Okay, so this is a vendor application note, but it's not written by company scientists. In fact, it appears to be the next edition of this sub-radar preprint from earlier in the year.
I've had this preprint open on my desktop for a while in tab 713, because it's the first time we've seen Astral vs Ultra vs 8600 (and 7600+).
As it said on our US HUPO poster this year "vendor instrument comparisons are boring" or "...because Ben (Orsburn) said vendor instrument comparisons are boring..." maybe that was it. In the preprint the authors completely and totally avoid any point where they set up 50ng of the human/yeast/ecoli mixture and the same relative chromatography and compare the results from these same instruments. That's not the point. The point is a current generation publicly available dataset to compare your proteomics algorithms on all the new shit out there.
The 8600 looks really nice whenever you see peptide IDs or quan, but if you also saw this back in February and were a big enough nerd to make it to page 17 of the Supplemental information you'll see this -
The Astral and Ultra2 chromatography looks pretty solid. Particularly, the refined Astral gradient vs the Ultra. ...and...the chromatography on the SCIEX's....looks like its having some issues..... And that was the problem when I had the 7600. I had the Waters HPLC and it really just didn't work properly all together.
Why this app note is interesting is that they seem to have refined those chromatography issues..... And this currently budget instrument seems like the next generation instrument that it might truly be. Look, y'all run the HYE digest all the time. I see it in the literature all over the place. I personally prefer just a human + E.coli spike. I think adding 5k new proteins to human is a little bit excessive, but I've looked at a lot of HYE digest data.
What I haven't seen is almost 11,000 protein groups in 15 f'ing minutes. At 50 nanograms? Maybe the Astral preprint from the Thermo marketing unit in Denmark has come close? I think they loaded more and ran longer. Given what the 11 minute EvoSep data from the preprint looks like in DIA-NN, despite what appears to be something wrong with the HPLC, it doesn't seem all that unlikely. People out there with the >$1M instruments should be very nervous about this thing. I did get an academic quote for one for $510k - with $25k/year service!!
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