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Topic: About the identification result. (Read 2490 times) previous topic - next topic

About the identification result.

Hi All,
 I found something wierd about the identification result of  my LC-MS/MS profiling data,  The identification score cut off was set as 90% (see the attached screen shot) and a list of metabolites were identified. However, the annotation  seems  performed only based on MS1 ions. All identified metabolites in the exported alignment result table were annotated as false "MS/MS matched"  while the  total  scores were mostly more than 90 (see attached table). I have checked some of the annoted candidates and  make sure that the MS2 spectral was not matched well with  the reference spectral. I can't understand the scoring rules because I think the candidate MS/MS spectral should matched very well with the library spectral when  a high score was given. Could you please help me to remove this confusion?

Thanks

Yong Li

Re: About the identification result.

Reply #1
Hi,

sorry for this confusing result in the current msdial output.
In processing tandem mass spectral data, there are two ways for annotation scoring.
(1) based on RT, isotope, m/z accuracy, and MS/MS similarity
(2) based on RT, isotope, m/z accuracy.
Both scores are normalized (in metabolomics project) to 100 as the maximum score.

The problem is
(A) when a peak is annotated by the first criteria, the annotation will be performed by the second criterion.
(B) the second criterion was basically for the peak that does not have MS/MS spectrum information. However, it will be also applied to the peak having MS/MS spectrum if the peak is not annotated by the first criterion.

If the peak is annotated by the second criterion, the "w/o MS2: " tag is assigned.
The current problem is that the annotation scores of first and second criteria are normalized to 100 in both cases.

>>I think the candidate MS/MS spectral should matched very well
Check your m/z accuracy for ms1 and ms2. As a trial, please use a wider mass tolerance for ms1 and ms2.

Thanks,

Hiroshi