Which LC & Flow?

Surprised that u go so low. With EvoSep 24 min method we can load lots more on our Ultra2 until reaching saturation especially with ICC2.0

How much are you loading per injection? Is ICC 2.0 enabled on the Ultra2? And which library are you using?

True — but the odd part is that the Human Reference Proteome is not really ‘canonical only’. Non-canonical entries from TrEMBL are included, yet the curated SwissProt isoforms are missing default. That’s what undermines the idea of a high-quality reference set.

On a separate note: I was surprised to find that none of the non-canonical SwissProt isoforms are included in the official human reference proteome (UP000005640).
Anyone know what’s going on here? 🤔
#proteomics #bioinformatics @pwilmarth.bsky.social il

By the way.. 43% of current TREMBL entries will be dropped soon anyway insideuniprot.blogspot.com/2025/06/capt...

Without #2, a lower ion count is needed just to be sure that the full MS range is scanned, but with more accurate ion counts, you can go to the max S/N without losing ions on the edges.
This could also work for the Orbitrap Astral.

Bonus: DIAPASEF on Thermo - patentscope.wipo.int/search/en/de...

Thanks @pwilmarth.bsky.social - also included the less-redundant "one protein per gene" db here ...Has anybody assessed potential benefits of the reduced search space on sensitivity?

aaah guess its "hidden" there :)

Great thanks! Where can I find the one protein per gene option?

💯

Is that narrow windowed thin-PASEF?

Using 32-Core Threadripper for DIA-NN. Gamechanger for large studies as multithreading is efficiently used. Also in case if several user need to process different jobs at same time.

If I got that correctly its not „truly“ open, as only predefined offset masses can be selected.

Have tried Fragpipe22? You can do ion mining from DIA data …

Sure. Why?

..diaPASEF down to 1 ng Hela looks ok (using E.Coli entrapment)