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Topic: Alignment list interpretation (Read 89 times) previous topic - next topic

Alignment list interpretation

Hello

I am processing Mzml files in MS-DIAL and I exported the Alignment results to Excel, however, it is not quite clear for me how to interpret the results in the columns. I understand that, roughly speaking, this is a list with all the possible metabolites that my samples could have, however, I don’t completely understand the post creation section.

What does “ion correlated with….. exactly mean? I checked such correlations with the numbers and some metabolite names happen to be same, but not all of them. Also, Does “w/o MS2:” mean that these metabolites were identified without using MS/MS and the ones that do not state this were identified using MS/MS?

Finally, the remaining columns in this spreadsheet, How do I interpret the fact that most of my rows state ‘False’ and ‘null’?

Thank you very much for your attention


Re: Alignment list interpretation

Reply #1
Hi,

>>What does “ion correlated with….. exactly mean?
The detail is described in the following article.
https://www.nature.com/articles/s41592-019-0358-2

1. The ion correlation linkage is made if users import >= 9 samples.
2. The peaks within +/- 0.06 min are currently evaluated.
3. The correlation value of ion abundance profile e.g. between alignment spot A and alignment spot B is calculated.
4. If the correlation value is more than 0.95, the spots are linked.


>>Does “w/o MS2:” mean that these metabolites were identified without using MS/MS and the ones that do not state this were identified using MS/MS?

Exactly. See the FAQ site.
http://prime.psc.riken.jp/compms/msdial/faq.html
What is the 'w/o' tag of identification results?
1. This program first tries to find a metabolite candidate from a MSP file by means of MS/MS similarity, accurate mass, isotope ratio, and retention time. A metabolite getting 'highest score' in the metabolite candidates is annotated. Note that this score is the total score from retention time similarity, isotope ratio similarity, accurate mass similarity, and MS/MS similarity.
2. But if the 'highest score' is less than user-defined identification cut off, 'non-MS/MS based identification' is performed. That is, this program next tries to find a metabolite candidate by means of accurate mass, isotope ratio, and retention time. Then, a metabolite getting 'highest score' in candidates is annotated. Note that this score is the total score from retention time, isotope ratio, and accurate mass. This result will be shown as 'w/o MS2:***'.
3. If any compounds are not found from the above two criteria, the result will be 'unknown'.


>> How do I interpret the fact that most of my rows state ‘False’ and ‘null’?
Many fields are filled (by TRUE or a value) if the metabolite is annotated by MSP spectral libraries.
Basically, they are used to clarify the "matched" criteria for annotating metabolites. And, the fact is used to generate the annotation code supported by MS-DIAL.
http://prime.psc.riken.jp/compms/msdial/annotationcode.html
The code is also described in PSI.
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo

Thanks,

Hiroshi Tsugawa