How to use .mzML files or to convert them into .imzML and .ibd

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Marco Fidaleo

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May 11, 2024, 11:44:30 AMMay 11
to Cardinal MSI Help
Hello everyone,

I've obtained results from a targeted MSI analysis using a Waters instrument. I managed to convert the RAW files into .mzML format, but I am not able to convert them into .imzML and .ibd formats. I'm wondering if it's possible to generate both .imzML and .ibd files directly from a .mzML file. I've tried various software tools like MZmine and imzMLconverter, but without success. I'm curious if there's a direct method to do this using Cardinal.

Thank you,
M

kbemis

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May 16, 2024, 4:30:25 PMMay 16
to Cardinal MSI Help
Hi Marco,

No, we don't provide functionality for conversion from mzML to imzML.

I would suggest reaching out to the maintainers of the converters for help.

-Kylie

Matthew Smith

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May 17, 2024, 9:43:51 AMMay 17
to Cardinal MSI Help
Hello,

I too ran into this problem with targeted MSI analysis with Waters. As a temporary fix until conversion tools cover this data type, I developed a parser which reads in the data to Cardinals 'MSContinuousImagingExperiment' object (as well as some additional functions I needed for quantification for instance).

Maybe it is helpful for you too - https://github.com/targeted-lipidomics/quantMSImageR.

Bw,
Matt

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