Are there any free tools for converting raw mass-spectrometry files into open formats? In particular, is there any way to convert Water's .raw MS files into a readable format in a batch-wise fashion (talking about hundreds of mass spectra, so it needs to be at the command line ...)? After a long search, I only found MassWolf which seems very outdated and which also doesn't seem to provide any command line batch processing. Isn't there something like OpenBabel for analytical chemistry file formats?
Waters Databridge actually allows the conversion of multiple files at the same time, but somehow it is not very intuitive to use (not a native UI) and also does not really work in batch mode. Still, it is somewhat possible to quickly export Waters .raw files using Databridge, and it is the best solution I found so far. From there, a simple python script allows me to average the mass spectra (that are still chromatograms), so that it at least doesn't take hours to export every single mass spectrum by hand.
For other people in my position, having to convert hundreds of Waters .raw files, I hope that helps at least somewhat.