About the identification result. January 13, 2021, 09:28:02 AM 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?ThanksYong Li Quote Selected
Re: About the identification result. Reply #1 – February 07, 2021, 05:15:51 AM 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 Quote Selected