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31
MS-DIAL / MS-DIAL beginner
Last post by ilaria. -
Hello everyone,
I'm just approaching to use MS-DIAL. I would like to ask some questions about it.

1) Is it possible to introduce METLIN library in the MS-DIAL searching? If not, do you recommend to use just the libraries downloadable from MS-DIAL website for the human metabolome?
2) Which file should I export for the metabolites quantification and which table column should I consider as a normalized value to quantify metabolites?
3) Is it possible to export only the validated metabolites after the post-processing analysis to discard the false positives?

Thank you to everyone who will reply  :)
Ilaria
32
MS-DIAL / MS Dial v5 keeps crashing + Mass normalization
Last post by mw_uwchem -
Hi all,

#1 I'm wondering if there is a solution to the newest version of MS Dial (v5) crashing? Soon after I press "Run", the software closes with no warning or error message. Also- I've updated to the newest pre-released version AND tried another user's solution to add msp files for IDs after running the initial search. When I try this, everything works fine but then the program crashes again once the msp files are uploaded. :( Is this an issue with too large of libraries or too many samples?

#2 I've started using v4.9 and am wondering if there is a scalar to normalize by sample mass? I originally was using the newest version's analytical factor column.

Thanks,
Mallory
36
MS-DIAL / Re: MS-DIAL error. Check polarity setting?
Last post by biswapriya -
Hello,

Please share the a) Parameters.text file that you can save after the analysis is concluded.
b) A link to a RAW file loaded onto Google drive or dropbox will also help me troubleshoot the issue.

Thanks,
Biswa
37
MS-DIAL / Re: No support for custom .msp library in the Lipidomics workflow in MSDIAL 4.9...
Last post by biswapriya -
Hello,
Here is a  solution that has worked for me by asking the software to run a metabolomics analysis, and uplading a lipidomics.msp spectral ibrary:

Hello,

Well, the way lipidomics workflow on MSDIAL is built is that "lipidomics spectral DB" is "inbuilt" and one can not upload external or additional libraries for spectral searches.

if you really have your own and very enriched .msp for lipids, then start as "metabolomics" in the  1st window, and then use the lipidomics .msp as reference spectral library for searching.

This should work for you!

Thanks,
Biswa
38
MS-DIAL / Re: Lipidomics MSP file can't be uploaded (lipid database setting poped up instead)
Last post by biswapriya -
Hello,

Well, the way lipidomics workflow on MSDIAL is built is that "lipidomics spectral DB" is "inbuilt" and one can not upload external or additional libraries for spectral searches.

if you really have your own and very enriched .msp for lipids, then start as "metabolomics" in the  1st window, and then use the lipidomics .msp as reference spectral library for searching.

This should work for you!

Thanks,
Biswa
39
MS-DIAL / Molecular network with MSdial
Last post by yj -
Hi everyone!

I use msdial for molecular network, but I use msdial for molecular network analysis （not for GNPS/FBMN）, and the exported node information contains color. I initially thought that the color corresponds to ontology, and that black represents unidentified compounds. However, I found that some identified compounds are black, and compounds from different ontologies have the same color. Therefore, I would like to ask how the color is assigned to the compounds.

thank you
yj
40
MS-DIAL / Lipidomics MSP file can't be uploaded (lipid database setting poped up instead)
Last post by taufiq -
Hello,

I just started a lipidomics project. When setting up the analysis parameter setting, I tried to insert/upload the MSP database in the Identification tab. However, it did not browse to the location of my MSP data, instead, the lipid database setting popped up.

Previously I was working with the metabolomics and had no problem inserting the MSP data during that time. Is there any setting that I mislook?

Attached are the screenshots of my problem. First is the Identification tab, and second is the lipid database setting.

I appreciate your assistance!

Edit: I'm using MS DIAL 4.9.221218