2023-05-11
This is Audrey's DBGI daily open-notebook.
Today is 2023.05.11
Todo today
- Collect plant at Jbuf
- Seminar at 3 pm
- Continue poster (mzmine treatment + MN)
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Done
1/ Collect plant from Jbuf (only the one in the syst. 1 / 2 and 3)
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Clematis heraclifoia
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Clematis recta
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Clematis vitalba
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Lonicera caprifolium
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Lonicera Kamtschatica
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Lonicera perclymenum
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Lonicera tatarica
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Lonicera xylosteum
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Euonymus alatus
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Euonymus europeaus
Plant were collected according the dbgi protocole Bachelor Work 2022 ; fews leaves of plant were collected and put into coffee filter and then into a falcon with pre drilled plastic caps. Falcon are placed into liquid nitrogen during the harvesting before beeing lyophilized. Falcon are placed at -70°C before being freeze drying.
Clematis florida, Clematis tangutica and Lonicera nigra from the system couldn't be collect (no leave or not enough).
2/ treatment Coleus with modification of level noise (not finish pb with transfer of the dataset)
Treatement of X072067ALC.dataCompass.mzxml ; X072068ALC.dataCompass.mzxml ; X072069ALC.dataCompass.mzxml (Bk, aerial part, roots)
Datatreatment :
a/ Conversion raw data to MzXmL using CompassBruker (or Preteowizard (MS convert) under windows si Thermo data)
b/ 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 2E3
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
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deconvolution : wavelet ; auto ; 0.025 Da ; 0,15 min
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isotope peak grouper : m/z 0.001 - 5 ppm ; rt 0.08 min ; max charge 2 lowest m/z
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aligment : (not the bk 1st) 0.01 m/z or 12 ppm ; RT tolerance 0.1 min
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filter : feature list rows filter : MS/MS + two ions in the isotopic pattern
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gap filling : same Rt & MS range gap filler
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feature list method - identification - adduct + complexe
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)
Notes
Todo tomorrow
- Collect 9 plants from the differents localisation