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34
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
35
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
36
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
37
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
38
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



39
MS-DIAL / No support for custom .msp library in the Lipidomics workflow in MSDIAL 4.9...
Last post by capkavl -
Hello all,
We made a custom .msp lipidomics library and would like to use it in MSDIAL 4.9.221218. However, in the lipidomics workflow, the program does not allow us to select the .msp file. The select button takes you to lipid subclass slection but does not allow us to browse to the library file. We tried to paste the path to the .msp file in the selection box but upon processing, this link is ignored and a default, build-in library is used instead.
Does anyone have any advice on how to solve this problem?
Thank you,
40
MS-DIAL / MS-DIAL error. Check polarity setting?
Last post by Oryza -
I have LC-MS（Shimadzu）lcd. files and need to analyse with MS-DIAL. I followed below steps and at the end I get a message "No peak information. Check your polarity setting."

1. Converted .lcd files to .mzML using ProteoWizard

2. Converted .mzML files to .abf using Reifycs Analysis Base File Converter

3. imported .abf files to MS-DIAL and ran with below settings:

4. MS1 Data type (Centroid data)

5. MS/MS (Centroid)

6. Ion mode (Negative)

7. Metabolomics

8. Libraries loaded (MSMS-Neg-Vaniya-Fiehn_Natural_Products_Library_20200109.msp / BioMSMS-Neg-PlaSMA.msp / MSMS-Neg-FiehnHILIC.msp)

9. Get below error
"No peak information. Check your polarity setting."