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41
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
42
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



43
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,
44
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."
45
Other / Extract backpressure information from Aglient .d LC-MS data.
Last post by joergbuescher -
I'm currently trying to set up a script that should automatically check if the backpressure of my LC-MS runs is within the ok range and then send a warning email if the pressure increases (rather than waiting for the system to crash with an overpressure error). To this end, I would like to automatically extract the backpressure information from the recorded .d files. I've tried conversion of .d to .mzML using proteowizard/msconvert, but unfortunately the backpressure information is not contained in the output. Any ideas for how to solve this (preferrably in R) are most welcome.
Thanks for your help!
47
MS-DIAL / Re: MSDIAL Beginner
Last post by James -
Hi phgreer,

Does the facility that ran your samples have any training support available for data analysis? This might be helpful for getting you started. You can also try to follow the MS-DIAL tutorial if you haven't already: https://mtbinfo-team.github.io/mtbinfo.github.io/MS-DIAL/tutorial.html

To try to answer your questions:

1. The most important thing is that you choose a library that matches the way your data were acquired. Were the data acquired with GC-MS or LC-MS/MS? If the latter, was it in positive or negative mode? If, for example, your samples were analysed using LCMS/MS, with positive mode electrospray ionisation (ESI), you could use the "ESI(+)-MS/MS from authentic standards (16,481 unique compounds)" library from MSDIAL's set of curated libraries. The facility might also have access to a more comprehensive commercial library. If you are unsure how your samples were analysed, you should check with the person who acquired your data.

2. The libraries we are talking about above are what is required in the identification tab - if you download from MSDIAL it will be in .msp format, which is basically just a text file. But if you have an excel file with retention times from your samples, it sounds like the facility has already done some data analysis of your samples for you? If so, depending on your needs you might not need to use MSDIAL at all. Hard to say with info in your post.

3. Yes that is OK, MSDIAL processing will run without standards, or QC samples for that matter. Standards are useful if you want to confirm the identification of particular metabolites or quantify the metabolites in your sample, but it is probably OK not to have them for a qualitative, untargeted metabolomics project.

Cheers,
James
48
MS-DIAL / MSDIAL Beginner
Last post by phgreer -
Hi everyone,

I'm just starting out with using MSDIAL and have a few initial questions. Would be great if anyone was able to help out with all or any of these please :) I am working with metabolomics data acquired from drosophila samples. My questions are:

1. In terms of selecting a library to use, I've had a look at the MSDIAL website and the downloads available on MONA at https://mona.fiehnlab.ucdavis.edu/downloads ,but I'm unclear on how to go about selecting one. For e.g. are they all suitable for all sample types or organism specific?

2. I understand that I also need to upload a library text file under the identification tab. I received an excel file with retention times from the facility that carried out the data acquisition. I'm wondering if this is what I would need to attach here (in text format) or if it's something else I would need to upload?

3. Finally, when I come to the section where I input samples to process:  from the files sent to me by the facility that acquired the data I don't think I have anything that can be input as a standard in the class ID column when adding all my samples. Is it okay only to be entering pooled, QC and sample info ( and not any standards) or am I missing something?

If anyone can offer me any advice re the above it would be a massive help to me. Thanks :)
49
R / QExactive MS1 metabolomics
Last post by np28 -
I have direct infusion positive mode MS1 data from the QExactive, multiple replicates gathered across several batches across many months. Most of the software / R packages I have seen like XCMS, MS-DIAL, etc. seem to deal primarily with LC-MS data. What would a data-processing pipeline for this data look like and is there already an established workflow in R for DIMS data? I would like to go from ThermoRAW files to a background corrected, deisotoped, adduct-collapsed matrix of samples vs features.
50
Other / File Conversion - LECO Data
Last post by Mark Bernards -
I am having trouble finding a way to convert Leco data (*.smp) from a Pebasus BT system into netCDF or mzML for import into XCMS. Can anyone suggest software or a mechanism to do this?

Mark