ProteoWizard

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)
• pure C# on .NET 10 (Windows and Linux), packaged as a library, msconvert, MSConvertGUI, SeeMS and BiblioSpec
• 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)

The original C++ implementation (libpwiz, the C++ msconvert, Bumbershoot, BiblioSpec-C++ and the Boost.Build tree) lives on with its full history in ProteoWizard/pwiz-cpp.

Official build status

Build	Status
Core Windows x86_64
Core Linux x86_64
Skyline master and PRs

Click here to visit the official download page.

Developer quickstart

Requirements: the .NET SDK pinned in global.json (scripts/ensure-dotnet.sh installs it on Linux), and on Windows the Visual Studio C++ toolset for the two remaining native pieces (Hardklor, MascotShim).

i-agree-to-the-vendor-licenses.bat   REM once per machine; enables the vendor SDK readers
build.bat                             REM restore + build Pwiz.sln + run the tests

Alternative entry points:

• Open Pwiz.sln in Visual Studio 2026 (other IDEs may work but are unsupported)
• build.sh on Linux (Thermo, Bruker and Waters vendor formats plus mzML/mzXML/MGF and friends; the other vendor SDKs are Windows-only)
• build.bat --help lists the flags (--without-mascot, --coverage, --automated, ...)

Key locations:

• pwiz/utility, pwiz/data/{common,msdata,identdata,tradata}, pwiz/analysis: the library modules, each with its tests in test/ and its fixtures beside it (CV ontologies in data/common, *.data under analysis)
• pwiz/data/vendor_readers/<Vendor>: one project per vendor SDK, next to Reader_<Vendor>_Test.data
• pwiz/utility/bindings: the native-host / Native AOT exports and the Bruker PRM scheduler P/Invoke
• pwiz_tools/Commandline: msconvert, msbenchmark
• pwiz_tools/MSConvertGUI, pwiz_tools/SeeMS, pwiz_tools/BiblioSpec, pwiz_tools/BullseyeSharp: the tools
• pwiz_tools/Skyline, pwiz_tools/Shared, pwiz_tools/Osprey: Skyline and its shared libraries
• build/: MSBuild targets shared by pwiz and Skyline (versioning, test-data extraction, vendor SDK pins)
• vendor-archives/: the encrypted vendor SDK archives the readers are built against
• scripts/installer/: the Inno Setup installer for the pwiz tools

Common tasks:

• Clean build outputs: clean.bat (clean.bat --all also wipes the extracted vendor SDKs)
• Run one test project: dotnet test pwiz/test/MsData.Tests -c Release

Skyline development

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

• Build Skyline and run its tests (recommended first step):

pwiz_tools\Skyline\build.bat

• Open Skyline in VS: pwiz_tools/Skyline/Skyline.sln

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:

• Prefer invoking build.bat / pwiz_tools\Skyline\build.bat; avoid ad-hoc compiler calls
• Do not reformat unrelated code; keep original indentation and spacing
• Use the existing solutions and Directory.Build.props chain instead of introducing new build systems