2023-05-22
This is Audrey's DBGI daily open-notebook.
Today is 2023.05.22
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
datatreatment project 28
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- Mass detection
MS level 1 : Noise level 1.5E2
MS level 2 : Noise level 2.5E1
- Built chromato (ADAP)
RT = 0.5 - 15.3 min ; MS1 ; centroided ; peak scan = 5 ; treshold 5E2 ; min 1E3 m/z = 0.01
- 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 : MS/MS + two ions in the isotopic pattern
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gap filling : same Rt & MS range gap filler 0.01 m/z or 12 ppm
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check that QC are group (select feature list + feature list method - data analysis - PCA)
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feature list method - identification - adduct (Na, K, NH3)+ complexe 0.001 M/z
==> feature list with less than 160 features (trop restrictif)
Done
Ornamental project
- Preparation of the sample for analysis (Grinding, extraction, labelisation of the 38 samples of clematis, lonicera & euonymus) ; blank is the solvant extraction which followed the same step than sample (extraction with 3 beads in eppendorf)
labellisation : DBGI_xxxxxx_01 refer to stock vial (conserved in the freezer)