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Messages - berrytf

16
MS-DIAL / Re: Retention times in MS-DIAL library.
Which library are you talking about specifically? There are two large conglomerate spectral library (+ & -) as well as a bunch of smaller individual libraries from various groups. The individual libraries likely all have different conditions specific to the group/labs that generated. If you can find the initial publications from those groups or the MS-Dial group you can often locate the LC-MS conditions.
18
MS-DIAL / How to update library with new compounds in MS-Dial
Hey everybody,

I wanted to touch on something that has me confused. I have both MS-Dial and MS-Finder on my computer, but if I'm being honest I'm not really sure how to properly use MS-Finder. I believe it should be useful for the process I'm about to mention, but I'm not 100%. The purpose of MS-Finder is less-than-clear even after reading through the documentation.

In short my lab has an in house library. We purchased it from IROA & utilized their processes & software to generate a 500-600 metabolite RT enforceable library. While it's useful, compared to the large public libraries without enforceable RTs, it is limited. We have a large number of analytical reference standards in house that we'd like to run on our system & incorporate into our in house library. Unfortunately IROA  doesn't allow for inclusion of standards that aren't included in their kit so we're looking to MS-Dial and/or MS-Finder to fit the role.

Ideally we would like to do the following:

-Generate a reference standard or mixture of standards
-Analyze standards by LC-QToF-MS in both (+) and (-) ESI
-Import data to MS-Dial
-Identify peaks of standards (likely under the 'unknown or suggested' features)
-Annotate reference standard peak spot with ID & RT information
-Update in house library file(.msp) with additional information

Would MS-Dial alone suffice for this or would MS-Finder be required? If MS-Finder is required how do we update/append the in house library file(.msp) properly? Is there an intended set of instructions?

I saw another forum post where a user provided an R script for it. Also saw responses demonstrating that one could open the library file(.msp) in a text doc & manually update it with cut&paste info from another library file(.msp).

That said I envisioned there was a way to do this easily, but I'm finding it more difficult than originally planned. Do you guys have any recommendations on best practices for this process? Do I need an extra program like MS-CleanR to do this properly?

Lastly - the times I've used MS-Finder I've found myself rather lost. The program is confusing & not being able to clear the cache of previous work is even more confusing. Are there plans to improve documentation on it in the future or is it about as advanced as it's going to get for now?

Feel free to link me to other resources if you feel this information has already been covered at length.

23
MS-DIAL / Re: MS Dial Alignment Export Errors
Sure.

What we were actually trying to do is figure out the best processing method for our data sets. Our PI has typically analyzed stuff in a single group without sample type distinction. The data is then cleaned up in Excel by sorting for MS2 ID'd metabolites, Blank subtracting by average area, and finally sorting for <10% CoV Features. We were trying to task MS-Dial to do the appropriate filtering, blank subtractions & prior to exportation to reduce the work in Excel. At present we're comparing the current way with a single group & sample type to a multip-group & appropriate sample type comparison. Unfortunately we started hitting the wall of alignment export issues which makes it difficult to compare the results.

I have other questions about how blanks, blank subtraction, and groups operate in this program. Not sure if I should float them now or wait.

Edit - My apologies. That's the wrong window. I'll have to fix it tomorrow when I'm back in the lab.

For the Alignment Export data pane we have the directory selected.

The alignment selected

Raw Data Matrix (Area) selected

Replace Null Values selected

.mgf format selected


We are playing with blank removal so that is also occasionally selected depending on the condition. Doesn't seem to change the likelihood of the error in any manner. Sometimes the export is successful. Sometimes it's not. Very strange since we hadn't had this happen until recently. Also another strange bit is that we seem to be getting less MS2 confirmed IDs from the large public metabolomics library hosted on MS-Dials website. It doesnt appear to be an issue on the side of our instrumentation, though it's always possible, so I wonder if this might have to do with the corrupted output files or not. Just spitballing here.

Anyhow I'll upload the appropriate export pane you requested tomorrow. Thank you!
24
MS-DIAL / MS Dial Alignment Export Errors
Hi All,

We've been using MS-Dial to parse untargeted LC_MS metabolomics files generated using a Sciex 5600 QToF.

Most typically we've been using MS-Dial for identification and alignment before exporting the alignment data out for stats processing in MetaboAnalyst.

Here lately, upon exporting data we keep getting an index file error(see attached). It generates 42 kb export data files that trail off to large numbers when you follow the index. Any clue as to why this is happening?

I'm happy to provide any info on the project, files, or processing steps if it helps resolve the problem. We've been using 4.7, but this also occurs on 4.6 when we revert back to it. We're utilizing raw .wiff files for the project as well if that helps.

Thanks,

TB