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mzmine source code repository
https://mzmine.github.io/mzmine_documentation/
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Batch xml file example for MZmine3 #1752

Open fbonnet08 opened 5 months ago

fbonnet08 commented 5 months ago

I am starting to use MZmine3, and I would like to use it in batch mode, I also would like to be able to read from the raw files directly. I am after two things.

I would like to use MZmine in batch mode but before I can do that I would need to have an example XML input file to process a set of Thermo raw files or others, if the Thermo raw files needs to be converted I would need to know what format that needs to be in to use the batch mode with the XML file.

Also, it would be really useful to have a Thermo raw file reader in Python3 so that I can use it in some other parsing code as well. Thermofisher has a C# version reader but that would require me to write the wrapper code for this to be useful.

Would it be possible to get an example XML file to run in batch mode in MZmine3 for command line use?

Also can MZMine3 export the raw file to a csv file from the command line using the xml batch file? Thanks.

robinschmid commented 4 months ago

Please refer to the documentation and our learners corner and youtube videos. You can use the mzwizard to setup a batch processing configuration. Start with the GUI to setup your batch and then use the file in CLI mode. You can always join the development in mzmine and add your own functionality. This is going to be much easier than working with the resulting files that we provide - in case you want to have stronger access to all data structures like scans and chromatograms.

Best regards Robin

robinschmid commented 4 months ago

Also we just released mzmine 4 so check it out

fbonnet08 commented 4 months ago

Dear Robin,

ok thank you for letting me know.

What would be very useful and super cool to have is a command line control mechanism to use MZmine to batch many raw files either from Thermo fishers to export into a mgf file. In fact what I would need is an example of xml file to use in batch mode that I can use with MZmine.

The second thing that would really help me is the python version of the thermofisher raw files.

Regards, Frederic.

On Mon, Apr 22, 2024 at 12:41 PM Robin Schmid @.***> wrote:

Also we just released mzmine 4 so check it out

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robinschmid commented 4 months ago

I am not quite sure what you are trying to do. There are Python packages that support mzml import or support further statistical analysis of mzmine results. So within mzmine you can put together any workflow and export results to many different formats. If you need more data the best is to get involved and you can access all sorts of information from each feature or spectrum in mzmine. It is quite simple to build your own module in mzmine.