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Messages - Seb

Is there a METLIN API available? Or is there any way to export results tables as .xml?


Hi Justin,

Thanks for the info.

Dear Paul,

OK, I'm looking forward to see the changes implemented. And the Bilbao circle is small and I will say hi to Oskar G when I see him :)


Dear Paul,

Thank you so much for your reply (and Reza for forwarding this to you). Clear annotation might indeed solve the problem.

In any case, could you provide a link to the software/literature to generate the spectra?

And I will say hi to Oscar (M?) :)


Dear Meow,

Although I'm sorry to hear that you wasted time on this issue as well, I am glad  that I was not the only one. Maybe this could motivate the METLIN people to address this issue.

Furthermore I would like to reiterate my point about the low quality of the in silico spectra. In Fig 1 I show a low (5 V, bottom) and high (20 V, top) energy spectrum of  LPC(18:0) (a lysophosphatidylcholine) at m/z 524 as measured on our SYNAPT G2 ToF instrument. Fig2 are the low (bottom) and high energy (top) predicted spectra as found in the METLIN database. The differences are obvious.

I know for sure that 104 and 184 peaks in Fig 1 are characteristic for (L)PCs on any type of MS, however these are not obvious or completely missed by the predictions. Yet the predicted spectra show a whole bunch of peaks that are nowhere to be found in the actual spectra. This is just an example; I found more obviously wrong spectra. I really think these in silico specs should be removed from the database or at least should not be shown in the current form.

I would like to hear some opinions from the METLIN db curators if possible. However I am not sure how to contact them besides this forum.



Fig 1) High (top) and low (bottom) energy spectra of LPC(18:0) as measure on a SYNAPT G2 ToF.

Fig 2) High (top) and low (bottom) energy spectra of LPC(18:0) in silico predicted as found on METLIN

METLIN / In Silico predicted MS spectra - A good idea?

I noticed that as of recently most of the compounds currently in the METLIN online database are accompanied by CID MS spectra in positive ionization mode. At first I was delighted because this information proofed to be extremely helpful for me identifying certain metabolites. However, my mood rapidly changed when I found out that most of these newly added spectra where in silico predicted.

My problem is that many of the in silico spectra are not indicated as such (e.g. Fig. 1), leaving me to think that they are based on actual empirical data (as was the case before). This caused me a great deal of confusion. Moreover, having seen many physical CID MS spectra, to me, all these predicted ones did not seem to have much to do with reality. I would like to know what program was used to make these spectra and how well this software preforms.

In conclusion, if you decide to add in silico spectra please indicate this very clearly and explicitly state the software used. But in all honesty I do not think they are very helpful and are going to cause a lot of confusion. I would like to hear some other opinions on this matter.



Fig. 1) An in silico predicted spectrum which is not indicated as such.