Native Linux Thermo/Bruker data conversion

[prvst]

Hello, would it be possible to integrate the native Linux libraries for Thermo and Bruker data conversion into msconvert? We have good examples of working projects, like the ThermoRawFileParser and timsconvert. This would be a considerable improvement and a very useful update to msconvert.

Thanks.

[chambm]

It would require a completely separate approach in our code and build system that wouldn't work for Skyline, because it is .NET that uses C++/CLI wrappers to access the core pwiz reading in C++. There's no C++/CLI compiler for Linux (as far as I know, I just did a brief search for it again). So this would be a lot of work that wouldn't be that useful for us.

We are already routinely using msconvert and Skyline on Linux via the Wine/Docker container (which you can also use with Singularity or Apptainer). Indeed I think after our latest Wine update, Thermo performance on Wine is almost as good as on Windows. Bruker TDF support is even closer to parity. And from my brief testing, msconvert on Wine is significantly faster than TRFP on Windows (I haven't tested TRFP on Linux). I haven't compared against timsconvert.

[prvst]

Thanks for the explanation, Matt.