Pwiz

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