Great to hear that you like it :)

To your question if that data is already in prDB - decryptM: YES it is ! e.g.
www.proteomicsdb.org/drug/107070/...

also i can recommend the interactive dashboards.html on zenodo to explore the data locally
zenodo.org/records/1609...

Yes crazy... I still remember the 1.8 million PDF pages we were printing to manually determine what a real dose-response was in the original decryptM paper. Luckily, this is over now :)

Let me know if you need some tricks for the time-dependent hack and good luck with the paper

At the Kusterlab, we have developed a statistical analysis tool (CurveCurator) to mine these proteome-wide dose-response curves. You may want to give it a try. github.com/kusterlab/cu...
3/3

A 1.5 orders of magnitude dose range is not really wide enough for a full dose-response curve, but if you have such a scaled-up workflow, you could easily extend it to more doses with good dose resolution. 2/3

I really like the regulome-wide profiling in a dose-dependent fashion. Going one step further, I would love to see actual TF dose-response curves in Figure 5. So not interpreting each dose individually as bar, but actually have a curve with potency and efficacy estimates for each protein. 1/3

Interesting.. that’s a long time for sure!

We are running the astral mostly without FAIMS and experienced for us normal exploris-like cleaning cycles.

It probably also means that a single publication by one group is not proving anything. Only if multiple independent groups report the same result it becomes trustworthy. Given the reproducibility crisis in biology, maybe this AI fabrication just accelerated a deeper problem, that we need to overcome

I just checked out our NAS..
there are exactly 222 active and alumni members in the folder structure. Wow quite a crowd by now :)

There is paper by now: (Checkout Figure 1E)

pubs.acs.org/doi/10.1021/...

It would be interesting to know what a potential company would charge.

In Europe, you pay ~ 8k for a TMT 16 plex (the 5 mg bag). This means: ~8k Eur / 50 batches / 16 samples = ~10 Eur / sample. If they could allow 5 to 2 Eur, that would be game changing.

No, I was not aware of it.. Thanks for sharing. :) .. interesting

This iTRAQ to TMT mass range should be fine and only C/N encoding. I just don't know how stable this free double bond is in the gas phase. The others always used a ring. But it's the same for all TMT channels, so maybe fine anyway.

I would always give it a try if it is cheaper, legally fine to import to Europe, and of similar isotopic/reactive quality.

But there are many small challenges to solve: bigger tags, which resolutions is needed, thermo would need to open the MS e.g custom phiSDM masses, how clean is the mz area…

Also, dose-response curves yield 4 key values:

- potency -> which target caused the effect? Does it meet my expectation?

- effect size -> what is the biological response strength to the perturbation?

- direction -> is it inhibitory or activating?

- significance -> can I trust this observation?

Dose-response curves help to identify real biological signal in omics data sets because one has a clear expectation about how they should look like. Our CurveCurator software has automated this “gold digging” for everyone.