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Topic: How to update library with new compounds in MS-Dial (Read 186 times) previous topic - next topic

How to update library with new compounds in MS-Dial

Hey everybody,

I wanted to touch on something that has me confused. I have both MS-Dial and MS-Finder on my computer, but if I'm being honest I'm not really sure how to properly use MS-Finder. I believe it should be useful for the process I'm about to mention, but I'm not 100%. The purpose of MS-Finder is less-than-clear even after reading through the documentation.

In short my lab has an in house library. We purchased it from IROA & utilized their processes & software to generate a 500-600 metabolite RT enforceable library. While it's useful, compared to the large public libraries without enforceable RTs, it is limited. We have a large number of analytical reference standards in house that we'd like to run on our system & incorporate into our in house library. Unfortunately IROA  doesn't allow for inclusion of standards that aren't included in their kit so we're looking to MS-Dial and/or MS-Finder to fit the role.

Ideally we would like to do the following:

-Generate a reference standard or mixture of standards
-Analyze standards by LC-QToF-MS in both (+) and (-) ESI
-Import data to MS-Dial
-Identify peaks of standards (likely under the 'unknown or suggested' features)
-Annotate reference standard peak spot with ID & RT information
-Update in house library file(.msp) with additional information

Would MS-Dial alone suffice for this or would MS-Finder be required? If MS-Finder is required how do we update/append the in house library file(.msp) properly? Is there an intended set of instructions?

I saw another forum post where a user provided an R script for it. Also saw responses demonstrating that one could open the library file(.msp) in a text doc & manually update it with cut&paste info from another library file(.msp).

That said I envisioned there was a way to do this easily, but I'm finding it more difficult than originally planned. Do you guys have any recommendations on best practices for this process? Do I need an extra program like MS-CleanR to do this properly?

Lastly - the times I've used MS-Finder I've found myself rather lost. The program is confusing & not being able to clear the cache of previous work is even more confusing. Are there plans to improve documentation on it in the future or is it about as advanced as it's going to get for now?

Feel free to link me to other resources if you feel this information has already been covered at length.

Re: How to update library with new compounds in MS-Dial

Reply #1

I think you can export all reference spectra into a single folder from MS-DIAL. Then you can import all these spectra into MS-FIDNER and then export to a *.msp file. I suggest you put positive and negative spectra into two folders so that you can finally get positive and negative libraries separately. Once, you have new reference spectra processed by MS-DIAL, then you can export to the same folder and re-import into MS-FINDER to export the latest *.msp file.

Another thing is that you can use the post-identification function in MS-DIAL. For example, I prepare a *.txt file (see below. please follow the MS-DIAL tutorial) for post-identification, where I put the name, InChIKey, Formula, SMILES, Adduct, and corresponding m/z (it is important as MS-DIAL use it for identification), but leaving RT as -1. currently, I only consider M+H, M+Na, M+K, M+NH4, 2M+H, 2M+Na, 2M+K as well as 2M+NH4 for positive mode. With all this information, you can easily check which feature could be the true one for your reference standard and the exported spectra will contain this meta-information as well. Otherwise, you will have to manually add meta information for each spectra in MS-FINDER.

You can also use LIMA software for the management of you *.msp libraries.

Qizhi Su

Re: How to update library with new compounds in MS-Dial

Reply #2
Thank you very much for the helpful information