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sgibb / MALDIquantForeign

Import/Export routines for MALDIquant
https://strimmerlab.github.io/software/maldiquant/
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Possible to add support for Shimadzu XML format? #34

Open mr-september opened 4 months ago

mr-september commented 4 months ago

Have this old Shimadzu MALDI that doesn't really allow bulk spectra exporting in the usual formats like mzml, but only in just .xml.

I tried using the default import function to try and parse this, but it said something about unknown file format.

I have attached an example XML file (zipped as per github's requirements).

Test Expor A2-D3.zip

Would this be something feasible to add support for?

sgibb commented 4 months ago

Is it supported by msconvert? e.g., Shimadzu LCD (except ITOF) distributed with ProteoWizard

I am not working in the MS field anymore. While I still maintaining MALDIquantForeign and fixing bugs I won't add new features. But I would happy to help with the existing code base if you want to add it yourself.

mr-september commented 4 months ago

Unfortunately msconvert doesn't seem to recognize it. It is a 7090 model, and while Shimadzu typically uses .lcd, I could not find them from this machine.

I have never worked with XML parsing before, but would be keen to have a go. If you just have a glance at the .xml file above, does it look somewhat similar-ish to perhaps mzXML? Would adapting from the existing mzXML parser be a good way to start?

sgibb commented 3 weeks ago

Sorry for the late reply. It isn't similar to mz(X)ML, e.g. mz(X)ML use as Base64 encoded string for all mz/intensity values. In this xml every spot has its own children with spot name, x center, y center, ...