Agilent files

[Former user]

Dear Zhixu Ni,

Congrats for the software! Really interesting. I've just installed and tested the tutorial files. They worked well. However, I use an Agilent instrument. Can I actually use mzml files from Agilent QTOF? When I tried my mzml file and set instrument to Agilent, it didn't work.

Regards, Manuela

[Zhixu Ni]

Hi Manuela!

Thank you for your interest in LPPtiger.

Please send us your mzML file and if it is possible also the original file so that we can have a look and find a solution next week.

Best regards,

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Zhixu Ni

[Manuela KS]

Hi Zhixu Ni,

Thank you for the promptly answer!

Example of the files and mzml: https://drive.google.com/drive/folders/1ly6xoHFcNtu_m1Yc6Elfu0fSLpR8CPMv?usp=sharing

Regards,

Manuela

[Zhixu Ni]

Hi Manuela!

This is one mzML issue due to the pymzml package used by LPPtiger.

Due to the release of proteowizard, you have to update the obo files in the obo folders.

If you run the LPPtiger_debug version (the LPPtiger_debug with grey icon version), you probably will have this error message:

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You can download the updated obo files from this link:

https://speicherwolke.uni-leipzig.de/index.php/s/g8dzPDQzwd4JGBG

unzip this file and overwrite the obo folder under your LPPtiger folder.

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Or you can download this patched version of LPPtiger and delete your previous version of LPPtiger:
https://speicherwolke.uni-leipzig.de/index.php/s/pBtdi3Rsj9bN2wm

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After that you can try again, please run the debug mode of LPPtiger and send us the screenshot.

If it's still not working, please send me your proteowizard version so that I can have a look when I back to work next week.

I’ve run the file 1 you sent me with oxPE from following PE lipids:

PE(16:0/18:1)

PE(16:0/18:2)

PE(16:0/20:3)

PE(16:0/20:4)

PE(18:0/18:1)

PE(18:0/18:2)

PE(18:0/20:3)

PE(18:0/20:4)

And I found oxPE like:

Wish you great success in your data analysis!

Best regards,

Zhixu Ni

[Manuela KS]

Hello Zhixu Ni,

Thank you the help!

I decided to download the patched version of LPPtiger and delete your previous version of LPPtiger.

I run the debug version and it worked fine.

[Zhixu Ni]

Hello Manuela,

It is great that the fix works for you! Thanks for the feedback!

I will try to upload this fixed one to the download page. And I will mark this issue as solved.

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It would be nice if you can send me an email so that I can inform you when new LPPtiger version is available later.

zhixu.ni(at)uni-leipzig.de

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Best regards,

Zhixu Ni

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[Zhixu Ni]

You can download the updated obo files from this link:

https://speicherwolke.uni-leipzig.de/index.php/s/g8dzPDQzwd4JGBG

unzip this file and overwrite the obo folder under your LPPtiger folder.

Or you can download this patched version of LPPtiger and delete your previous version of LPPtiger: https://speicherwolke.uni-leipzig.de/index.php/s/pBtdi3Rsj9bN2wm