SYFT Data support

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SYFT Data support Christina lucas  2021-02-22
 

Hi there,

I was wondering whether anyone has every tried to implement data of a SIFT MS of syft technologies for small molecules (mainly VOC's). Datafiles are *.csv and *.xml, unfortunatly no mzML or mzXML available.

Data is quite simple you select a reaction ion (First Q), Reaction, product ion (Second Q), supported are SIM and Fullscan in the Second Q.

I attached some Datafiles in csv /XML, there no proprietary data format.

It would be great to get it into Skyline :)

Best, Christina

 
 
Brian Pratt responded:  2021-02-22

Hi Christina,

I'm not aware of any existing solution. Generally the instrument vendors provide a converter to mzML, perhaps as a customer you can lean on them to do so. You might also be able to do a bit of Python or similar programming to get the data into a format that txt2mzML (http://proteowizard.sourceforge.net/tools/tools_base.html) can process.

Thanks for using the Skyline support board!

Brian Pratt

 
Christina lucas responded:  2021-02-22

Hi Brian,

thanks for the help.

Where can I get access to txt2mzML or see the input needed?
Cause on the link, its greyed out, so no more information about it accesable.

Kind regards,

Christina

 
Nick Shulman responded:  2021-02-23
Christina,
There was a question on the ProteoWizard support board about txt2mzML that I answered a few months ago:
https://sourceforge.net/p/proteowizard/mailman/message/37183625/

I don't think you can see the file attachments there, so I will forward you the original message.

There are other really simple and well documented mass spec data formats which you might find easier to produce than figuring out how to get txt2mzml working.
The simple formats I'm thinking of are called ".ms1", ".ms2", and ".mgf".

Here's the documentation for .mgf (which seems to be ms2 only):
https://fiehnlab.ucdavis.edu/projects/LipidBlast/mgf-files

You can find a description of the .ms1 and .ms2 formats in this paper:
https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.1603

-- Nick
 
Christina lucas responded:  2021-02-23
Hi Nick,

thanks a lot for your help.
I'll try to get it running :)

There is no body at Syft Dealing with this topic, so I've to get a workaround myself, as it is a very small company.

I'll let you know if I succeed!

Have a nice day,

Christina