2023-05-03
This is Audrey's DBGI daily open-notebook.
Today is 2023.05.03
Todo today
[] create label to collect samples next week [] Next Tuesday collect at jbne
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Treatement of X072067ALC.dataCompass.mzxml ; X072068ALC.dataCompass.mzxml ; X072069ALC.dataCompass.mzxml (Bk, aerial part, roots)
Datatreatment :
1/ Conversion raw data to MzXmL using CompassBruker (or Preteowizard (MS convert) under windows si Thermo data)
2/ treatment Mzmine 2.53
- access to mzmine cf http://www.dbgi.org/dendron-dbgi/notes/mn44v5c7fa6f4qqoz117s8k/
- Raw data import
- Mass detection
MS level 1 : Noise level 5E3
MS level 2 : Noise level 1E2
- Built chromato (ADAP)
RT = 0.5 - 21 min ; MS1 ; centroided ; peak scan = 5 ; treshold 5E2 ; min 1E4 m/z = 0.01
- deconvolution : wavelet ; auto ; 0.025 Da ; 0,15 min
-
isotope peak grouper : m/z 0.001 - 5 ppm ; rt 0.08 min ; max charge 2 lowest m/z
-
aligment : (not the bk 1st) 0.01 m/z or 12 ppm ; RT tolerance 0.1 min
-
filter : MS/MS + two ions in the isotopic pattern
-
gap filling : same Rt & MS range gap filler
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check that QC are group (select feature list + feature list method - data analysis - PCA)
-
feature list method - identification - adduct + complexe
-
creation list metadata
3/ FBMN on GNPS
4/ Sirius
Paused
Done
Notes
Todo tomorrow
- faire tuto nouvel arrivant"
- création identifiant directus
- création des étiquettes