How to install Proteome Discoverer 1.4 on *ubuntu Linux 14.04 via PlayOnLinux

*ubuntu linux OS are frequently used in scientific research. However, commercial software to analyse data originated from mass spectrometry measurements often relies on Windows as operating system.

One of such commercial software is Proteome Discoverer (version 1.4) from Thermo Scientific. Although this (great) software is made for Windows, it is possible to install it via wine on Linux & I will show you how to do that …

First of all, we need Proteome Discoverer. Fortunately, there is the possibility to download a 30-days trial version from The download is about 147.5 MB (2015, March 15th) in size.

The next thing we need is PlayOnLinux. The developer describe it the following: „PlayOnLinux is a piece of software which allows you to easily install and use numerous games and apps designed to run with Microsoft® Windows®.

In *ubuntu Linux system, we get this software by opening a terminal and typing in:

$ sudo apt-get update

$ sudo apt-get install playonlinux

This will install a stable version of PlayOnLinux. If this version is to outdated for your purpose, please download the verification code (#1) and add the source to your reprository (#2)

$ wget -q „“ -O- | sudo apt-key add –

$ sudo wget „$(lsb_release -cs).list“ -O /etc/apt/sources.list.d/playonlinux.list

Afterwards, refresh and install it as described above. Afterwards, we can start the program via the terminal ($ playonlinux) or via your system start menu.

The main window of PlayOnLinux

The main window of PlayOnLinux

As shown in the image above, we first go to Configure & select to create a new Virtual HardDrive (see image below)

PlayOnLinux New Virtual HardDrive

It is important to use a 32-bit windows installation. For my installation, I used wine 1.7.38. This was one of the most current versions available at the point of writing. Principally, all higher versions of wine should work as well as 1.7.38. At the end, simply name the Virtual Drive.

The next step is to install some .Net frameworks. It may happen, that a mono feature request will pop-up.

Mono Installation Request

Luckily, the entire process of installing mono is straightforward and should finish without any issue. The next step is to activate your Virtual Drive and go to the Install Components tab and install Microsoft Framework 2 to 4. On vanilla *ubuntu system, you will get an error during the installation process.

PlayOnLinux Error Message

To „fix“ this problem, we need to open the terminal again an run the following command [see here for details]:

$ sudo gedit /etc/sysctl.d/10-ptrace.conf

This will open a new gedit window. In case, you do not have gedit installed, simply replace it with kate if you are running KDE. Then, set this option:
kernel.yama.ptrace_scope = 0

It is important to reboot your PC. Without restart, I still was not able to install Microsoft .Net framework software. After rebooting, start PlayOnLinux again and go back to the Configure tab and install the .Net frameworks. The installation downloads and configures the frameworks (almost) automatically.

After finishing these processes, we will install the Proteome Discoverer software. Therefore, go to the  install tab in the main window of PlayOnLinux. A new window will pup-up and select „install from a non-listed program“ in the lower left corner. The next two information are important:

  1. Leave the default location during the installation unchanged and
  2. Do NOT tick the tickbox „run the program“

Keep on by clicking „next“ until you have to chose which Virtual Drive to select. Here, please chose the Virtual Drive you have created before by choosing „edit or update an existing applications“ & select the Virtual Drive in the next step.

Edit or update an existing application

Edit or update an existing application

Virtual Drive Selection

In the next window leave all ticks unselected (that is „use another version of wine, configure wine and install some libraries„) plus select „32 bits windows installation“ in the next setup point. Browse to the installation file you downloaded before and go on by clicking „next„.

After some seconds, the installation window for Proteome Discoverer will lunch. In this case, I will install Version

Proteome Discoverer installation Window

The installation is identical to an installation on a windows PC and includes also the installation of „Microsoft Visual C++ 2008„. During the installation, you have to activate the software. Using wine alone (without PlayOnLinux), the activation always failed. To circumvent this problem, I used PlayOnLinux to run Proteome Discoverer on *ubuntu Linux.

If all goes well, you will receive a message, that the installation was successful. In order to create a shortcut to run Proteome Discoverer, select Thermo.Discoverer.exe as shown below.

Create a shortcut for the Thermo Proteome Discoverer .exe file

If you want to create a further shortcut, repeat the process; otherwise select „I don´t want to make another short cut“ and click „next„. The window will close and you will be redirected to the main window of PlayOnLinux. By selecting Thermo.Discoverer and clicking on run, Proteome Discoverer 1.4 will start.

The program works well on *ubuntu, as you can see in the next image.

PD running on Ubuntu Gnome

Although it is more than nice to see Proteome Discoverer 1.4 to be running on *ubuntu Linux (here Ubuntu Gnome 14.04), the program crashes if you try to export spectra. However, this is the only problem is recognized so far, which, from my point of view, is acceptable. All other functions, such as exporting the results to .txt or .xls files work without any problem.

I hope, this post blog was helpful for you to setup a Proteome Discoverer installation on an *ubuntu Linux system using PlayOnLinux and wine.


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