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mwang87 / ReDU-MS2-GNPS

User interface to reanalyze and explore all public data in Metabolomics Public Data
https://redu.ucsd.edu/
MIT License
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Addition to ReDUMS2_controlled_vocabulary (MicrobeMASST) #257

Open Panzenboeck opened 2 years ago

Panzenboeck commented 2 years ago

Hi, could you please add the following entries to the controlled vocabulary for ReDU:

SampleExtractionMethod:

  1. boiling 80% EtOH
  2. Folch

ChromatographyAndPhase:

  1. reverse phase (C30)
  2. 2D - HILIC and reverse phase (C18)

MassSpectrometer:

  1. ORBITRAP ID-X
  2. Bruker Daltonics timsTOF fleX
  3. Q Exactive HF

NCBITaxonomy: Pichia pastoris (Guillierm.) Phaff 1956 (Komagataella phaffii Kurtzman), Taxonomy ID: 460519 (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=460519&lvl=3&lin=f&keep=1&srchmode=1&unlock)

Thank you!

alan-jarmusch commented 1 year ago

SampleExtractionMethod: boiling 80% EtOH = added as 'ethanol-water (4:1),boiling' Folch = please specify composition

ChromatographyAndPhase: reverse phase (C30) = 'reverse phase (C30)' 2D - HILIC and reverse phase (C18) = '2D:HILIC and reverse phase (C18)'

MassSpectrometer:

ORBITRAP ID-X = 'Orbitrap ID-X|MS:1003112' Bruker Daltonics timsTOF fleX = 'timsTOF fleX|MS:1003124' Q Exactive HF = 'Q Exactive HF|MS:1002523'

Panzenboeck commented 1 year ago

Thank you!

Folch would be 2:1 (v/v) chloroform/methanol

mwang87 commented 1 year ago

@alan-jarmusch Will be able to help on this front.