Hi Hamid,
Not sure how we would analyze these data. We are definitely open to suggestions. Almost every DIA spectrum is chimeric so we rely on using the unique combination of precursor and sequence specific product ions to provide a specific measurement. We have been thinking about using complementary ions to analyze TMT data (https://pubmed.ncbi.nlm.nih.gov/33929851/) but that is definitely far off and a research project as the complementary ions from TMTPro aren't ideal.

Not sure how we would demultiplex these data. All of our efforts in the past have been focused on staggering the isolation windows (https://pubmed.ncbi.nlm.nih.gov/30671891/) -- that should work if you staggered the precursor isolation windows. We also did a fair amount with multiplexing the precursor isolation windows (https://pubmed.ncbi.nlm.nih.gov/23793237/) but moved away from that in the use of the staggered windows.

Cheers,
Mike