I made more tests with DIA from 100 pg to 150 ng, with gradients from 10 min to 90 min. Anything below 5 ng suffers from gradients above around 20 min. With higher inputs , longer gradients actually give you a tiny little bit more precursors. Full report incoming after I'm back from holidays :)

smh... 🤦‍♂️

VSCodium

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Also, the number of peptides/proteins/precursors do not increase above 50 ng.

#bruker TimsTof Ultra is definitely seeing signal saturation with 50 ng of sample injection.

@fcyucn.bsky.social Any update on diaPASEF compatibility with FragPipe? :) You just tease me with new papers, now about the Analyst, but I can't use it as I measure everything with DIA on TT instruments. Greets

Testing goes further: Two weeks of Hela runs with BSA once per 4 samples. RT and IM and pressures stay steady on the PepSep ULTRA (the variation in the metrics mentioned above is random, and not related to the measurement time). #timstofultra#bruker#proteomics

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