I have a question regarding the (post-)alignment process, i.e. the option to filter „blank features“.
In the alignment settings, I checked the blank filter option using an average intensity ratio of sample to blank of 3. Thus, the number of features decreases from 1836 to 933. That means, about 50% of the features were also detected in the solvent blanks with respect to the above-mentioned settings, and consecutively these features were not reported in the corresponding feature list (export by selecting „height matrix list“ and „blank filter option“).
However, when you look into that feature list, there are still a lot of features in there, which still have average intensity ratios below 3 or even below 1. Approx. 70% of all features belong to that category of features. So in my case, the blank filter process seems not to work properly.
Do you have an idea what the problem might be and how I can get a better feature list?
And a general question, what is meant with „Average Sample Intensity“: the average intensities from all sample files, but including or excluding QC samples?
By the way, I used MS-DIAL version 4.24.
Thanks for your response.
sorry, I cannot reproduce your result on my side. Can you share your small data set with me to understand your problem with some experimental slides?
>>but including or excluding QC samples?
QCs are included.
Please consider this scenario as well...
You need to check the ID of the peaks, some of them were generated in silico (as explained in the link).
Did you untick "Keep 'reference matched' metabolite features" and "Keep 'suggested (w/o MS2)' metabolite features" in the alignment tab? In my understanding, if you tick any of these two options, then you will have some match/suggested features kept in the list even though they are in blanks as well. I had the same confusion before, but now, when I untick them, the final list is good now.
I really ticked some of the "Keep..."-Options in the alignment tag. After unticking everything is fine.
At his point, I did not check the gap-filling option. But I will keep the remark by UFZ-Stef regarding gap-filling algorithm in mind.
Thanks for your help.
You are welcome. It's my pleasure to help.