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Topic: in silico side chain problem (TGs) (Read 106 times) previous topic - next topic

in silico side chain problem (TGs)

I've noticed an issue with the side chains for the insilico TGs.  As can be seen in the screen shots below, the first three compounds that show up have different side chains but show the exact same MS/MS fragments.  This issue seems to repeat every three compounds (groups of three).  This issue is not present every time, but fairly often.  This is with version 4.38.

 

Re: in silico side chain problem (TGs)

Reply #1
Thanks Bryan, we will check it soon.
Hiroshi

Re: in silico side chain problem (TGs)

Reply #2
Hi Bryan,

my staff has checked this feature.
These are not the exactly same fragments but the slightly different spectra as the decimal values.
I just pasted the detail of MS/MS spectra for these metabolites.

NAME: TG O-16:0_10:0_16:0
PRECURSORMZ: 726.697
PRECURSORTYPE: [M+NH4]+
IONMODE: Positive
FORMULA: C45H88O5
SMILES: O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COCCCCCCCCCCCCCCCC)CCCCCCCCC
INCHIKEY: FKBSAQBKXJSFMO-UHFFFAOYSA-N
COMPOUNDCLASS: EtherTG
RETENTIONTIME:
COMMENT:
Num Peaks: 5
726.697001   100
709.670452   50
537.524122   999 "NL of SN3 [3]"
467.409487   999 "NL of SN1 [1]"
453.430222   999 "NL of SN2 [2]"
NAME: TG O-17:0_10:0_15:0
PRECURSORMZ: 726.697
PRECURSORTYPE: [M+NH4]+
IONMODE: Positive
FORMULA: C45H88O5
SMILES: O=C(OCC(OC(=O)CCCCCCCCCCCCCC)COCCCCCCCCCCCCCCCCC)CCCCCCCCC
INCHIKEY: DDYDVVZXHMHMOL-UHFFFAOYSA-N
COMPOUNDCLASS: EtherTG
RETENTIONTIME:
COMMENT:
Num Peaks: 5
726.697001   100
709.670452   50
537.524122   999 "NL of SN3 [3]"
467.445872   999 "NL of SN2 [2]"
453.393837   999 "NL of SN1 [1]"
NAME: TG O-11:0_15:0_16:0
PRECURSORMZ: 726.697
PRECURSORTYPE: [M+NH4]+
IONMODE: Positive
FORMULA: C45H88O5
SMILES: O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COCCCCCCCCCCC)CCCCCCCCCCCCCC
INCHIKEY: KXAAUHFLKJXVON-UHFFFAOYSA-N
COMPOUNDCLASS: EtherTG
RETENTIONTIME:
COMMENT:
Num Peaks: 5
726.697001   100
709.670452   50
537.487737   999 "NL of SN1 [1]"
467.445872   999 "NL of SN2 [2]"
453.430222   999 "NL of SN3 [3]"

Currently, the intensity differences for cleaving ether and ester linkages are not defined, and therefore, those spectra look very similar. And it indicates that currently it's very difficult to distinguish them unless we can use very high resolution/accuracy MS instrument for MS2!

Thanks,

Hiroshi

Re: in silico side chain problem (TGs)

Reply #3
Thank you!  This clears it up.