Florian P Bayer
banner
flobayer.bsky.social
Florian P Bayer
@flobayer.bsky.social
PhD student in PTM proteomics @kusterlab
This is very useful.
Thanks for the effort !!
January 9, 2026 at 5:56 PM
Yes. 100% agree.. That is bad MS2 co-isolation and ratio distortion :)
December 16, 2025 at 3:41 PM
Good question how the *spectra* S/N is calculated by Thermo for the Astral...
December 16, 2025 at 3:24 PM
Looking at the recent MacCoss paper, one needs to divide intensities of a OTs by 10x to get to intensities of ITs and Astrals pubs.acs.org/doi/10.1021/...
Evaluation of a Prototype Orbitrap Astral Zoom Mass Spectrometer for Quantitative Proteomics─Beyond Identification Lists
Mass spectrometry instrumentation continues to evolve rapidly, yet quantifying these advances beyond conventional peptide and protein detections remains challenging. Here, we evaluate a modified Orbitrap Astral Zoom mass spectrometer (MS) prototype and compare its performance to the standard Orbitrap Astral MS. Across a range of acquisition methods and sample inputs, the prototype instrument outperformed the standard Orbitrap Astral MS in precursor and protein identifications, ion beam utilization, and quantitative precision. To enable meaningful cross-platform comparisons, we implemented an ion calibration framework that converts signal intensity from arbitrary units to ions per second. This benchmarking strategy showed that the prototype sampled 23.1% more ions per peptide than the original Orbitrap Astral MS. This increase in the ion beam utilization resulted in improved sensitivity and quantitative precision. To make these metrics broadly accessible, we added new metrics to the Skyline document grid to report the number of ions measured in a spectrum at the apex of the elution peak or the sum of ions between the peak integration boundaries. Taken together, our results demonstrate the Orbitrap Astral Zoom prototype as a high-performance platform for data-independent acquisition proteomics and establish a generalizable framework for evaluation of MS performance based on the number of ions detected for each analyte. Data are available on Panorama Public and ProteomeXchange under the identifier PXD064536.
pubs.acs.org
December 16, 2025 at 3:24 PM
One would need to multiple with MS1 intensity to get better quantities, because otherwise it depends when the TMT was picked how much intensity (ions/sec) you end up with in that moment of time, how many peptides you sum, etc... TMT is "only" excellent in conserving ratios within a TMT experiment.
December 16, 2025 at 3:24 PM
I don't see *spectra* S/N ratios reported in table S3.

They have mean vs. STD *protein intensity* over three replicates. I didn't go deep enough to their analysis, but normally people just sum up TMT report intensity to protein level. This intensity is however not indicative of actual quantities.
December 16, 2025 at 3:24 PM
my understating was that the S/N cutoffs are the sum over all TMT reporters. So a threshold of 1440 S/N for an 18plex would be average 80 S/N per reporter.. are the purple numbers retained spectra?

Thanks for sharing this analysis. Just sad that good signal leads to poor resolution in TOF world.
December 16, 2025 at 1:24 PM
What I was always wondering is if you could do a normal ion processor/HCD-MS2 scan and then for the MS3 scan do first HCD in the IRM and then select N Fragments (by optics n=1, SPS in the IRM?) and do the second HCD in the processor?

But happy that you guys are thinking about it :) :)
November 20, 2025 at 11:32 PM
(2/2) For me, the problem with the Astral rather is that it currently does not support MS3. I don't mind running the MS at a lower Hz if I can get much better data from it. Every time I meet someone from thermo, I try to spark the MS3 idea. It hasn't ignited yet ..
November 20, 2025 at 2:50 PM
The Deu-TMT requires careful planning of which samples go to which channel and requires a Deu/nonDeu-"bridge" sample to remove the Deu-RT effect. Then it works as expected.
(1/2)
November 20, 2025 at 2:50 PM
A sneak preview is already online in proteomicsDB (www.proteomicsdb.org/analytics/KSR).

If you have questions, comments, or ideas, feel free to reach out.
ProteomicsDB
www.proteomicsdb.org
November 19, 2025 at 11:02 AM
In summary:
* 133 clinical kinase inhibitors x 5 cell lines
* >17 million peptidoform DRCs
* Critical re-evaluation of existing KSRs
* Proper FDR control for KSRs
* Identification of thousands of high-confidence KSRs
* Exposing how kinases shape cell line models and cancer patients
November 19, 2025 at 10:44 AM
The authors used CurveCurator to fit and evaluate all dose–response data across different omics assay types. CurveCurator’s scores let you set custom thresholds and interactively identify high-quality curves in ProteomicsDB.
November 18, 2025 at 8:50 PM
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...
ProteomicsDB
www.proteomicsdb.org
August 13, 2025 at 4:38 PM
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
July 3, 2025 at 1:25 PM
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
July 3, 2025 at 12:37 PM
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
July 3, 2025 at 12:36 PM
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
July 3, 2025 at 12:36 PM