I would like to export .mat files for selected features from the alignment tab like it was possible to do with previous versions. When I right-click on the alignment tab there is no option to "search formula and structure". Ideally I would like to "add compound to search list" as .mat file. Is that possible in another way using the new version of MS-DIAL? If not, is it planned to have the option?
I was wondering if I could ask you a question when you injected multiple samples in different batch. In the sample description it is possible to set different batch numbers for the files (and analytical order). Therefore I was wondering if MS-DIAL can account for the batch effect (described in this paper for example: https://doi.org/10.1021/ac302877x). Is it done in the LOESS regression? If so, could I have some information on how the data is normalized?
thanks for the detailed answer. I have exactly the same problem and you described the situation I am in. Now, I am not sure I understood what I could do to export the "alignment result B" (obtained with the MSP file B). Should I just start a new project using the same parameters so the feature list won't change (I hope) but this time it will look for annotations with MSP file B?
I would like to use QC normalization using the LOWESS option. Unfortunately MS-DIAL crash after I click on "done" in the span option. I am using MS-DIAL 4.24 (also had the same problem with version 4.20), and a LC project (acquisition in SWATH). It seems to be working with a LC project in DDA acquisition.
Also with both LC projects we have trouble changing the Span (it looks like a mild bug is preventing us to write a span of 0.22 for example like the minimum size suggested).
Anything we could do to use QC normalization for a LC project in DIA?
I was wondering if there is a possibility to export only selected peaks in an .mgf file. I can explain what I'm trying to do: I run a number of samples in MS-DIAL and looked for MS2 matches using the available databases. With the remaining peaks (which on MS-Dial have these filters: MS2 acquired, Blank filter, and Unknown) I would like to export only these ones into SIRIUS (for formula and structure prediction). Via the ion table, I can send only these peaks to MS-Finder which is great but if it's possible I would like to compare the results from MS-Finder with what I would obtain by using SIRIUS. Any idea?
Thanks a lot for the wonderful software you've developed. Unfortunately, in our lab, we are two scientists to have recently install MS-DIAL 4.16 on our windows computers and the software keeps crashing when we want to create a new project. After selecting a project file path and all the correct conditions related to our files, when we click "next" the software closes. We both have the same issue. Any suggestion?