get an iPad 3 or reduced-price iPad 2 on the screen quality. As you probably have read on the rumours pages, it is likely that the iPad 3 will have twice the screen resolution as the two generations before. In my opinion, a better screen will by far outweigh the maybe $100 difference in price if one of your main uses of the iPad is to read PDFs. I will be very tempted to upgrade, as reading PDF articles in full screen right now is a little pixely on my veteran iPad 1.

      Thanks for commenting, come back soon!

  3. Shakirt says:

    God iPad 2 few days ago and found some useful apps for myself for working with notes and documents. These are ReaddleDocs and NotesPlus. Both of them can make annotations in PDF files. Bud if ReaddleDocs is more like GoodReader and is perfect for organizing files, BotesPlus is good for making researches.

    • Jo says:

      Hi Shakirt,

      I also like NotesPlus, maybe this is a post at some other day. Will check out ReaddleDocs, thanks for pointing that out!

  4. Randy says:

    Thanks for the review and article. I didn’t understand why you said you did not think writing margin notes with a stylus on a PDF is useful? I am an attorney and that is one of my main goals; however what I want is to be able to highlight text in a document, make handwritten notes (using a stylus) in a text box that links up with the highlighted text; and have some kind of character recognition to translate the handwritten note to text. I’d like to be able to export the result to some kind of PC-readable file, even if it is just the highlighted text and the note excerpted into a Word document with a page reference. Does anything like this exist? Is this what you were talking about with the “sticky notes”? Thanks

    • Jo says:

      Hey Randy,

      I came with pretty much the same idea to reading PDF articles as you just described. But if you think about it, this is an analogue workflow applied to a digital device. I am not aware of any app that lets you use a stylus to make margin notes AND THEN OCR’es the handwritten notes into machine-readable text.

      Instead, it is much better to use “sticky notes”: these are typed comments that can, depending on the app you use, either just float around in the document or can be assigned to a particular text segment. The drawback is that you have to type, which might not be your “thinking style” (some people like to think holding a pen in their hand), but on the upside you can view all your comments in a single spot (e.g., Sente). If you have a third-generation iPad, you might be even able to use the dictation function for making these notes, depending on whether dictation works for you (e.g., how long your notes are, whether your pronunciation is recognized by the OS).

      If you are Mac based, Sente might be interesting for you. It is developed for academics, but the way you can add comments to certain text passages might also work well for you. If you need to view your comments on a Windows PC, then you can check out Papers (now also for Windows), iAnnotate, and PDF Expert. I know from iAnnotate (I use this one too) that the comments can be viewed in any other PDF viewer.

      Hope that helps, let me know if you have more questions!


      • Jag says:

        Hello Jo
        Great piece! I think the ability to write in margins would be a powerful feature, as it mimics how we mark up paper-based articles. As you point out, the challenge is that these notes aren’t machine-searchable. Though if that’s not essential (e.g. grading student papers), I’m wondering, is it still possible to hand-write in margins with an ipad 3 with stylus? Practically the hand-writing would need to be clearly reproduced on the doc, and also there can be problems with not enough margin-space to write in because of the layout of the doc (& esp. a pdf).

        I know all this points to using sticky-notes, but inquiring about your experiences of actually hand-writing in margins and whether an ipad lacking an active digitizer can do it well enough. (On Win-based PC, hand-writing can be translated real-time into text to fill comment boxes, though it still can involve making time-consuming corrections).

        Thanks for any feedback.

        • Jo says:

          hey Jag,

          That depends on the app. Sente and Papers can’t, but iAnnotate and other apps as mentioned in the Allrounder category will work OK for this. It won’t be the same as on paper though, because you probably won’t be able to write as narrowly on the iPad as you can on paper. At least I found this method to be less effective, so I gave up and transitioned to sticky notes.

  5. blankblank says:


    Great article – thank you, and well-done. As you say, this seems to be the most handy thing on the web to adress a lot of our concerns. There are a couple of issues that I face, that I am sure others also face, and which would be great to see addressed if you are following up in the future.

    I use a PC for work; this will not change, and I can’t easily change. It seems that ipads are going to be much easier on the eyes than the competition.

    – Is there a way use a papers-like system that can work with/synch with a PC. And/or, accepting that interface with a PC will be ‘clunky’, which is the least bad system?

    – Doesn’t Mendeley have an ipad version now? How dpoes it compare to the competition that you address?

    – During the process of writing this comment, I have seen that they have recently released Papers for PC. How far behind the mac version is it, and how easily does it interface/synch with ipad?

    I may even constitute a user-type, but I’ll leave the naming up to you,



    • Jo says:

      Hey Andy,

      Good you found the Sente for Windows article! That would have been my first suggestion as well. Right now, Papers for Windows is still in pre-release, and I don’t know when version 1.0 will hit the market. As the chart in the Papers for Windows post shows, the pre-release version is still lacking highlighting and iOS sync. In other words, the gap is pretty large. I am sure that mekentosj (the developer) is working hard on this, and I hope that they will bring highlighting also to version 1 (it wasn’t implemented in the Mac version at the 2.0 launch, though,… so I have my doubts).

      Anyways, in your situation Papers is the best bet I think. You are right that there is Mendeley, but its feature set and user interface is so poor that I didn’t even include it as a possible candidate in my Papers vs. Sente face-off series ( Mendeley is a free software, which is great, but it also means that the development is often a little slower.

      If you try out the Papers pre-release version, please give us a shout (or drop me an email) how it works for you. I am sure that others would be interested in that as well.

  6. blankblank says:

    just saw your link to papers for windows; perhaps that caetgory typeshould refect this !

  7. francesco says:

    Hi all,
    I agree, this is the best article ever!! I finally begun making sense of the mess. I am midway between the 2nd and the 3rd profile (actually I am a bit of the first as well, I HATE spending money on applications).
    I use a pc at work, at the moment with endnote (I may consider switching to papers, maybe in a couple of releases?)
    I just bought, yesterday, a very expensive (64gb!!) ipad, with the objective of storing, cataloging, but also annotating all my papers (I dream of my desk empty like in a furniture store).
    This is what I would do, but I’d like feedback to make sure I am not asking too much to the programs currently existing:
    - install goodreader (no doubt there, large consensus on the fact that it is the best pdf annotator) to annotate the paper
    - Use a PC management software (say endnote for the moment) to organize, tag, categorize etc my papers.
    - synch trough dropbox.
    What do you guys think? Does it make sense? And crucial question, are the papers physically on the ipad as well? The day I go in a no wifi area, will I still be able to open and annotate the papers? I have the feeling that no, that the dropbox app only indexes content, and actually downloads the paper only when it is selected. If yes, the ipad will never be autonomous. And if yes, I need to find another sync method, that actually STORES the papers on the ipad as well. Any hint as of a), whether I got it right; b) what could I use to sync an ipad with a pc if not dropbox?

    Thank you guys, and again, Jo, great post! It really made me understand better what direction should I take. Before reading you I would not even be able to know what to ask :-D

    • Jo says:

      Thanks for the kind words, Francesco. I am glad I can help.

      About your workflow: that makes sense. I can’t speak about Goodreader, as I am using iAnnotate (if not Sente or Papers), which has good annotation capabilities as well. Syncing with dropbox on iAnnotate works great, and you can store the files locally on the iPad. In order to see your annotations on the PC, you would have to sync them back to dropbox though.

      Switching over to Papers at one point might let you access all your previous annotations if you bake them into the PDFs, but you won’t be able to edit them later on. My intuition is to rather take the jump now. It would be a little bumpy in the short run, because Papers for Windows isn’t in full release yet, but long-term you would have a stable solution. And you would be able to edit all the annotations you are doing now later on.

    • Leslie says:

      Hello Joachim. Thank goodness for your work here. I’m an academic down the highway from you and I am trying to implement a workflow system. (I have spent far too much time reading/researching online, and need to make a decision!) Like F before me: PC laptop, iPad 3, iphone and dream of the fully integrated system that does everything, and need to work offline and collaborate with others. I haven’t invested in any productivity apps yet, (paralyzed by too many choices), I use google docs just to engage in co-authoring, in reality , I am starting from scratch. If you were starting from point zero: what would you recommend as a system of 1) (annotation/reader tool), 2) PDF / file management and 3) synching/collaboration/storage,, with a Pc desktop to which i must remain faithful. As asked earlier, am I asking too much?

      I would greatly appreciate your insight, but I don’t want to take you away from finishing your dissertation! :-) best, Leslie

      • Jo says:

        Hi Leslie,
        Answering your questions in depth would be three posts or more, so I hope its okay that I don’t go into too much detail here. In your situation, given that you are linked up with a PC, I would recommend:
        - Papers as an annotation / reader tool. Papers for Windows is still in beta and lacks iOS sync I believe, but long term this will be a good choice
        - Either Dropbox or Sugarsync for file management and syncing. If you consider signing up for a paid account, I am inclined to say sugarsync might be better. Check out, and please use the links there so I can get a little bit more space with them :-)

        Where about down the highway are you? Toronto, Ottawa?

        • Leslie says:

          Utoronto :-)
          Thank you for the advice! Apps etc in place, now to change my behaviors and habits!
          Hope to be paperless soon! Merci! Great site, btw, I passed it along to UT librarians. L

  8. ranjeev says:

    What about reading and annotating djvu files? Is it even possible on an iPad?

  9. Korien says:

    Thanks for a great post and please forgive if I ask questions you have already answered. I am a PhD studet and like a number of other people at the start of setting up a paperless system. I want to buy an iPad mostly because I have seen with friends that it is much better for reading than my PC (Mac again very expensive). There are some challenges in South Africa, specifically that Internet access is very very expensive (I’ve just resigned my paid job to study, so must watch the budget) I started using Mendeley at the beginning of the year and was very disappointed to see the bad feedback about their app.
    I have read all the comments, but still want to ask:
    1. Will I need a “big” (i.e. 64GB) iPad? Or will a 16GB do? (Again a BIT cost difference between them)? Does the apps you talk about store the files on the iPad?
    2. Will I be able to sync the iPad and my PC directly (i.e. without having to send data via Internet – the cost issue I talked about)? I want to have the annotated .pdfs back on the PC (old-fashioned maybe:-)
    I will read your other posts as well.
    Thanks in advance,

    • Jo says:

      Hi Korien,
      Thanks for your comments! Mendeley hasn’t had a decent iPad app (read: with an annotation workflow) last time I checked, so this won’t help you much in your paperless workflow with an iPad. With a PC as your other computer, Papers is the best bet for you, since they working their way into the windows world.
      Papers (and all other apps described in this article) will save a copy of the PDF on your iPad, so it is always with you even without internet access. Also, Papers syncs via local WiFi or via cable and iTunes, so no internet connection required for exchanging PDFs between iPad and PC. In order to have the annotated PDFs back on your PC (not old fashioned at all), you will need the Papers Windows app though (that is, if you use Papers. Different story for the All-Around Reader apps). I think the current Papers for Windows beta is still freely available, so you can find out if this is for you.
      About your iPad size question: The PDFs you store on your iPad won’t eat too much space. I think unless you are into storing videos or lots of music or photos on your iPad, you won’t need 64 GB. I have a 64 GB first-gen iPad, and I have free space after using it for more than 2 years. My preference is 32GB, but I am sure it is possible to live with 16GB, especially when you define the iPad as a tablet for work. Check out this post:
      Best luck!

  10. CaptSolo says:

    Thanks for a nice summary. Text-based highlighting is essential for me and the table clearly showed that only paid apps do that (a bit inconvenient as you can not know in advance what you are gonna get).

    Good that it’s not the case any more — the Adobe Reader is available for iPad (for free) and has all the functionality you’d expect. Might be a good idea to add it to this guide.

  11. Jerrey says:

    Which app allows printing afterwards?

    I still prefer phyiscal printed paper when revising for exams, but seems i have an ipad3 i was thinking of first scribbling and annotating my notes digitally first then save them and print them at the end of each chapter that way it would be much neater

    • Jo says:

      My understanding is that printing is part of iOS. So you can print out your annotated pages from every app.

    • Shirl says:

      Jo – are you talking about airprint enabled printers? they are listed on the apple store and yes you can print directly to them from ipad or iphone etc
      or another option is an app, sadly writepdf is not mentioned here, not only do i use it to direct edit my pdfs from the cloud but also to print to my hp ;)

  12. Wow, superb blog layout! How long have you been blogging for?

    you make blogging look easy. The overall look of your website is fantastic, let alone the content!

  13. Mark says:

    I just came across your blog (nice job!) and can add a few points and desires based on my experiences as a university professor.

    My current workflow is with BookEnds on the Mac. All of my pdf files sit on a folder in DropBox, while my BookEnds database sits on Dropbox as well. The benefit of this is that I can work across many Macs and, so long as I keep only one BookEnds database open at a time on one Mac, can keep everything current. On the iPad, I’ve been using PDF Expert for annotation. I have found this app to be great at working with large documents, DropBox syncing and annotation features. However, I am still confused about how / if I can really get an annotated PDF from this app back to my Mac in a way that I can edit the annotations that I made on my iPad. This is a HUGE limitation if not possible, and something that a lot of users will want to consider. In many cases, I don’t want to distribute a marked up PDF file to a class, so it would be great if I could duplicate the PDF on my Mac and then remove all annotations for distribution. What we really need is one developer who can come up with a Mac desktop AND iPad PDF editor to allow for seamless use. PDFpen is about as close as we can get to this, and I have heard that their iCloud syncing is pretty slick. With that said, annotating in PDFpen on the Mac feels really clunky and is not as streamlined as other editors.

    On another note, you mention in your table that BookEnds on Tap syncs via “ cloud syncing through Bookend’s server.” Unfortunately, this is not correct. At this time, BookEnds on Tap only syncs across WiFi. Syncing databases across iCloud has turned out to be a developer’s nightmare (note that apps like Devonthink and Yojimbo have not figured out how to do this yet and Yojimbo worked quite well across MobileMe before that plugged was pulled), and most developers are better off to offer dropbox syncing (with the caveat of conflicts mentioned above) or better yet, a webdav service of their own.

    I will end this with a bit of a warning. If any readers are currently graduate students and considering staying in academics, really take your time and consider how you will move to a paperless workflow. The further you get in your career, the less time you will have to futz around with new software. Likewise, as your database gets larger it can become a lot harder to deal with moving it over to a new app or platform.

    • Jo says:

      Thanks for sharing your workflow, Mark. I definitely agree with you on developing digital workflows, not only with respect to journal articles, but also about all kinds of information management. Thats a big topic here on academiPad as well.

  14. William says:

    In prep for going back to school (embarking on a new journey, very excited!) I found your site and have been brought back to it several times as I ask questions of the Google-machine. Thanks for all the great information, it’s very useful coming up to speed on what technology is out there, given I’ve been out of school for quite a few years. Many thanks!

    A note about Dropbox, you mentioned you only get 2GB free – I went to SugarSync, where you get 6GB in their free account for just that reason, but recently I discovered there is a way to get up to that same amount of free space on Dropbox by performing some simple tasks – here is the article I read (it’s not mine, I just used the suggestions and now have 5.9GB of free space from Dropbox), It doesn’t take long at all before you perform the easy tasks and get a big bump in free space, highly recommended!

    Again, thanks for all the great info and advice on here.

    - William

  15. Kim Flintoff says:

    Not fond of the “penny pincher” comments t- they come across as cynical and smug and ignore the plurality of contexts in whihc people can be using ipads – there are a lot of kids in school who are provided with an iPad for use in class – free apps are their lifeline to quality learning opportunities…

    • Jo says:

      Hi Kim,

      Thanks for voicing your concerns. I think you have a valid point there, and have thus changed that section of the article.

      It was also a good chance of adding Adobe’s free PDF Reader to the list of good free apps.

      I am confident that you will find the current form of the article to be more inclusive.


  16. Some valuable and useful research has gone into this ‘blog’ which doesn’t even read like one! Love your work Jo and have added you to my favs – and always link your info to my academic social network ‘Yammer’ – thanks again! Maria

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  18. Steve says:


    I may have missed this piece but what I have tried a couple of apps to annotate and then am not able to search on the text notes I have made… it sticky notes or floating text in the margin….

    What are the best apps for that? Or is this a function of the document management app?


  19. Chris says:

    Great article but I think one thing’s missing in the comparison. I’ve spent better half of the last year or so trying (well… not very hard perhaps) to find an app that would allow for searching in annotations (and/or bookmark names) across many pdf files rather than inside a specific one.

    In my workflow I might add a couple of bookmarks (or annotations) with a specific title/text to a number of pdfs and need be able to find them at a later point (tagging would not work because I also need to be able to go to the specific page within each file where the annotation was made).

    Hope you can recommend an app with that kind of robust search. .

    • Jo says:

      Hi Chris,

      I know that Sente can do this. It won’t find search terms in text (yet), but if you highlight something as a quote or add a comment to a text selection, you can find this section in a global search (using a word that it is the comment or quote). This way, some form of page-based and even line-based tagging is possible.


  20. steve gartner says:

    What about Notability. I really like it and it’s very usefull for annotations.

  21. Amarendra says:

    How do I move across different annotations ?
    Say I have a big document and like to read only annotations.
    Thanks for nice article.

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  25. wole says:

    Hello Joachim.I am in love with your articles! Only God knows how much effort you must have put in .I am an engineer and a medical student that needs your advice on whether I shoould buy an ipad or blackberry playbook . My major need is taking notes during classes ,drawing and annotating ,especially lots of anatomical diagrams, and reading and annotating (jotting on )my ebooks ( mainly pdf files ). I am not much of a gamer but I do watch movies .I would also want to ask a question on the issue of palm sensitivity of screen which makes people loose written materials on a page,how do you prevent or overcome palm must not touch screen when writing issue? Please , can ipad 1( cheaper) be used for this purpose ? Thanks .

    • Jo says:

      Hi Wole,

      There are a couple of ways to prevent accidental palm input. None of them is really good right now. First there are many note taking apps that have some palm rejection function. Penultimate does this on the fly (and you can tweak it by telling how you normally hold a pen), but its not working all the time. Other apps can pull up an area where to rest your hand, but I find this quite cumbersome.

      Then there is the hardware fix: You can wear a glove for drawing sessions or put a micro finer cleaning cloth under your wrist. This is even more effortful.

      So right now, we are stuck with accidental hand input. There is at least one stylus solutions right now (iPen, I believe), but it is very expensive, requires to put in some accessory in the cable port, and is slow in response time. In the near future, when bluetooth 4 styluses become more prevalent, there should be some advancements in making scribbling on the iPad a more pen and paper like experience. Right now, it is not. See more info here:

      • Jag says:

        Re. active styluses, you mentioned in your post linked to, the Pogo, appears to be properly released now. Great if you can review it!

        • Jo says:

          I personally are more interested in trying out the soon to be released Adonit palm-rejection stylus. once this one is out and I find time to review it, I will surely post it here. I am using the flip now and the adonit type tip works well for me

  26. Definitely happy I stumbled across this blog today has cheered me up quite seriously

  27. Jon Stephens says:

    Also check out Explain Everything – it’s a recorder tool but has pretty robust import/export & annotation features.

  28. The next time I read a blog, I hope that it won’t disappoint me just as much as this one. I mean, I know it was my choice to read, but I actually believed you would have something helpful to say. All I hear is a bunch of whining about something you can fix if you weren’t too busy seeking attention.

  29. An impressive share! I’ve just forwarded this onto a co-worker who has been doing a little homework on this. And he in fact ordered me breakfast simply because I found it for him… lol. So let me reword this…. Thanks for the meal!! But yeah, thanks for spending time to talk about this topic here on your site.

  30. ACFELLNER says:

    I am a narrator and record books for a few different outlets.
    I read my scripts from my iPad, and the scripts usually arrive in PDF form.
    To keep characters and voices straight, I need to sometimes place the name of the character in the margin so that I can quickly recognize whose voice I need to use.
    What annotating system would you suggest for that purpose?
    Thanks in advance.

    A C Felner

  31. Ur post, “The ultimate guide on how to annotate PDF files on the iPad” was well worth commenting on!
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  32. Theo says:

    Hi Jo,

    First thank you for all these very clear and helpfull informations for a Mc dummy like me. I bought yesterday my first Mc device (Ipad4).

    However there one info i find nowhere. I am looking for an app which is doing the following special tricks with pdf files:
    1) With an Original pdf file: annotate (underline, highlight, posts, etc…easy), edit annotation list (classify per type of annotation, for each annotation indicates page number, possibility to select and modify annotations,etc…) and export annotations (in pdf file for example). One example can be: with a study book, i annotate all the formulas and sentences i am interested in to learn, i export it in a file and magic i have my learning document ready and can print it, and may be bring it to the exam…;-)
    2) The same than above but with a pdf file done by scannning a book. This i think more tricky.

    Did you heard about some apps that can do this? I watched the videos of apps you advice for but these tricks are not shown.

    Thank you for your help, and one more time congratulations for your blog!

    Theo from Paris

    • Jo says:

      Hi Theo,
      That is quite specific. The closest thing that comes to my mind is Sente. It won’t export your annotations into a special file or book, but it lists them up front on the cover of the file.
      There might be a better solution, but I don’t know it.
      That won’t work with a scanned book, though.

  33. Herfried Hartl says:

    Halli Hallo, bin auf der suche nach einen App für mein IPad II zur
    Notenverwaltung – ca. 500 Titel
    (auch3-4seitig) wichtig ist mir eine flotte Suchfunktion für live Auftritte.

    Vielen DANK im VORAUS.


  34. Ehud says:

    Thanks for the professional review.
    I downloaded PDFpen. The first look is impressive but then, after about an hour of work, it saved the file. The process took few sec and at the end I saw a brief msg “save failed, aall changes are lost” and indeed they were lost forevever. I tried two more times and for the same outcome (stupid me, I could have predicted that).
    I wrote the PDFpen guys and hope they can find a way around this bug. But as it is now, PDFpen is absolutely useless for me.


  35. Rohit says:

    Hi Jo,
    Thank you for a very informative article.
    May I request you to please help me with the following queries:
    1) I believe you are using multiple apps – iAnnotate, Sente etc. Are the pdfs portable between these apps. If they are, do the annotations, highlights, etc. also remain intact when the pdf is opened in a different app.
    2) You also touched upon the limited storage capacity on iPad. So, if I remove my older pdfs from ipad to accomodate the new pdfs, what happens to the annotations, highlights on the older pdfs….where are these stored and can these we used again seamlessly.

    - Rohit

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  43. thintieguy says:

    I appreciate this article. So far, I have not found exactly what I am seeking. I want to find the fastest, most intuitive way to annotate a PDF with straight lines in a graph format that looks a bit like economic charts. The purpose is to show above a written text the shape of a melody for those who cannot read music. My problem is that the best solution I have found is using my iMac and painstakingly make this kind of graph with Wondershare PDF Editor. Stuck using a mouse, I get cramps in my right hand very quickly and would much rather have a system where I could do this using an iPad and a finger/stylus (I’ve not yet purchased one but would do so if only to accomplish this single task). Also, Wondershare only lets me use straight lines in one thickness and in red (a BIG hassle). Any thoughts out there?

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  54. George R says:


    I must say I don’t fully agree with the author about handwritten annotations. Yes, they don’t show up in searchable form in the list of annotations. However, together with text notes they present extra information at a glance when you are skimming through the PDF you once read. I personally find it extremely useful, though it very much depends on one’s workflow and diligence in making self-contained notes for each paper they read.

    The inability to add handwritten and textual notes as well as shapes has been one of the things preventing me from switching from GoodReader to Papers. The other thing being that I really appreciate Android OS and did not want to commit to an iOS only app.

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