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Support GOLM style MSP files #604

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hechth opened this issue Feb 22, 2024 · 0 comments
Open

Support GOLM style MSP files #604

hechth opened this issue Feb 22, 2024 · 0 comments

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@hechth
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hechth commented Feb 22, 2024

The keywords in the GOLM msp style are currently not supported.

We need to add a column GOLM to the export function and include the mapping for the following keys

  • Synon: METB InChI -> InChI
  • Synon: METB InChIKey -> InChIKey
  • Synon: RI: 986,12 -> retention_index: 986.12 has to be handled with the different decimal sign
  • Synon: MST N -> compound_name
  • MW -> exact_mass
  • Synon: METB CAS -> casno
  • Synon: METB KEGG -> kegg
  • Synon: METB N: -> synonyms -> these should all be written into a list as they are present multiple times.
  • Synon: METB CLASS -> class

I think those should cover most usecases. Those keywords have then also be added to the accepted keywords list and the handling of multiple : in the metadata keys needs to be handled.

Example Spectrum:

Name: M000412_A100001-101-xxx_NA_986,12_TRUE_VAR5_ALK_Glyoxylic acid (1MEOX) (1TMS)
Synon: MST N: Glyoxylic acid (1MEOX) (1TMS)
Synon: RI: 986,12
Synon: RI VAR5 ALK: TRUE
Synon: MST: A100001-101
Synon: MST ISOTOPE: 101
Synon: MST ID: A100001-101-xxx_
Synon: MST SEL MASS: 160|116|89|100|144
Synon: METB: M000412_no_preferred
Synon: METB N: alpha-ketoacetic acid
Synon: METB N: formylformic acid
Synon: METB N: Glyoxalate
Synon: METB N: Glyoxalsaeure
Synon: METB N: Glyoxylate
Synon: METB N: glyoxylic acid
Synon: METB N: Glyoxylic acid
Synon: METB N: Glyoxylsaeure
Synon: METB N: oxalaldehydic acid
Synon: METB N: oxoacetic acid
Synon: METB N: oxoethanoic acid
Synon: METB CAS: 298-12-4
Synon: METB KEGG: C00048
Synon: METB InChI: InChI=1S/C2H2O3/c3-1-2(4)5/h1H,(H,4,5)
Synon: METB InChIKey: HHLFWLYXYJOTON-UHFFFAOYSA-N
Synon: METB CLASS: Acid (Oxo)
Synon: GMD LINK: http://gmd.mpimp-golm.mpg.de/Analytes/60565248-bf50-49fb-b739-3920cf0162da.aspx
Synon: GMD VERS: 21.Nov.2011 21:54 hummel
Formula: C6H13NO3Si
MW: 175,258
CAS#: 55493-91-9
Comment: consensus spectrum of 2 spectra per analyte, MPIMP ID and isotopomer, with majority threshold = 60%
DB#: 21
Num Peaks: 26
85:201 86:55 87:10 88:4 89:315 
90:29 91:22 92:1 99:2 100:64 
101:27 102:9 103:4 116:137 117:51 
118:10 128:1 129:5 132:2 144:30 
145:13 146:1 160:1000 161:100 162:38 
163:2 

Regarding the synonyms, basically this

Synon: METB N: 3-Aminopropanoate
Synon: METB N: 3-aminopropanoic acid
Synon: METB N: 3-Aminopropionic acid
Synon: METB N: Alanine, beta-
Synon: METB N: b-alanine,N,O-TBS
Synon: METB N: beta-alanine
Synon: METB N: beta-Alanine
Synon: METB N: beta-aminopropionic acid
Synon: METB N: H-beta-Ala-OH
Synon: METB N: omega-aminopropionic acid

should be parsed to this:

{
    "synonyms": [ "3-Aminopropanoate", "3-aminopropanoic acid", "3-Aminopropionic acid", "Alanine, beta-", "..." , " omega-aminopropionic acid"]
}
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