kaibioinfo
commented
3 years ago Woah, this is a mean one: the subtree of [C42H41O18 + 1] looks perfect: several hexose moieties, water losses - sure it gets high score and is picked, although the "OH" loss and the "O" loss are both strange.
By default, there is no special treatment of isotope peaks. You have to enable this option explicitely. In the CLI you can do that with the --IsotopeMs2Settings SCORE option. Instead of SCORE you can also write FILTER (not implemented yet for some reason, I already added a ticket) and IGNORE (default).
Just a few words to the Isotope detection in MS/MS: The idea of the FILTER option is to just remove isotope peaks before starting computation. Its a very simple heuristic that checks for monotonic decreasing peaks with the right mass following high intensive peaks and removes them. It is not enabled by default, because isotope peaks usually only appear for specific instruments (like Bruker) and setups (like DIA). So we do not want to accidentally remove real signal peaks on an Agilent Q-ToF where we do not see isotope peaks in MS/MS anyways. The SCORE option however integrates the isotope peaks into the optimization problem. This makes the optimization problem much harder (because isotope peaks violate the assumption that parent peaks do always have larger masses than their children; this assumption is necessary for many tricks to speed-up the computation). Thus, expect that computation will take more time when enabling this option. Second problem: Isotope peaks in MS/MS can look very different. To be honest, I have never seen so clean isotope peaks as in your example above. Usually, their intensities are totally disturbed and "strange". This is because the isotope intensity in MS/MS depends totally on the instrument and the isolation window setting. It is really hard to find some general setup or scoring for isotopes that work for all kind of instruments and isolation windows. In DIA, of course, you have perfect isotopes. But so far we had rather bad experiences with DIA methods: they produce WAY less fragments than the DDA and a lot of chimeric peaks from isobar compounds. Thus, I would not recommend to use SIRIUS on DIA, without tuning it on DIA beforehand. Which kind of instrument/setup did you used for the measurement above?
nirshahaf
mfleisch
chrispook
AharoniLab
Hi,
There is a possible bug in the output format of the fragmentation tables of the Sirius output (the parent MF, C42H42O19 is correct): As fragments and heavier isotopic peaks are co-occurring in the data, I would expect them to be labelled according, however in the output table the isotopes are labelled as independent chemical entities, which are wrongly labelled as a +[H] of the monoisotopic mass, see:
Additionally, the corresponding fragmentation tree seems mistaken - with the [M+1]+ and [M+2]+ taken as distinct fragments and become parents of subsequent sub-trees: