Does anyone running MS-DIAL command line know how to assign class IDs to samples (useful in filtering at alignment)? I assume it could be generated in a .txt and uploaded, but there is nothing in the FAQ or documentation on the MS-DIAL website.
Can someone please provide a reference for the exact chromatography conditions used to generate the RTs embedded in the default MS-Dial lipids database? It would be very nice to just use that exact chromatography instead of RT correcting the values from my current method.
I am processing time-course data right now (but this is applicable for all studies). I am finding a number of features with poor spectral matching in the alignment result, but when I check the "Spectrum reference file name" column I find the spectra are commonly from samples with very low levels of the metabolite. If I then go to a file with high levels of that same feature I find a very highly scored match.
So my question is: Is there a way to force MS-DIAL to select the MS2 spectra (in the aligned peaks list) from the sample with the most intense response?
Perhaps a relevant note: This feature found using an mz-RT list.