The ProteoWizard Library and Tools are a set of modular and extensible open-source, cross-platform tools and software libraries that facilitate proteomics data analysis.

The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

Core code and libraries are under the Apache open source license; the vendor libraries fall under various vendor-specific licenses.

Features

• reference implementation of HUPO-PSI mzML standard mass spectrometry data format
• supports HUPO-PSI mzIdentML 1.1 standard mass spectrometry analysis format
• supports reading directly from many vendor raw data formats (on Windows)
• modern C++ techniques and design principles
• cross-platform with native compilers (MSVC on Windows, gcc on Linux, darwin on OSX)
• modular design, for testability and extensibility
• framework for rapid development of data analysis tools
• open source license suitable for both academic and commercial projects (Apache v2)

Official build status

OS	Status
Windows
Native Linux
Wine Linux

Click here to visit the official download page.

Unofficial toolsets

OS	Toolset
Linux	GCC 13
OS X	Clang 12

Developer quickstart (Cursor)

This repository uses native builds (MSVC on Windows, GCC on Linux) and Boost.Build/Jamfiles. For a fast local build on Windows:

• Open a PowerShell or Developer Command Prompt
• Run: quickbuild.bat

Alternative entry points:

• Open pwiz.sln in Visual Studio 2022 and build the solution
• Use quickbuild.sh on Linux/macOS

Key locations:

• C++ libraries and tools: pwiz/, pwiz_tools/, pwiz_aux/
• Command-line apps (e.g., msconvert): pwiz_tools/commandline/
• MSVC build output (after quickbuild): build-nt-x86/msvc-release-x86_64/
• Third-party deps and Boost.Build: libraries/

Common tasks:

• Clean build outputs: clean.bat
• Build quickly with defaults: quickbuild.bat
• Documentation entry point: doc/index.html

Skyline development

Skyline lives under pwiz_tools/Skyline and depends on pwiz_tools/Shared and the full ProteoWizard tree. Always work from a full checkout of this repository, not just the Skyline subtree.

• Build entire repo (recommended first step):

bs.bat

This calls the app toolset build (e.g., pwiz_tools\build-apps.bat 64 --i-agree-to-the-vendor-licenses toolset=msvc-14.3 %*) to build ProteoWizard libraries, command-line tools, and Skyline.

• Open Skyline in VS: pwiz_tools/Skyline/Skyline.sln
• Ensure .NET Developer Pack is installed if prompted

Full setup and troubleshooting guide: How to Build Skyline.

Skyline C# coding conventions: see STYLEGUIDE.md.

Threading Guidelines

The project avoids async/await and .NET Task support in favor of deterministic threading:

• Use CommonActionUtil.RunAsync() (in Shared projects) or ActionUtil.RunAsync() (in Skyline) instead of Task.Run() or async/await
• Avoid .NET thread pool - Use allocated threads for more deterministic behavior and easier debugging
• Prefer synchronous operations on background threads when possible
• Thread marshaling - Use Invoke() for UI thread operations from background threads

Executables note: Projects under pwiz_tools/Skyline/Executables are separate solutions (most build stand-alone EXEs or developer tools, some ship with Skyline). They are not built by Skyline.sln, but should generally follow the same coding conventions unless a local project override is required. See the Tool Store: https://skyline.ms/tools.url

EditorConfig: Repository-wide .editorconfig enforces core C# naming/formatting so separate solutions (including pwiz_tools/Skyline/Executables) inherit consistent style in Visual Studio.

Notes for AI/code assistants (Cursor):

• Prefer invoking quickbuild.bat on Windows; avoid ad-hoc compiler calls
• Do not reformat unrelated code; keep original indentation and spacing
• Use existing Jamfiles/solution instead of introducing new build systems
• When adding C++ files, update the appropriate Jamfile or Visual Studio project as needed