Start loving to organize your PDFs with Papers for Mac

Papers 2 for MacThe best apps offer a simplistic and beautiful interface that allows people to use the software in an intuitive way. Papers by mekentosj is one of these apps: Through its iTunes-like interface, Papers allows you to organize and annotate your endless collections of journal articles in an easy and fun way.

This post is part of a series exploring the two leading PDF management systems on the Mac and iPad: Sente and Papers. Previous posts have explored the benefits of PDF management systems (in comparison to stand-alone PDF readers) and offered an in-depth review of Sente for Mac. The current post checks out Papers, following the same structure as the Sente for Mac posts: it introduces the Papers ecosystem, reviews how you can add and annotate references, and briefly talks about how you can insert in-text citations and bibliographies into your write-ups.


Overview of the Papers ecosystem

Papers is available for the Mac ($79, students can get a 40% discount) and as a universal application for both iPad and iPhone ($15).

You can sync your library across devices every time your iPad and your Mac are connected to the same wireless network. Some university’s wireless networks won’t allow for WiFi sync, in which case you can create your own computer-to-computer network through your Mac’s Wi-Fi icon in the menu bar. Linking your iPad to this ad-hoc network does the same trick.

Papers Ecosystem

Paper's ecosystem includes apps for the Mac, iPad and iPhone. You need to be on the same wireless network though in order to sync your library across devices.


The benefit of this WiFi sync is that Papers will sync pretty much everything between the Mac and iOS version, including your smart folders and manual collections (see below).

However, the downturn with WiFi sync is that both devices must be in the same network. If you, for example, are rushing to the airport and had no time (or forgot) to sync before you left, you won’t be able to read that latest article that you have left on your Mac at home. Also, you won’t be able to easily share your library with co-authors from different universities, as sharing a library pretty much requires to be in the same room or, at least, campus.

The main window: iTunes for PDFs

Once you open Papers for the first time, you quickly see why it has been dubbed the iTunes for PDFs. You are presented with a clean and playful interface that consists of up to four elements: The library list that shows you all your papers and your collections, your articles view as a list, a cover-flow or preview of your PDFs, and an inspectors plane holding some info about the article, notes, reviews, and supplements.

Here is a look on Papers’ main window (click on image to read short version of this post):

Its beautiful and simple design has earned Papers the title of being the "iTunes for PDFs"

Its beautiful and simple design has earned Papers the title of being the "iTunes for PDFs". The great strengths of Papers is its flat learning curve and its convincing Magic Manuscript workflow through which you can cite papers without touching the mouse.


You can read PDFs in Papers either in their own tab or in the fullscreen reading mode. Unfortunately, it is not possible to drag tabs into their own windows in order to read multiple PDFs side-by-side. However, you can at least re-arrange the open tabs, which makes it easier for you to switch from one article to another.

Reading an article in the Tab view of Papers.

One way to read your articles in Papers is to use the reading tabs. You can highlight in here and assign keywords and notes. One good feature is that you can re-order the reading tabs, so it is easier for you to browse through them. However, you cannot de-couple the reading tag from the main window to read two or more articles side-by-side.


Paper’s has done a fine job in offering a dedicated fullscreen reading mode in addition to the reading tabs in the main window. The fullscreen reading mode gets rid of most user interface elements and lets you fully focus on the current article that is displayed against a grey background.

Fullscreen Reading Mode on Papers.

The fullscreen reading mode allows you to focus just on a single article at a time. You can add annotations and notes while reading fullscreen.


Adding references to your database

Papers lets you add any file to your reference.

Papers lets you add any file to your reference.

Like Sente, Papers lets you add a host of different references to your database, and it will attempt to identify the papers you are adding by matching them with online repositories. In most cases, this works fully automatic, but even matching the paper yourself often doesn’t take more than three clicks with your mouse.

Besides dragging existing PDFs into your Papers library (or onto the Papers icon in the dock), you can also add papers by open your library website or pages like google scholar from within Papers. Any papers you download from here will end up in your “Recent Import” inbox, from where you can match the paper. Papers will warn you if you are adding a paper that already exists in its database.

One nice addition that was included in the release of Papers 2 is Supplements in the inspector plane. You can simply drag any file into the target area to attach it to the currently selected article. This might be very useful, for example, when you want to keep sketches, reviews,  or data files together with your or others’ publications.


Organize your library with collections

Organizing your articles is one of the task where PDF management systems leave stand-alone PDF reading and annotation apps in the dust, as in PDF management systems you can associate one and the same file with as many different collections as you like. Papers goes a slightly different way than Sente in how it wants you to organize your library, making this task one of the main differentiators between Papers and Sente.

Papers allows you to organize journal articles in a hierarchy of manual collections.While Sente gently pushes you towards organizing your library via tags, Papers is much more okay with you using manual collections to sort through your articles. You can create a hierarchy of collections and simply drag all relevant papers into the collections that are relevant. Again, these can be as many collections as you wish. Papers will even list the collections each paper is associated with in the context menu of each reference as well as in a column of the library list.

Papers is able to sync these manual collections (unlike Sente), so it is perfectly okay to use them. In fact, because Papers is only able to make a hierarchy of manual collections, but not of smart collections, manual collections are the best way to organize your library in Papers.

Of course, Papers also lets you create smart collections based on all kinds of attributes (e.g., journal, flagged, rating, notes, and keywords). Keywords is the Papers name for tags, but unlike in Sente, it is not possible to assign often used tags into a hierarchy of tags. Instead, every keyword you have ever assigned is offered you in a list which soon becomes very difficult to navigate.

Papers lets you assign keywords to individual articles.

Papers lets you assign keywords to individual articles. However, you cannot organize your keywords into a hierarchy.

These two factors combined – the ability to sync manual collections and the inability to sort keywords into a hierarchy – makes manual collections the best way to organize your Papers library.


Papers’ long and winding road to annotating PDFs

Before Papers 2 came out, being able to annotate on the Mac version of Papers was a often-uttered wish by its current and would-be users, especially since the iOS version of Papers Touch has offered a decent annotation workflow for quite a while. Disappointment was great among Papers fan when highlighting didn’t make the cut into the Papers 2.0 release, but the guys at mekentosj soon after added annotation support in the Papers 2.1 release.

However, annotating on Papers for Mac is still somehow a long and winding road, especially when compared to Sente’s top-notch annotation workflow, which is surprising giving the normally polished feel of Papers.

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Annotating on Papers for MacChanging the color of a highlighted passage in Papers for MacIn order to highlight a passage of text, you need to select the text and chose “Highlight Selection” from the context menu. If you want to change the color of the highlight (Papers will use the same color you have used last time), you need to open up the context menu again and choose the new color in the “Change Highlight Color” part. There is no separate annotating menu or floating box that comes up, which makes annotating on Papers a somehow interrupting experience.

Tip: You can use the keyboard shortcut “Control+Command+H” to somehow streamline your annotation workflow, especially when you are working with BetterTouchTool, one of my favorite Mac OS tweaks.

Besides highlights, Papers lets you add sticky notes to your text and overall notes to your reference. It is not possible to assign different colors to your notes, and there is no dedicated notes plane which shows you all your notes in one spot.


In-text citations and end-text bibliographies

Even if the annotation workflow is a little disappointing, Papers surely made a big leap forward when it comes to how you can add citations into your writing projects. Its new Magic Manuscript function lets you insert references to your documents pretty much without leaving your keyboard. As you would expect, Magic Manuscript works with pretty much any application that accepts text inputs.

In order to bring up the Magic Manuscript dialogue, simply press your Control key twice and start writing the name of the author you wish to cite. Papers will offer you a list of matching references, and you can simply select and insert the desired reference through with your keyboard.

Papers Magic Manuscript

Papers' Magic Manuscript allows you to insert references into your writing projects without using your mouse. You can search for the paper you want to cite by its author, name, or keyword.


You can also select multiple references and insert them all at once. Regardless how many references you have selected, Papers will insert a citekey at your current position that will look similar to these ones: {Scholz:2011df, Scholz:2013ff}. You can also customize how citations are displayed in the text by adding citation modifiers that add a prefix, suffix, or page number, and of course you can choose to suppress either the author or the year (see the Citations Modifiers post in the Papers Knowledge Base for more info).

Adding the bibliography at the end of your document is also easy and painless. Simply open up the Magic Manuscript dialogue again and choose “Insert Bibliography”. The dialogue will notify you if any citekeys cannot be resolved. Once all your citekeys are clear, you can chose “Format Manuscript”, which will open up a new, formatted document.

As you would expect, Papers follows citation guidelines (e.g., changing from “Scholz, Smith, and Mitchell 2013″ to “Scholz et al. 2013″ after the first citation), and you can select what citation style you want to apply from an impressively long list of built-in formats. Also, Papers offers you a free serial number if you send in a new citation style. So download the trial version and get busy!

I must say that Papers did a fine job with Magic Manuscript. You don’t even have to remember who wrote the article, as you can simply type into Magic Manuscript a keyword or what you believe might be in the title, and chances are good that the reference you are looking for is popping up.

However, Papers will make your life harder if you just want to insert citations on your own. It is a miracle for me how Papers picks the letters behind the year in its citekeys, and I haven’t found a way to customize the citekey (e.g., to use abbreviations for your favorite papers, such as KH04 or LTG10). Simply typing in {S11} or {Scholz:2011} won’t be resolved, so unless you remember the actual citekey you will have to use Magic Manuscript.


Wrapping up: bonus features and shortcomings

Papers 2 IconPapers for the Mac is a beautifully designed application that offers you a tightly integrated ecosystem for organizing and annotating your PDFs without burdening you with a steep learning curve. The user friendliness is really one of Papers greatest advantages. Beside the iTunes-like take on PDF management, you will also find a ton of video tutorials online that give you a step-by-step introduction of how to use Papers to its full potential.

Papers also offers you a couple of other things that Sente, Papers closest competitor in the race for the best PDF management system, is lacking. Papers has scanning functionality built-in (including OCR support), and it attempts to mimic Mendeley’s social network features through its Livfe feature. The latter lets you share and discuss your favorite papers with colleagues, friends or the whole wide world. I haven’t tested any of these two, but they might be an important reason in your own decision what PDF management system you are going to get (you know you want one).

While Papers is doing a lot of things right with their version 2.1 release (after a rather bumpy version 2.0 release), there are a couple of things that I would like to see improved upon. Although it is nice that Papers allows you to re-order your reading tabs, it would be even nicer to de-couple reading tags from the main window so that you could read two or more articles side-by-side.

Neither Sente nor Papers allow for side-by-side reading.

Unfortunately, neither Sente nor Papers allow to open references in their own window to read them side-by-side. Standard PDF viewers such as Skim let you do this, and it is a great way to justify to yourself buying that larger screen you really only need to watch movies on. I hope a window view will be added to Papers and Sente sometimes in the future.


While the missing side-by-side reading feature is a common oversight of PDF management systems, the biggest disappointment for Papers is its somehow choppy annotation workflow. Using the context menu for adding and changing the color of highlights is just too disruptive to your reading flow. Also, there is no way to customize the highlighting colors (if you are using orange or red as a color code, you are out of luck), to assign colors to notes, or to view all your notes at one single place.

There is some hope though that Papers will continue to improve on its annotation workflow, and maybe it could even take some clues from the annotation workflow offered by Sente or from how annotations are done on the new iBooks textbooks.

Overall, Papers is having a good run with its Magic Manuscript function and simplicity of use, and it is a promising candidate to become the centerpiece of your Read-Annotate-Cite workflow.

But before you go out and buy Papers for Mac ($79) and Papers Touch for iPad ($15, iTunes link), read more about the iPad apps of Papers and Sente, as well as the big shoot-out between Papers and Sente. And to stay up to date with all your other Mac and iPad related needs, please subscribe to the RSS feed, to the email subscription, or to my twitter account in order to hear about updates.

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Next, I want you to do three things:

First, check out the other post on Sente for Mac, if you haven’t done yet.

Second, download the 30-Day Trial versions of both Papers and Sente and get busy! By the time your trial ends, this mini series on PDF management systems will have come to an end as well, and you will have all the information and first-hand experience you need to pick your favorite ecosystem.

Third (if you have 10 seconds), please share this article with your colleagues and twitter followers. I know its a shameless plug to advertise my blog, but it is easy (there are buttons for this below) and would be a huge help and motivation for me to keep writing. Thank you! :-)

Disclaimer: The developer of Papers granted me a review license for Papers for Mac upon request. Featured image by, Papers ecosystem and the Magic Manuscript images from mekentosj. All other images by academiPad. Please consider sharing this article if you found it useful.

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  1. Pedro says:

    man how i wish they would set hierarchical tags on papers2!!! ive been writing to support asking if they have something in view in their road map that will support hierarchical tags but still no response. Do you know anything about it??

    cheers from Argentina, Pedro
    p.s: big fan of your posts here, its been great help!

  2. Mike_B says:

    Just want to add on the nonexistent support, no response for weeks and, yes, my question is in a private discussion in which only I contribute. We have been testing different software for our research group and “Completely nonexistent customer support” is now added on the Con side for Papers.
    And the inability to export annotated papers outside of the Papers universe with annotations.

  3. TJ says:

    Your review is very good and the program worked just as expected, BEFORE it was rewritten to Papers2. I was mac user of Papers 1 program. Now I moved to Windows and bought upgrade license for Papers2 and what a disappointment. Its super buggy (and they take pride in total rewriting of the program). The support is pathetic and almost all the question you ask them are made PRIVATE so that you have no clue what other users are asking or complaining. I have 4 questions open within last 2 months and no answers. I agree the questions are critical (i.e. not applauding their program but very civil).

    I use laptop with i3 processor with 4GB RAM on 64-bit Windows 7 and the program uses upto 1GB of RAM at a times. I can work with photoshop much faster than Papers2. Its very very slow. I have about 1000 articles in my library and its frustrating. I never had this problem with with Papers1 on Mac.

    Now that they are acquired by a big scientific articles publisher, I don’t think they give a hoot to your complaints. Keep an eye on open source program Qiqqa. Its not as polished but I hope they too get their act together and make it a pretty good program.

    I seriously loved Papers1 and encouraged everyone in the lab to purchase it. Out of 11 members 7 bought the license but now I doubt, I will recommend this program to anyone. If Qiqqa improves, I will abandon Papers2 for sure. I really wanted to love this program but at this moment, I am very disappointed.

  4. Harrih says:

    I am new to Papers, first impressions are promising. However, is it a fact that I can not see my higlights and annotations as a list, nor I can not export them?

    • Jo says:

      You can see a list of your highlights and annotations in the Notes plane of the Inspector. I do not know of any way to export the notes. Maybe contact the guys from mekentosj and see if they have a way or want to add one. Sounds like a good idea.

  5. Shaibelle says:

    I was actually an early beta tteesr for Mellel and was one of those who argued forcefully (and successfully) for allowing two sets of footnotes, such as found in the Aramaic Bible series. That being said, Mellel never quite worked for me. On the other hand, I have used Nisus since 1994 and if you search long enough you can find emails from me to the support group dating back to the mid 90s. NWP is the best environment I have found on the Mac for the kind of work I do. Again, to each their own (But I do most of my office work in Word for obvious reasons.)

  6. Hi Jo,

    Awesome review, and glad to see you like the app so much. To address your main concern, the choppy annotation workflow, are you aware that all you need to do to highlight a sentence is to hold the command (Cmd) key while selecting text? We don’t believe there’s any app out there that can beat the speed of this method. Same with notes, simply Cmd-double click anywhere in the PDF to create a sticky note.

    With regards to the randomness of the letter added to the inserted citekey, this is actually far from random. In fact, the whole idea is to create consistent cite keys that even work if you work with collaborators that happen to have inserted or imported their references in a different order then you did (in other apps this would lead cite keys like griekspoor2001a and griekspoor2001b to be reversed, most likely without you even noticing but potentially with disastrous effects). You can read more about these “universal citekeys” here:

    CEO & Founder

    • Jo says:

      Hi Alex,
      Thanks for bringing in some celebrity flair to academiPad, and thanks for all your good work with Papers.
      I can see that the command key could work for some people, but for me that is still one key too much to press. I used Skim a lot and always enjoyed just activating the highlighting mode and to highlight by simply selecting text. Are you guys considering to add a “highlighting mode” similar to Skim that could be toggled on or off?
      Your reasoning about the citekey makes sense. Its just that for the user it is hard to guess a citation if he/she does not know what citekey Papers created. No big deal in my opinion, as the Magic Manuscript is really fast. For those papers that I am citing all the time, I am sure I will pick up the two letters at the end very soon, anyways 😉

      • Dunia says:

        I’ve mentioned Sente on my blog breofe, it is indeed good software. One of the main differences between Sente and Papers beyond what you mentioned is that it is not a bibliographic manager, properly speaking. It does not work with a word processor to generate footnotes and bibliographies (though I think they may be working on this).One major lacking thing in Sente (for me at least) is that it cannot import a list of abbreviations into its journal dictionary. In our discipline, there are a whole wack of abbreviations that we need to work with for book series and journal articles. There is currently no way in Sente to import a whole list, you need to put them in one by one. I’ve asked the developer to address this, but another voice asking wouldn’t hurt (hint hint).For what it’s worth, Bookends is also working on an iOS app. Mendeley also has an iOS app I believe. And there are rumors of a Zotero app too. Sente, though, may well remain unique in its syncing of PDF highlights.

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