Comet MS/MS

Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool written primarily in C/C++. The original Comet repository lived on SourceForge since 2012. It was migrated to GitHub on September 2021.

The project website can be found here. This includes release notes and search parameters documentation.

To compile on linux and macOS:

• Type 'make'. This will generate a binary "comet.exe".

To compile with Microsoft Visual Studio:

• We current use build tools v143 with Microsoft Visual Studio 2022.

• Load "Comet.sln" in Visual Studio.

• Set the build to "Release" and "x64".

• Right-mouse-click on the "Comet" project and choose "Build". This should generate a binary "Comet.exe" in x64/Release.

Comet integrates:

• Mike Hoopmann's MSToolkit library for reading various file formats.
• Matthew Belmonte's C implementation of the Twiddle algorithm used in generating modification permutations.
• C++ port of Gygi Lab's AScorePro for modification localization.
• Barak Shoshany's BS::thread_pool C++ thread pool library.
• Thermo Fischer's RawFileReader .Net assembly.

Reading Thermo .raw files on Windows

comet.win64.exe reads Thermo .raw files directly using Thermo's RawFileReader .NET library. This requires three DLLs to be present in the same directory as Comet.exe:

• ThermoFisher.CommonCore.Data.dll
• ThermoFisher.CommonCore.RawFileReader.dll
• OpenMcdf.dll

No installation or registration step is needed -- just place the three files next to Comet.exe (or in the same folder you run Comet from). This is a deliberate improvement over the older MSFileReader COM library Comet used previously, which required a separate installer that registered COM components in the Windows registry.

These DLLs can be obtained from Thermo's official thermofisherlsms/RawFileReader GitHub repo (the Libs/Net471 folder matches the .NET Framework version Comet is built against). Comet has been built and tested against version 5.0.0.93.

.raw support is Windows-only. mzXML, mzML, and mgf/ms1/ms2-family inputs work on every platform without any of the above and require no additional files.