Comments (5)
jorainer
commented on August 16, 2024
For ChEBI (2018-12-03):
- No. of compounds: 46765
- No. of compounds without inchi: 7075
- No. of compounds with inchi: 39690.
- No. of unique inchis: 38946
So, we don't have an InChI for all of them and we have compounds with the same InChI! Apart from the name and the ID these compounds are however identical:
compound_id compound_name
8564 CHEBI:17775 7,9-dihydro-1H-purine-2,6,8(3H)-trione
18506 CHEBI:46811 2,6-dihydroxy-7,9-dihydro-8H-purin-8-one
18507 CHEBI:46814 9H-purine-2,6,8-triol
18509 CHEBI:46817 7H-purine-2,6,8-triol
18513 CHEBI:46823 1H-purine-2,6,8-triol
27249 CHEBI:62589 6-hydroxy-1H-purine-2,8(7H,9H)-dione
inchi
8564 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
18506 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
18507 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
18509 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
18513 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
27249 InChI=1S/C5H4N4O3/c10-3-1-2(7-4(11)6-1)8-5(12)9-3/h(H4,6,7,8,9,10,11,12)
inchi_key formula mass
8564 LEHOTFFKMJEONL-UHFFFAOYSA-N C5H4N4O3 168.028
18506 LEHOTFFKMJEONL-UHFFFAOYSA-N C5H4N4O3 168.028
18507 LEHOTFFKMJEONL-UHFFFAOYSA-N C5H4N4O3 168.028
18509 LEHOTFFKMJEONL-UHFFFAOYSA-N C5H4N4O3 168.028
18513 LEHOTFFKMJEONL-UHFFFAOYSA-N C5H4N4O3 168.028
27249 LEHOTFFKMJEONL-UHFFFAOYSA-N C5H4N4O3 168.028
>
Question is whether these compounds would have different MS2 spectra? If so it would not make sense to combine them!
Some of the compounds without an inchi are listed below:
compound_id compound_name inchi inchi_key
3 CHEBI:10003 ribostamycin sulfate <NA> <NA>
15 CHEBI:10036 wax ester <NA> <NA>
91 CHEBI:10283 2-hydroxy fatty acid <NA> <NA>
140 CHEBI:10545 electron <NA> <NA>
148 CHEBI:10583 kappa-carrageenan <NA> <NA>
154 CHEBI:106304 sphingomyelin d18:1/16:0 <NA> <NA>
formula mass
3 C17H34N4O10.(H2O4S)n NA
15 CO2R2 43.990
91 C2H3O3R __ C2H3O3R(CH2)n 75.008
140 <NA> 0.000
148 (C12H17O12S)n NA
154 C39H79N2O6P 702.568
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SiggiSmara
commented on August 16, 2024
In the case of CHEBI:46814 and CHEBI:46817 for instance (and I suspect the rest of them) then they are not the same chemical at first glance (see below, different locations of a hydrogen), but in fact they are tautomers of each other. This is also indicated in the CHEBI entries of some of them if you look them up in CHEBI. That means they readily convert from one to the other without any external input (energy or otherwise) and thus should really be thought of as a mixture of all of them. The MS2 spectrum "should" be similar if not identical, buut the actualy ionization conditions (pH, buffer ions etc) might also have a big effect leading to different MS2 spectra.
Here I would suggest to get input from people that are actually working with tautomers to hear what they have to say about it.
46814
and
46817
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jorainer
commented on August 16, 2024
Thanks for your input @SiggiSmara ! I'll try to get some input from people actually working with MS2 spectra and identification.
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stanstrup
commented on August 16, 2024
I have no experience with tautomers but one option could be to use the SMILES where this is explicit. You can also generate a non-standard InChI with the fixed-H layer from the SMILES.
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jorainer
commented on August 16, 2024
Had also feedback from Steffen. They use the same approach than pubchem: a compound table with unique InChI and a substance table with additional annotations (eventually multiple entries per compound).
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