Modal Geometry Governs Proteoform Dynamics arxiv.org/abs/2508.20004

We preprinted a method of measuring phosphosite stoichimetries (occupancies) in just two mass spectrometry acquisitions, using internal stable isotope labelled controls. In fact, we measure phospho stoichiometries in two ways, using dephosphorylation and using known relative ionisation efficiencies of phosphopeptides, compared to their unmodified forms: the measurements correlate well. In either case, estimates are well below on average compared to what was reported in some previous works. Link in comments below.

Our machine learning driven quantification algorithm for proteomics now published in Nature Biotechnology. Optimal protein quantification and, for the first time, error estimates for individual quantities. Paper link in comments below.

QuantUMS is the default method in our DIA-NN software. nature.com/articles/s41587-0…

Cleland immunoblotting can be used to quantify cysteine proteoform ensembles sciencedirect.com/science/ar…

We are delighted to present DIA-NN 2.5. Redefining LC-MS proteomics with up to 70% more proteins identified and powerful capabilities for statistics, visualisation and biological interpretation.

Nature Aging published a great piece presenting perspectives on the aging field from ~30 leading experts. Few areas of research make it as challenging to separate good science from hype as aging, which makes this article particularly valuable: nature.com/articles/s43587-0…

Biology isn’t just chemistry, it’s geometry in motion. This new Nature Biotech work shows that when we change the envelope geometry of a delivery particle, the efficiency of gene transfer into stem cells shifts dramatically. In VFD, this is expected: Geometry → Field Coherence → Cellular Response. Cells don’t react to molecules alone, they react to harmonic structure. When the geometry aligns, the information flows. VFD-BioSim models this directly, connecting φ-geometry, torsion, and receptor coherence into a unified biological framework. The closer biology moves toward geometry, the clearer the deeper mechanism becomes. @NatureBiotech @Nature #VFD #BioSim #GeometryOfLife #GeneEditing #Biotech @drmichaellevin @StuartHameroff

We acquired a large-scale mixed-species benchmark, with variable background, to comprehensively assess quantitative accuracy of proteomics. Key features: - 192 runs, 0.75ng - 15ng of variable human cell line backgroud. - Can dissect the impact of both random and systematic errors. - Can test how quantitation algorithms scale with experiment size and sample heterogeneity. Our insights based on the data: biorxiv.org/content/10.64898…. PRIDE repo will be made public in the next days.

Solving the computational challenge of phosphoproteomics with 𝐏𝐡𝐨-𝐓𝐢𝐩: dephosphorylation on-tip identifies the sequences of phosphorylated peptides. This serves as a basis for predicted spectral libraries, reducing the search space 10x-20x. biorxiv.org/content/10.1101/…

Is “oxidative stress” a useful concept in biology? In this work, led by Nikos, we argue that the term “oxidative stress” is devoid of biological meaning and, even worse, misleading.

If you believe that the current framework of redox biology (oxidative stress/redox signalling) is vague, then the approach introduced in this paper offers a geometric/physical basis for how redox modifications (cysteine oxidation) happen, interact, and shape biological outcomes.

Was a great pleasure to contribute to this work pubs.acs.org/doi/10.1021/jas…. DIA-NN release with support soon.

A prevailing idea in exercise physiology seems to be that the only erythrocyte factor affecting performance is hematocrit and hemoglobin levels. Is it really that simple? 1/3

Is the erythrocyte a simple cell that just passively carries oxygen during exercise? NO. In our new study in @SportsMedicineJ with @dalessandrolab we show that erythrocyte energy and redox metabolism affects muscle oxygenation and exercise performance. link.springer.com/article/10…

Time and time again, it's always the same picture. DIA-NN controls FDR correctly as data reliability has been the main goal at DIA-NN's conception back in 2017 and a priority since then. Data from a very nice paper introducing the Thin-diaPASEF concept: doi.org/10.1093/dnares/dsaf0….

Preprint on information and chaos in redox proteomics preprints.org/manuscript/202…

Assessing FDR in proteomics using full proteome recombinant libraries: pubs.acs.org/doi/full/10.102…. A very elegant work and a benchmarking dataset useful for many other things too. Protein FDR higher than precursor FDR likely due to paralogues - and this needs to be researched further.

🚀 Check out our preprint on the new Thermo Scientific Orbitrap Astral Zoom MS 💫👇🏼 biorxiv.org/content/10.1101/…

A sharp, thought-provoking critique of the Bayesian brain hypothesis. Bold ideas, fearless writing. Essential for anyone in neuropsychology, motor control, biomechanics or concerned with falsifiability and biological plausibility. link.springer.com/article/10…