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Topic: Few issues about MSDIAL and MSFINDER (Read 554 times) previous topic - next topic

Few issues about MSDIAL and MSFINDER

Hi,
here are some issues and my own expectations for MSDIAL and MSFINDER.

MS-DIAL (data independent LC-MS/MS)
   a. When dealing with Waters MSE data, in my experience, it is better to remove function 3 files (_FUNC003.DAT, _FUNC003.IDX, AND _FUNC003.STS, they are for the lockmass) from the *.raw file before converting into *.abf file for MSIDAL processing. Otherwise, the deconvoluted MS/MS spectra might weird. 
   b. There is always an error "library information should be imported". But I have MSP library downloaded from RIKEN, and use it for the identification. Is it only available when the spot hit any library?
   c. I am wondering if MSDIAL allows manually identification of any feature since the requisite of uploading spectra to MoNA is that the feature has to be fully identified. If I wanna submit the spectrum of a compound, I know which spot is the compound, but how can I assign metadata to that spot and then submit it? And I think it will be useful to allow to export the identified spot as local database, e.g. *MSP file.
   d. Can anybody tell me what is  correlation based deconvolution? I could not find useful information to fully understand what is it for.

MSFINDER
   a.Is it possible to the selected rather than all local databases for formula scoring? I think it will be nice for research areas other than metabolomics.
   b. Is it possible to allow us to mark down the probable correct structure we think? It seems like the "reflect MS-FINDER result to MSP/MAT file" function. The difference is that it would be better to permit us to select the one we want instead of to choose always the top 1 candidate. And it would be very nice to allow exporting the "identified" compound (meta data) together with MS/MS spectrum as a MSP file. It will facilitate building library and then submit to open library since metadata are already there.
Using predicted retention time to structure elucidation is really a good idea. However, is it possible to allow user to integrate their well train model (for example trained and tested by Retip R package) for the prediction instead of using the simple XLogP method?
       


Re: Few issues about MSDIAL and MSFINDER

Reply #1
Hey Sukis,

I think I can answer C and D for you. C, If you want to annotate a feature by hand, you can click the spot and then "show ion table," from here you can type whatever you like into the comment box. If I understand you're asking, that should help. D, if you're doing SWATH or something similar, the deconvolution works by matching EICs of fragment ions with that of parent features. Fragments that have similar EICs are displayed as the deconvoluted MS2 of that feature. The MS-DIAL paper has more details.

~Matthew

Re: Few issues about MSDIAL and MSFINDER

Reply #2
Hi Qi-Zhi,

I wrote my answers below.

MS-DIAL (data independent LC-MS/MS)
 a. When dealing with Waters MSE data, in my experience, it is better to remove function 3 files (_FUNC003.DAT, _FUNC003.IDX, AND _FUNC003.STS, they are for the lockmass) from the *.raw file before converting into *.abf file for MSIDAL processing. Otherwise, the deconvoluted MS/MS spectra might weird.

According to my understanding, the function storing lock mass data is not stored in abf. If you see such an issue, we have to ask the developers of abf converter. Please send me an example .raw file of Waters if you face on such an issue.


b. There is always an error "library information should be imported". But I have MSP library downloaded from RIKEN, and use it for the identification. Is it only available when the spot hit any library?

I checked the source code, and the error is displayed if the msp information is not imported. If you face on the problem even though you imported your msp file, please send me the demo files to reproduce it on my PC.


c. I am wondering if MSDIAL allows manually identification of any feature since the requisite of uploading spectra to MoNA is that the feature has to be fully identified. If I wanna submit the spectrum of a compound, I know which spot is the compound, but how can I assign metadata to that spot and then submit it? And I think it will be useful to allow to export the identified spot as local database, e.g. *MSP file.

As Matthew said, you can put your "comment" to commend field in the peak/alignment table viewer. But there is no way to organize InChIKey and SMILES etc in MS-DIAL application. I will make a method of "private MSP-builder" in MS-DIAL program.


d. Can anybody tell me what is  correlation based deconvolution? I could not find useful information to fully understand what is it for.

The CorrDec algorithm is now submitted to a journal. Sorry for the delay.
There is one publication including a brief feature of CorrDec here: https://www.mdpi.com/2218-1989/9/11/251


MSFINDER
a. Is it possible to the selected rather than all local databases for formula scoring? I think it will be nice for research areas other than metabolomics.

OK. I will edit the program.


b. Is it possible to allow us to mark down the probable correct structure we think? It seems like the "reflect MS-FINDER result to MSP/MAT file" function. The difference is that it would be better to permit us to select the one we want instead of to choose always the top 1 candidate. And it would be very nice to allow exporting the "identified" compound (meta data) together with MS/MS spectrum as a MSP file. It will facilitate building library and then submit to open library since metadata are already there.

OK. As I said in MS-DIAL, I will also write the source code of the private MSP builder in MS-FINDER as well.


c. Using predicted retention time to structure elucidation is really a good idea. However, is it possible to allow user to integrate their well train model (for example trained and tested by Retip R package) for the prediction instead of using the simple XLogP method?

Currently, users can use their own rt library having the pair of RT and InChIKey.
http://prime.psc.riken.jp/compms/msfinder/main.html#Templates

But unfortunately, there is no method to import the model file (for example developed by R). So you have to prepare the list of rt-inchikey pairs.

Hiroshi

Re: Few issues about MSDIAL and MSFINDER

Reply #3
Many thanks Matthew. The comment box helps as well. I will refer to the article about correlation-based deconvolution for further detail.

kind of regard,
Sukis

Re: Few issues about MSDIAL and MSFINDER

Reply #4
Hi Hiroshi Tsugawa,
1. I am sorry that I cannot remember where I have the confusion regarding lockmass in the .raw file. Maybe I have made a mistake, but I am not sure. Anyway, I will keep my eyes on the issue in future use. 
2. As for the problem about importing the library. I found it my fault. The problem was that my library was suffixed with capital "MSP". I now change it into lower cases "msp" and it works fine. It is a little bit odd that my GC-MS library was suffixed with capital "MSP" as well, but it works well.
3. Thank you very much for developing and maintaining the Softwares. They are really excellent and useful.


Best regards,
Sukis

Re: Few issues about MSDIAL and MSFINDER

Reply #5
Hi Hiroshi,

" a. When dealing with Waters MSE data, in my experience, it is better to remove function 3 files (_FUNC003.DAT, _FUNC003.IDX, AND _FUNC003.STS, they are for the lockmass) from the *.raw file before converting into *.abf file for MSIDAL processing. Otherwise, the deconvoluted MS/MS spectra might weird.

According to my understanding, the function storing lock mass data is not stored in abf. If you see such an issue, we have to ask the developers of abf converter. Please send me an example .raw file of Waters if you face on such an issue."

I recently encountered this problem again. i think i find a good example now.

I upload two screenshots here. after removing the function 3 from the raw file, the deconvoluted MS/MS is much better.

maybe I can send you my file when you have time.



Re: Few issues about MSDIAL and MSFINDER

Reply #6
OK Sukis: now I have time to check the raw data. Please send me the raw data file.
Thanks,

Hiroshi

Re: Few issues about MSDIAL and MSFINDER

Reply #7
Hi Sukis,

at least, the raw data/converted abf from you was fine in my side when checking the result of deconvolution.
I also confirmed that Function 3 was excluded in abf.
Could you please check the parameter setting again?
Thanks,

Hiroshi

Re: Few issues about MSDIAL and MSFINDER

Reply #8
Hi Hiroshi,

Thanks a lot for testing. I understand now it was because of the abf converter I used (an old version probably). Downloading the latest abf converter, it works fine now.

regards.