MSDIAL Beginner

November 22, 2023, 11:36:46 AM

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

Re: MSDIAL Beginner

Reply #1 – November 26, 2023, 05:07:06 PM

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