MS clean or blank filter not functioning for LC-IM-MS (PASEF) .d bruker & differences between IM & non IM?

[Elwingoh]

MS dial-version: MSDIAL.v5.5.250530-net48

For me, using Bruker .d files works for LC-IM-MS (PASEF), mzML wont.
To perform conventional LC-MS analysis with .d files (containing ion mobility information), conversion to .mzML is required — otherwise, the software crashes.

I have two file
i) Blank
ii) Sample files

The main issues were

1. Blank filtering in LC-IM-MS
   After feature detection using Bruker .d files (for LC-IM-MS with PASEF), I’m unable to remove blank/ghost peaks using MS-CleanR. Selecting the blank filter function (in alignment) is not working for me as well. (However, it is working for convensional lc-ms using .mzml file)
   would ask for suggestions to remove blank/ghost peaks effectively from LC-IM-MS data (using .d files)

2. Removal features without MS2
   using Bruker .d files (for LC-IM-MS with PASEF). I am able to remove features without MS2

Howevere, after selecting the alignment in alignment navigator (between blank and sample). I am unable to remove features without MS2

3)Feature count differences between the same data (ims and ims-less)
Using .d for LC-IM-MS (w ion mobility) extracted alot of features (5-6 times more), much more compared to convensional LC-MS (without ion mobility, using .mzML). When using .d files with LC-IM-MS (ion mobility enabled), I observe 5–6 times more features compared to conventional LC-MS analysis using .mzML files. Is this significant increase due to ion mobility allowing detection/separation of features that are otherwise unresolved in conventional LC-MS? Or is this simply because .mzML conversion causes loss of data (e.g., MS/MS, mobility resolution, or peak fidelity)?

Here attached the parameter selection for alignment etc.