We have used MS Dial a decent bit. Typically we collect small molecule metabolomics data on a UHPLC-Sciex 5600 QToF set up. Typically we're collecting IDA data in 10 minute runs. Most experiments involve collection of the following data types:
Pooled Samples MS2
Pooled Sample MS1
Individual Sample MS1
Blank
We do not convert the data to a common centroided format before ingesting it into MS-Dial. We churn the data on a dedicated Dell work station that has a 6 core/6 hyperthreaded Xeon CPU, 32 GB of DDR4 RAM, and a mechanical HD. For small projects(5 - 30 samples) its fine, but for larger projects (>30 samples) we run into issues. Specifically the issues arise after the individual samples are processed and during the 'peak filling, identification, and alignment' stage. Add gap filling in there too.
The program bogs down the PC to the point where it's unresponsive or slugging. MS Dial's progress bar during that period often freezes at a low %. Sometimes the project completes and other times it does not. It could take half a day or multiple days to complete.
I've pulled up task manager and other monitoring software during the processing to see what's happening. During the initial sample processing the CPU use is most intensive, but since it can multi-threaded in parallel it's quick. During the aforementioned 'peak filling, identification, and alignment' stage the CPU usage drops to almost nothing where as the RAM and the Disk activity shoot up to 90-100%.
I have a few questions
Are there tips on improving the speed at which larger projects can be computed?
Would a faster writing data component, like a soild state drive, improve the speed of that step?
How can we tell if the 'peak filling, identification, and alignment' is actually progressing or the program has stalled out as unresponsive?
I'd be happy to provide any information on our process, computer system, or software if it would help us tackle the problem. We like a MS-Dial a lot, but the slow down and questionable completion of the data processing has us questioning using it further.
I was excited to try out the new MS-Dial v5.1.22, but was surprised to run into some issues with file import. I was doubly confused by the tutorial videos provided which demonstrates import of Sciex files in a way that I cannot replicate.
The video is 'Creating new project' @ ~50 seconds it shows the user going to the file folder to retrieve the raw files. They have to use the file type selection choice to change from the default (.ABF) to the Sciex (.Wiff) file. When they do that the expected (.Wiffs) appear & can be selected for import. When I do that nothing shows up as it did in v4.9 & previous versions.
Doubly confounding is that the field for 'Analysis File Path' --> Browse which leads to the aforementioned window claims that, among other things, that '(Only ABF files now)' which you can briefly see in the video.
In converting my (.Wiff) files to (.ABF) I can see them when I repeat the process. Going forward with the project using the (.ABF) files I cannot get any usable ref matched IDs for the data files using similar project settings as we had before. I've tried several times to no avail. I've ensured the polarity and fragmentation types are all correct. I've tried our in-house RT enforceable library with many different settings. In addition I've also tried with both centroid and profile settings to be sure. Nothing improves the results in a way that comes close to the results we get in v4.9
This is quite confusing. Any thoughts on why this might be?
I just wanted to say as a user of your software that the new tutorial videos posted on YouTube are a huge boon for use of the software. While the written tutorials on github are also welcome it appears that many of them were made with older version of the software that have changed. Unfortunately the written tutorials don't necessarily reflect the changes that have been made to the software since. The video versions of the tutorial are a nice touch to show up-to-date information on the wonderful software this group has put together. Thank you so much for both the software & the informative videos.
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.
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.
