Hello Hiroshi, I don't know if anyone has asked about this in the forum before. I have difficulty understanding what "gap-fill" is and when/how does the program gap-fill. I am currently using version 4.18. For instance, under the EIC plot window on the top, there is a table-viewer function on the right-click menu where I can view chromatograms of the specific alignment across samples. In one of the columns, it tells whether the peak was gap-filled (shown as -2) or not. However, what I don't understand is the last column where it shows the peak with points in the chromatogram: for those that are gap-filled, does it make up the points of a peak? If it is gap-filled meaning that the peak does not exist, why would it create points of a non-existing peak? On the other hand, if the points were based on an actual/existing peak, why would the program gap-fill? If it sounds confusing and you prefer some screenshots, please let me know. I appreciate your help!
In the current program, you will see such a result in GC-MS project, and if I were you, I just simply delete one of the features in the excel program. Another option: you can tick the option of "only report top hit" in the identification tab of MS-DIAL parameter setting. One of the duplicates or more same annotations from the same database ID is selected by considering the identification score. That is, the peak having the highest score for metabolite annotation will have the metabolite name and the others are assigned as "Unknown".
Anyway, I will improve the program as much as possible.
Hello everyone, I have had issues for my recent MS dial results where there are two alignment results that have the same identification and almost the same information except that the Quant mass (which I don't know how the program picks) is different. Please see the attached screenshots. One shows Quant mass of 149 and the other shows 105. However, 105 is not even a significant m/z in the spectrum. Two spectra looks very similar but the program generates two alignment IDs. I have tried to play around with the parameters, such as average peak width, but it didn't fix the issues. Anyone has any idea what could possibly the issues? Thanks a lot!