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!
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.