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Topic: MS-DIAL (version 4.16) MSP database selection and mass tolerance (Read 3300 times) previous topic - next topic

MS-DIAL (version 4.16) MSP database selection and mass tolerance

Dear users,

I encounter an issue of the MSP database selection in metabolomics in MS-DIAL as follow,

I performed the plasma metabolomics test and followed the MS-DIAL paper (nature method, DOI:10.1038/NMETH.3393). The polar metabolites extraction and LC-MS conditions were similar to the paper description.

My MS data (Waters, Mse data)  was processed by MS-DIAL and the MSP database file was chosen All Public (please see the attached figures). The ref. matched metabolites are around 400. However, the ref. matched metabolites are 0 when I chose the Fiehn HILIC database. (Because I used HILIC column and follow similar LC-gradient). Why is so large difference by using two databases and at least some metabolites should be overlap?

In addition, another important value is Accurate mass tolerance (MS1). When I put 0.025 Da (follow tutorial), the ref. matched metabolites are 0 but I put 0.05 Da, the ref. matched metabolites are around 400. I checked my MS raw data, the mass accuracy could be 0.025Da tolerance but not sure why the MS-DIAL can't recognize it well.

Any comments and suggestions are all welcome and hope the experienced user could help me solve them.

Thanks for your attention

Best,

Bingpeng

Re: MS-DIAL (version 4.16) MSP database selection and mass tolerance

Reply #1 –
Hi Bingpeng

The msp files that I currently uploaded on my website do not include retention time information.
So, if you use my files, you should not tick "use RT for scoring and filtering" in annotation process. If you use RT info for (e.g.) Fiehn HILIC DB, please directly download it from MoNA.

>>In addition, another important value is Accurate mass tolerance (MS1). When I put 0.025 Da (follow tutorial), the ref. matched metabolites are 0 but I put 0.05 Da, the ref. matched metabolites are around 400. I checked my MS raw data, the mass accuracy could be 0.025Da tolerance but not sure why the MS-DIAL can't recognize it well.

I do not know the reason by the information only. Because all of the precursor values on my website' msp files was theoretically calculated, the annotation should based on the mass accuracy of MS machine.
Was the accuracy checked by MS-DIAL GUI? or MassLynx?
One possibility is that in some conditions, the lock mass calibration data is not reflected into the abf file. Please check this. Then, if you see that the abf data does not have a correct calibrated mass, please try to use msconvert (followed by mzML creation) to get the correct mass value.

Thanks,

Hiroshi
 

Re: MS-DIAL (version 4.16) MSP database selection and mass tolerance

Reply #2 –
Dear Hiroshi,

Thanks a lot for your explanation and suggestions.

I think the problem may be associated with the option of "RT for scoring and filtering". In addition, the MS-DIAL internal library (lipidblast) need to be clicked the option (RT for scoring and filtering), right?

Another issue of "Accurate mass tolerance (MS1)" was also stranged.

I used to perform multiple lipidomics data with MS-DIAL and the value was set 0.01 in the option of "Accurate mass tolerance (MS1)" under the identification tab (please see the attached figure). Then it could obtain a lot of ref. matched lipids in final results.

However, the 0.025 was set for metabolomics could not match well. I will check the mass accuracy later.

Thanks again.

Best,

Bingpeng