EAD information lost

[Panzenboeck]

Hi Adriano,
Thank you for your great work! I wanted to use CentroidR for centroiding my ZenoTOF 7600 data. However, the information on EAD fragmentation electron kinetic energies does not seem to be included in the .mzml files generated from .wiff format, but only when you create them from .wiff2. Do you have an idea how to cope with this? I saw that you recommend using .wiff files for centroiding with your package…
Best regards,
Lisa

[Adafede]

Hi Lisa,

Oh, happy someone found it useful!
I had issues with some values being NaN using the .wiff2 files in MSConvert, which was not the case using the .wiff files. This is the reason why I recommended using .wiff.

For the EAD...I know the issue (and saw yours in mzmine/pwiz)...also the activation time is not reported. We already mentioned it to Sciex. Let's hope they come with a good solution soon! 😊

Maybe you can try using the .wiff2and hope you won't get any NaN?

Happy to hear your feedback,

Best

Adriano

[Panzenboeck]

Hey Adriano,
thank you for your fast reply. Could you please let me know as soon as you've got some news from Sciex?

Best,
Lisa

[Adafede]

Hi @Panzenboeck,

It will probably not solve the whole issue as part of the information isn't in the profile mzML, but you should now also be able to use .wiff2 files without NaN issues.

We are still trying to look for a better conversion.

Best,

Adriano

[Panzenboeck]

Hi Adriano,
Thank you for the update – that sounds great!
Best,
Lisa

[Adafede]

Looks like we could get there sooner than expected, see: sneumann/mzR#308