mzmine4 support

[Sam-Will]

Is it possible to add mzmine4 as a support feature table type for FERMO? Current realase is 4.1.0 (https://github.com/mzmine/mzmine/releases/tag/v4.1.0)

Seems to be differences in the coloumn naming which is causing issues (example below)

Thanks!

row ID	row m/z	row retention time	row ion mobility	row ion mobility unit	row CCS	correlation group ID	annotation network number	best ion	auto MS2 verify	identified by n=	partners	neutral M mass	PostRunBlank01.mzML Peak area	PreRunBlank01.mzML Peak area
766	100.0756	1.63615				371	7	[M+H]+		1	761	99.06828	0	0
5295	110.0085	13.41073				83							932.3195	693.3513
36	110.0088	0.9634				87							68.06902	24.68771

[mmzdouc]

Hi @Sam-Will

thank you for your interest in FERMO!

Officially, we are indeed only supporting output from MZmine3 at the moment. Given that we have just released FERMO, we are currently busy with ironing out bugs and preparing the publication. We do not plan to include any additional features until FERMO has officially been published.

That being said, I tried running a peaktable that I produced with MZmine4.1.0 and it worked out for me - see here. However, the table format I got is different from the one that you provided in your issue - did you export it with Feature List Methods -> Export feature list -> Molecular networking files?

I have also attached the csv peaktable for reference
mzmine4test_quant_full.csv

Kind regards,

Mitja

[Sam-Will]

Hi @mmzdouc,

Thanks for the quick and detailed response!

Interesting, it looks like this becuase I use the 'Processing Wizard' feature, you also get a molecular networking feature file at the end but it names the row headers differently. I will run the steps manually to get the compataible feature table as suggested :)

If you had any time after FERMO has been published it be a nice feature to have it compatible with these tables too

Best wishes,
Sam