I have a question regarding the creation & selection of MSMS spectral libraries in MS-DIAL.
Is it possible to select several distinct .msp files in one data processing workflow for annotation or is it necessary to have it as one msp-file?
The background of my question is that we are currently creating our Inhouse MSMS spectral library in MS-DIAL. Therefore, we already measured several hundred reference compounds with our LC-QTOF machine.
In general, we prefer to create our own separate msp-file. However, are you able to select these library as well as the database package of MS-DIAL in one data processing workflow. Or would this mean you have to annotate every data set twice, one time with “our file” and one time with the “MS-DIAL file”?
Absolutely you can merge the in house .msp file and the open source spectral .msp files into a single .msp file and use just one file for your annotation purposes!
Follow steps something like this : Steps for Building an Open Source EI-MS Mass Spectral Library for GC-MS -based Metabolomics:https://www.protocols.io/view/steps-for-building-an-open-source-ei-ms-mass-spect-8txhwpn and get it done!
To differentiate between spectra that will be from your "in house" library vs the "OS" for say, "glucose", just "tag them differently in the "NAME" field in the individual spectra in the .msp files:
But if you need an automated R or Python based solution then check out here:http://www.metabolomics-forum.com/index.php?topic=1686.0
Hope it helps!
Thanks you for your recommendations. I tried to follow the workflow you proposed, i.e.:
1) Converting raw files (I converted into abf and not mzmL for some reason)
2) Processing by MSDIAL using a pre-prepared post-processing list to be able to identify the correct MS2 spectrum more easily
3) Exporting the respective MS2 spectra as single .msp-files for each reference compound (At this point, I changed the NAME descriptions of the msp files, e.g. by adding the prefix "MRI_MS2_..." )
4) Taking one single msp-file as starting point and sequentially adding the content from the other .msp-files (via Copy &Paste in Notepad), thereby creating my in-house MSMS spectral library (.msp) file
After finishing steps 1) to 3) and starting with step 4) (putting a few .msp-files together), I wanted to check if everything worked fine. So, I took three abf-files (belonging to single standards runs: Apigenin, Apigenin 6-glucoside and Apigenin 7-glucoside). For proofing MS2 matching quality I used the following files examplerily:
1.) post processing (.txt) file including all reference compounds from my mzRT list
2.) MSMS (.msp) file consisting of approx. 20 spectra (compounds) including the apigenin compounds mentioned above.
But as I checked the results, I noticed that none of the three standard compounds shows a MSMS matching hit, although their spectra (that had been exported from the same files I used here) were put into the In-house library (.msp) file.
In order to test if the error has to do with the merging of msp-files, I also select a single .msp-file (spectrum of Apigenin 6-glucoside) for annotation. But again, there was no MSMS match for Apigenin 6-glucoside.
So I think there is still a problem with the .msp-files but I don´t know what it is.
Could you see the error?
Thanks in advance.
Thanks for following up! And doing a good job actually.
I can comment if I see the .text paramters file" and if you can share that small .msp file (this would be essential) over here or email!
These 2 files will tell me the story and I can cross check with a quick run at my end....
Happy to help further.
Thanks for your support.
Of course I can send you the required files. Unfortunately I can´t send you the msp-file here (data format not accepted).
Could you therefore send me your e-mail?
I convert the msp-files into txt-files. Hope this helps you.
as some time has passed since my last post, I want to ask, if you already had time to look for the problem? Do you see any problems regarding the attached msp-files?
Really thanks for your support.