TMT-labeled DIA

TMT-labeled DIA beikih2  2023-09-07 10:19

Dear Skyline Support Team,

We are trying to use Skyline to process our TMT-18plex-7-tags DIA MS proteomics dataset. Could you please let us know if there is a good set up for this type of data? Also, how can I demultiplex this data?

Thanks in advance.


Mike MacCoss responded:  2023-09-07 11:01

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 ( 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 ( -- that should work if you staggered the precursor isolation windows. We also did a fair amount with multiplexing the precursor isolation windows ( but moved away from that in the use of the staggered windows.