in silico side chain problem (TGs) November 17, 2020, 01:14:04 PM 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. Quote Selected
Re: in silico side chain problem (TGs) Reply #1 – November 19, 2020, 10:10:05 AM Thanks Bryan, we will check it soon.Hiroshi Quote Selected
Re: in silico side chain problem (TGs) Reply #2 – November 23, 2020, 01:45:51 AM 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_16:0PRECURSORMZ: 726.697PRECURSORTYPE: [M+NH4]+IONMODE: PositiveFORMULA: C45H88O5SMILES: O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COCCCCCCCCCCCCCCCC)CCCCCCCCCINCHIKEY: FKBSAQBKXJSFMO-UHFFFAOYSA-NCOMPOUNDCLASS: EtherTGRETENTIONTIME:COMMENT:Num Peaks: 5726.697001 100709.670452 50537.524122 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_15:0PRECURSORMZ: 726.697PRECURSORTYPE: [M+NH4]+IONMODE: PositiveFORMULA: C45H88O5SMILES: O=C(OCC(OC(=O)CCCCCCCCCCCCCC)COCCCCCCCCCCCCCCCCC)CCCCCCCCCINCHIKEY: DDYDVVZXHMHMOL-UHFFFAOYSA-NCOMPOUNDCLASS: EtherTGRETENTIONTIME:COMMENT:Num Peaks: 5726.697001 100709.670452 50537.524122 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_16:0PRECURSORMZ: 726.697PRECURSORTYPE: [M+NH4]+IONMODE: PositiveFORMULA: C45H88O5SMILES: O=C(OCC(OC(=O)CCCCCCCCCCCCCCC)COCCCCCCCCCCC)CCCCCCCCCCCCCCINCHIKEY: KXAAUHFLKJXVON-UHFFFAOYSA-NCOMPOUNDCLASS: EtherTGRETENTIONTIME:COMMENT:Num Peaks: 5726.697001 100709.670452 50537.487737 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 Quote Selected
Re: in silico side chain problem (TGs) Reply #3 – November 24, 2020, 12:07:55 PM Thank you! This clears it up. Quote Selected