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MS-DIAL / Re: MSDIAL Beginner
Last post by James -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