mmzdouc / FERMO

Dashboard for analysis of liquid chromatography (tandem) mass spectrometry data.
https://fermo.bioinformatics.nl/example
MIT License
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mzmine4 support #34

Open Sam-Will opened 5 days ago

Sam-Will commented 5 days ago

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!

<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

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 commented 4 days ago

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?

image

image

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

Kind regards,

Mitja