Metabolomics Society Forum

Software => MS-DIAL => Topic started by: metabolon1 on May 06, 2020, 06:34:29 PM

Title: GNPS export files empty when Filtering by the ion abundances of blank samples
Post by: metabolon1 on May 06, 2020, 06:34:29 PM
Dear Developers and Community,

Today I came across an odd behavior in MS-DIAL. When I export alignment results as GNPS export, all of the files are empty of any data; this only seems to happen when "Filtering by the ion abundances of blank samples" is selected. When it is not selected, all of the files look fine.

However, when I am exporting as "Raw data matrix (Area)" or "Representative spectra", it works whether or not I have selected the "Filtering by..." option. In fact, the file sizes are the same in both cases.

I tried this with several of my project (.mtd) files that I have successfully exported GNPS files from. I tried with three different versions of MS-DIAL (4.12, 4.18, 4.20). The same thing seems to happen.

I'm surprised I didn't notice this before, but I think I never actually selected "Filtering by..." when exporting. I generally set up my analysis parameters with the option "Remove features based on blank information" using "Sample max / blank average = 5 fold change".

Is this a known issue? Am I doing something wrong?

Thank you for your help,