Barchart doesn't match chromatogram in MSDIAL 4.9

[typewritermonkey]

Hi

I want to compare the feature distrubution in different sample types but the bar chart results look different from the EIC results. For example in top barchart in the screenshot it looks like the feature represented by the red bar is the main feature and the others are barely there but in the EIC it looks like its the second biggest feature and there is a lot of that feature in all the sample types.

Also what does gap filling mean? The non red peaks say they were gap filled but I already unchecked the option for "gap filling by compulsion". I read Hiroshi's answer on the forums and he said gap filling should only be when the peak was present in one sample above the detection threshold but in other samples below the detection threshold. But in my case even the green peak said it was gap filled but it was bigger than the red peak which was not gap filled. Maybe if I'm getting a lot of gap filled peaks that means I need to lower my detection thresholds?

I guess its good to have gap filling otherwise you might think a certain feature was only present in one of your samples when actually it was present in other samples as well, just below the detection threshold you set. But it looks like the EICs show you the gap filled features but the bar charts don't. But if that is true means the bar charts can be misleading and its better to use the EICs for comparisons, right?