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Messages - JeanFroment

1
MS-DIAL / MS-DIAL 5.1.221118 export .mat files
Hello,

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?

Thanks for the help if you can
Jean
2
MS-DIAL / Taking into account the batch effect
Hi everyone,

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 a lot
Jean
3
MS-DIAL / Re: Exporting Error
Hi,

thanks, will do like that. If possible in future versions that might be useful to improve to allow users to easily look for the same features  in different msp libraries (just an idea  :) ).

Thanks again for the help
Jean
4
MS-DIAL / Re: Exporting Error
Hi Hiroshi,

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?

Cheers
Jean
5
MS-DIAL / Using LOWESS normalization for LC data
Hi everyone,

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?

Cheers
Jean
6
MS-DIAL / Selecting peaks to export as .mgf
Hi everyone,

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
Jean
8
MS-DIAL / Can't start a new project
Hi,

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?

Thanks
Jean