Visual Studio 2017

  • Skyline requires Visual Studio 2017 to build. You can have multiple versions of Visual Studio on your computer, but the only version that can build Skyline is Visual Studio 2017.


You can use this or any Git client you like, as long as it provides C:\Program Files\Git\cmd\git.exe

  1. Go to

  2. Click on TortoiseGit 32-Bit for a 32-bit operating system or 64-Bit for a 64-bit operating system

  3. Just accept the defaults during the installation.

  4. If you don't already have a git.exe, let TortoiseGit help you download and install Git For Windows.

  5. If you're installing Git For Windows, just accept the defaults. If it asks you for your GitHub login, provide that if you have one, or tell it you'll do that later.

  6. it's recommended to edit your settings so that some commonly used operations are promoted to the main right click menu:
    Create Branch, Log, Diff, Check for modifications, Add, and Switch/checkout

  7. It's also recommended that you run this git command to set your CRLF defaults: "git config --global core.autocrlf true".  Otherwise you may have the VS IDE Team Explorer window claiming a bunch of file changes that never happened, due to line ending changes.

Mascot Parser

  1. Go to to register with Matrix Science
  2. They'll send you an email, follow the instructions to download v2.6 for windows, both 32 and 64 bit.  You need at least the VS2015 folder (you probably don't have it if you are updating from the VS2013 build system).
  3. After downloading,and run each 7zip .exe as Administrator.
  4. Run (as administrator) the 32 bit self-extractor, extracting to "C:\Program Files (x86)\Matrix Science\Mascot Parser\"
  5. Run (as administrator) the 64 bit self-extractor, extracting to "C:\Program Files\Matrix Science\Mascot Parser\"

Checking out Skyline (as part of ProteoWizard)

  1. Create a ‘Proteowizard’ folder somewhere (i.e. under I:\proj)
  2. Right-click in the folder and select Git Clone (if that's not there, you skipped TortoiseGit install)
  3. Under URL of repository, enter, and click OK

To Build Skyline and ProteoWizard

This step builds the ProteoWizard core library used by Skyline to read mass spec data, as well as Skyline itself, and runs tests on both.  Once you've done this, as a Skyline developer you'll mostly work in the Visual Studio IDE.  If you need to work on the ProteoWizard core, it's back to the bjam-based build system (though you can follow the debugger from Skyline into the pwiz core, if pwiz is built with the "debug" option). 

In these instructions, <root> refers to that umbrella directory you set up earlier as an antivirus exclusion.

  1. In a command prompt, change directory to the root of the project that you cloned from github
  2. Create the batch file qb64.bat in this directory by creating a new file text file with a single line like:
    quickbuild --i-agree-to-the-vendor-licenses -j4 toolset=msvc-14.1 address-model=64 --without-compassxtract %*

  3. Type qb64.bat in the command-line.\
  4. For the quickest possible build without tests type "qb64.bat pwiz_tools\Skyline//Skyline.exe"
  5. It will build, then you'll see lots of Skyline windows flashing by as the tests are run.

Test and Begin Skyline Development

Note that the first time you open Skyline.sln, you are likely to be asked to download and install an update dotNet package - do that.

  1. In Windows Explorer navigate to <root>\proj\Proteowizard\pwiz\pwiz_tools\Skyline
  2. Double-click Skyline.sln
  3. Be sure that your build configuration (x64) is set correctly.
  4. Make sure your test settings match your build configuration:
    Test > Test Settings > Select Test Settings File
    and browser for either TestSettings_x64.runsettings in the Skyline folder
  5. On the Tools menu, click Options, select Debugging, select General, and uncheck the 'Enable Just My Code (Managed only)' option.
  6. On the ReSharper menu, click Options, under Tools, select Unit Testing, and uncheck the 'Shadow-copy assemblies being tested' option.
  7. In the Test menu, choose Run and click All Tests in Solution
  8. Once all of the tests have passed, you are ready to explore the code, debug and implement new features.

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