2023-04-28
This is Audrey's DBGI daily open-notebook.
Today is 2023.04.28
Todo today
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 1E3
MS level 2 : Noise level 0
- 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
Group isotop : 0.02 mz or 8 ppm ; 0.08 min charge max = 4 ; most intense
aligment : (not the bk 1st) 0.01 m/z or 12 ppm ; RT tolerance 0.1 min
Export to gitrepo (serveur)
3/to push files on git :
- powershell :
git repo / coleus_projet etc etc.
git pull
git add "chemin du fichier"
git commit -m "blabla"
git push
- visual code "dendron gitrepo" pull (to load document locally)
'PS C:\Users\Lecab\gitrepo\coleus-project> git pull'