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Topic: MS/MS Spectrum Match is available now (Read 8028 times) previous topic - next topic

MS/MS Spectrum Match is available now

Hi METLIN users,

I'm very glad to announce that we recently launched a new tool for MS/MS Spectrum Match, which allows users to ID known/unknown compound with a score (based on the modified X-Rank Algorithm).  The current version requires to enter m/z, intensity (of the user's MS/MS data) with a few parameters to search against METLIN's MS/MS database (currently ~5400 LC MS/MS data).

Please feel free to use the new feature, and give us some feedbacks regarding the tool.

You can check the awesome feature at http://


Re: MS/MS Spectrum Match is available now

Reply #1
Thanks! This is FANTASTIC!

A question: I want to make sure that I'm interpreting my search results correctly; is there an explanation somewhere for how to interpret the lines in the spectra listed under "spectrum matching"? I believe that the upper half of the spectrum is what I submitted, but I'm not sure why sometimes the line is blue and sometimes it's black, and the bottom must be what is in the database. How are you determining the length of the line? On the top, is that what I submitted and then the bottom is the residual of the fit to what's in your database?

Thank you very much for a great tool!



Re: MS/MS Spectrum Match is available now

Reply #2
Hi Laura,

Thank you for using METLIN, and I am very glad that you like the tool :)
Answering your questions,
- I am working on creating a manual for users, which will be available on the web shortly.  Please visit the site frequently :)
- You are correct, the upper half of the spectrum is what you submitted, and the bottom half of the spectrum is from the METLIN MS/MS data of the standard compound analysis, the blue line(s) indicate(s) the matching peaks between your data vs. METLIN's data, and black lines are the rest of peaks that you submitted or our data that do not match with your peaks.
- The length of the peak is a relative intensity from your data and METLIN's data.  We recalculate your maximum intensity peak as 100%, and then other peaks are relative to the strongest intensity peak.

So, based on your data and our data, we compute the possible matching score, and display it in the METLIN score column.

Please feel free to contact me if you have further questions, and leave me comments if you have advices.


Re: MS/MS Spectrum Match is available now

Reply #3
Hi, Kevin.

A question: To see the exact m/z of a peak in an MS/MS spectrum from a METLIN hit, I need to MouseOver that peak. Is it possible to get the m/z and intensities in a csv or other numerical format? I want to compare the peaks I see in the database side by side with the peaks in my spectrum, and it would be much faster if I could just download the numbers rather than mousing over each and writing down the value.



Re: MS/MS Spectrum Match is available now

Reply #4
I am facing some issues in METLIN Batch and MSMS spectrum search.

1. I am unable to download the searched results by batch analysis of input masses.

2. I am unable to search MSMS Spectrum. It is not showing any hit, even for your example data.

Is there any technical problem goin on?

Please help.

Re: MS/MS Spectrum Match is available now

Reply #5

I have one same problem, I can open the metlin database website, but I have a trouble to open the metlin msms spectra, i don't know why it doesn't show up in my computer in China. How to resolve this problem?

Thanks a lot! Please help!