MSMS match main page feature does not show up in compound search list

January 15, 2020, 05:59:33 PM

I've noticed when using both metabolomics and lipidomics msp that several times per set, the feature that shows up on the main gui page when I have a feature annotated by MSMS will not show up in the list of possible features when I click the compound search button.

As hopefully can be seen from these screen shots, the compound that shows up in the main page of the gui is PE P-33:1|PI P-16:0_17:1, but this compound does not show up as one of the matched options in the compound search page. Only PE O compounds show up.

I just wanted to report this issue. I've seen it in past versions and am seeing it in the current version 4.12 as well.

Re: MSMS match main page feature does not show up in compound search list

Reply #1 – January 19, 2020, 09:33:49 AM

Hi,

yes, it's true. Sorry, probably, all users will be able to know what ms-dial does in the program for lipid annotations once I can reach to the publication of MS-DIAL 4 paper. All algorithms are there actually. I hope, it will be published in this summer...

Simply: the current MS-DIAL program performs a "hybrid" annotation system including
(1) a classical similarity matching (dot-product and reverse dot product) algorithm
(2) a rule-based decision tree algorithm to describe an appropriate structure representation of lipids by considering the mass fragment ions.

Now, the MSP file records are actually used for the first purpose (dot-product and reverse-dot product). And the spectrum similarity score is used to filter out the noisy spectra. Currently, in lipidomics project, if the dot product score is less than 0.1 AND the reverse dot product score is less than 0.5, the spectrum is recognized as "Unknown" at this stage.
Then, the mass fragment ions are evaluated by the decision tree program. In the ether PE case, the experimental spectrum is evaluated to judge if it's from plasmanyl type- or plasmenyl type. Then, if the spectrum was estimated as "plasmenyl (plasmalogen) type", the representation is changed from PE O-XX:X_YY:Y to PE P-XX:X-1_YY:Y.

Does it make sense for you?

Hiroshi

Re: MSMS match main page feature does not show up in compound search list

Reply #2 – January 21, 2020, 04:29:18 PM

Yes that makes sense. That gives me a better idea about what I'm looking at. Thanks!