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Messages - Sukis

3
MS-DIAL / Re: Problem with converting NIST library to MS-DIAL
Hello Hiroshi and Biswapriya,

Thank you for your comments and contributions in the field. I tried your suggestions and it worked well for converting my NIST 08 MS/MS library into MSP using LIB2NIST. But I am really interested in converting the main library which  contains the EI GC-MS data. Unfortunately, I did not find any file for the mainlib to be converted. Also, I tried to export a selected spectrum from the ms search as Biswapriya suggested but it did not contain the retention index data and I think this approach can not be implemented for the whole library (batch export). Any ideas or tips to integrate the NIST GC-MS library (compiled EI-spectra with their retention indices)  with MS-DIAL.
Thanks a lot for your help.

Ahmed Serag, PhD
Assistant Professor
Department of Analytical Chemistry
Al-Azhar University School of Pharmacy



Hi Ahmed Serag,
Did you succeed in converting NIST 08 MS/MS library into MSP using LIB2NIST?


Best,
Sukis
7
MS-DIAL / Re: MSDial crashes after closing Table viewer
Dear Martin,
In my experience, if I am editing the alignment table (see picture below), and at the same time press Ctrl + D to change the feature to unknown, the program will crash. It happens all the time. So, to change the feature to Unknown in the alignment table, we have to make sure that we are not editing the table.

I don't know if this is your situation. Hope it is helpful for you.

Best,
Sukis
8
MS-DIAL / Re: How to convert NIST library (GCMS) into .msp format to use in MS-DIAL?
Hi Kumar M,
Please take a look here. http://www.metabolomics-forum.com/index.php?topic=1439.msg4270#msg4270

Besides,
 GCMS library is not suitable for LCMS data as GCMS uses hard ionization while LCMS uses soft one and the fragments of a given substance in these two systems could vary a lot. For annotating LCMS data, Hiroshi's team has compiled publicly available libraries in both positive and negative modes. You can download libraries here http://prime.psc.riken.jp/compms/msdial/main.html#MSP.

Best,
Sukis
9
MS-DIAL / Re: Importing Sciex Data for Building In-house Mass Spectral Library in MSDIAL
Hi FalcoB,
Maybe you can take a look at this paper (Tada, I., Tsugawa, H., Meister, I., Zhang, P., Shu, R., Katsumi, R., Wheelock, C.E., Arita, M., Chaleckis, R., 2019. Creating a reliable mass spectral–retention time library for all ion fragmentation-based metabolomics. Metabolites 9. https://doi.org/10.3390/metabo9110251).

In my experience, I used target analysis (prepare a target list that contains all injected standard for MS-DIAL) without considering retention time. Then MS-DIAL will annotate all features with the matched mass, and I exported these features into a folder. Then you can import these features to MS-FIDNER and export them to *.msp in MS-FINDER. If you have all metadata prepared in the target list then they will be included in the *.msp file. Of course, you can also edit them in MS-FINDER. You can do this in a batch way, for example 10 standard as a batch. But just be careful not to put standards with the sample formula into a same batch because you will not able to distinguish which is which.

Best,
Sukis
10
MS-DIAL / Re: Processing CCS files from Waters Vion ?
Dear Hiroshi,
According to Dr. Kyo Bin Kang, if one works with normal QTOF (not IMS-TOF) and UNIFI software, then he/she can export data as *.RAW which is readable by Masslynx. With the *.RAW files, then he/she can follow your MS-DIAL tutorial. However, I still fail to process IMS-TOF data from UNIFI software.

Best,
Sukis
13
MS-DIAL / Re: Updates of MS-DIAL and MS-FINDER for Windows/Mac/Linux
Happy new year! Wish everything goes well with you.

Thanks a lot to you and your team for the fantastic work!
By the way, do you think it is feasible to implement structure viewer in MS-DIAL in the future? That would be fantastic! If a feature is identified in MS-DIAL (with SMILES), then we can see the structure directly in MS-DIAL.

Best,
Sukis
14
MS-DIAL / Re: (Post)Alignment Processing - Blank filter option
Hi FalcoB,
Did you untick "Keep 'reference matched' metabolite features" and "Keep 'suggested (w/o MS2)' metabolite features" in the alignment tab? In my understanding, if you tick any of these two options, then you will have some match/suggested features kept in the list even though they are in blanks as well. I had the same confusion before, but now, when I untick them, the final list is good now.

Best,
Sukis