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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 After a long search, I only found MassWolf which seems very outdated and which also doesn't seem to provide any command line batch processing.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?

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    $\begingroup$ Long time ago I remember converting some *.raw data files with Bruker CompassXport. I'm not sure though if it can handle your data. Last time I used it, it was a free command-line tool which you can get for free from Bruker after you register on their website. Also, check out the manual beforehand. Or just upload an example of your data so that me and others could test their suggested converters before posting the ideas here:) $\endgroup$ – andselisk Sep 11 '17 at 14:13
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    $\begingroup$ @andselisk Thanks for the quick reply : ) I checked the manual, but couldn't really find anything on the Waters .raw format in there (.raw is really a stupid name for a format...). I am already at the point of thinking about using a Hex editor just to reverse engineer that format because a batch solution would be so much better! $\endgroup$ – logical x 2 Sep 11 '17 at 19:40
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    $\begingroup$ In the lab we use MSConvert from ProteoWizard (proteowizard.sourceforge.net/downloads.shtml) to convert Waters files to mzXML format. It is not exactly batch mode but you can input a list of files to process. The .raw to interpretable is done through a DLL provided by Waters, so they did not reverse engineer the format, which is not quite trivial (at least from my first attempts at it). $\endgroup$ – PLD Sep 14 '17 at 15:42
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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.

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