Naive question: I thought targeted was about sensitivity -
why ng?

Not a conference, but worth flagging:
EMBO Practical Course “Targeted proteomics: advanced tools for biomedical research” Barcelona, 8–13 Nov 2026

Line-up not announced yet, but previous editions organized by @maccoss.bsky.social with invited speakers incl. Alexey Nesvizhskii and Vadim Demichev.

I agree MaxLFQ isn’t meant for absolute quantification.
But that still doesn’t explain the complete lack of correlation with UPS2.

From my experience, iBAQ and MaxLFQ usually correlate well (R² ~0.78, non related example dataset shown), suggesting they track the same MS1 signal.

As shown in the DIA-NN paper, the mobility term contributes only negligibly to the discriminant score, suggesting that measured CCS -even with good IM resolution - might simply be too affected by gas-phase ion–ion / ion–neutral interactions to provide a stable, high-specificity constraint …

With a quadrupole we know exactly which precursor m/z window was isolated -the precursor mass is tightly defined with a well-characterised error. My question was whether CCS can provide anything close to that level of search-space restriction for database searching.

My point rather was whether precursor CCS can actually constrain the search space during database searching not just what Da-equivalent tolerance it has.

Asking for a friend: Is intrinsic specificity of CCS high enough to serve as an effective in silico precursor filter during database searching?

“Very interesting! Do you know whether ProteomeSciences is already testing the new DXT tags with selected customers or collaborators, or is it still entirely in-house at this stage?”

Bonus, info about DIA multiplex tags, up to 30-plex:
"trademark DXT for our DIA multiplex tags...advances have been made in DXT multiplexing since ASMS with the number of tags increased from 6 to 11 and with the potential to
increase these to beyond 30"

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?