Not yet, setting this up for plasma seems complex enough for now. We touched upon other fluids towards the end, so if this works, one can imagine to expand into urine, CSF, WB or DBS…

Looking forward to seeing those observations!

Can you comment on whether the ratio between glyco- and non-glycopeptides changes with NP enrichment (as compared to neat samples)?

Interesting! Did you also try to first enrich of glycoproteins or remove the modifications prior to particle enriched MS? Would be curious to understand the impact of glycosylation on such a workflow.

We think it will be a win if we can convince the community to add 3-6 extra samples to theirs and "invest" into such connecting analyses. Once have data from our first pilot, we can reshape such schemes with input from you and others"

While these can serve as starting point for future refinements, many (pre-analytcial) aspects appeared that compliactes this effort. Obtaining donor-derived matrial from certain populations, for example, might create a bias, and producing serveral variants of one protein might still be too costly.

Thanks Karsten - even though we briefly mention how single-nucleotide polymorphisms or sequence variants influcnce protein measurements using affinity-based tests and MS, this aspect is certainly underdeveloped for now. We tried to focus on how we could overcome buidling a first set of references.

Differences between mouse and humans are expected but longitudinal effects hopefully follow more common mechanisms.

We (+ others) have compared proteomes in capillary and venous samples - differences driven by penetrated tissues (skin) and blood preparation (whole blood vs plasma).

More soon…

Can you elaborate why it doesn’t make sense to you?

We assume equilibrium in blood and no gradient due to sampling location or distance to an organ. Total blood volume is ~ 2 mL and sensitivity is far from 1 protein per 1 uL.

You can even browse the data to search for your favorite longitudinal protein signature

mouse-dbs-profiling.serve.scilifelab.se/app/mouse-db...

@scilifelab.se @kthuniversity.bsky.social
@ki.se

Pretty tidy and refreshing for those who dare.