A mission control for frontier technology An ambitious perspective on technological innovation and scaling by @convergentresearch.bsky.social youtu.be/L5W-lV1K_xQ?...

I do not know if the result reflects just collider bias, but collider bias is certainly highly relevant to this analysis. The discussion raises awareness of collider bias, which is a good thing. Collider effects are relevant at the molecular level too ! 1/2

A new study evaluated Alzheimer’s disease neuropathological changes (ADNCs) based on plasma tau phosphorylated at threonine 217. The results suggest a high prevalence of ADNCs: ◼️Prevalence approached 1/4 even in the cognitively unimpaired group aged 70 years or older.

Post-translational modifications on tau isolated from postmortem Alzheimer's disease brains. Although incomplete, these modifications illustrate that the protein products of a single gene are often diverse. Their functional characterization remains an open challenge.

This article suggests that cancer treatment contributes to mutagenesis: "More than 25% of driver mutations in normal tissue exposed to systemic anti-cancer therapy, including in TP53, could be attributed to treatment."

This article is from people who have thought about FROs for years and have experience with what works and what doesn't. I have always appreciated the restraint in defining the niche of FROs in the broader ecosystem; it comes out clearly in this piece. www.essentialtechnology.blog/p/the-future...

The accuracy and precision of protein quantification by MS depend on sampling frequency. An effective way to improve them is ...

Question for the #proteomics community 👇 What should proteomics repositories be doing today (use cases, features, research) that we’re currently missing? Would love your input—RT to reach more voices. #opendata #mass-spectrometry #proteomics

We won’t understand brains by wiring diagrams alone. Single neurons are not transistors: they’re powerful information processing units with rich logic and capabilities. Mapping topology is just step one. We also need the computational physics of each neuron. 1/2

Biocatalysis is awesome! When I learned about enzymes as a student, I spent an entire summer trying to understand protein design and dreaming of making enzymes. I didn't succeed, but that didn't stop me from learning & enjoying the process. The recollection brings a smile.

I love playing with data ♥️

Large-scale investment in research is welcome and needed. However, it does not inherently favor higher risk and creativity. Engineering scale-ups seem more predictable and are likely to outcompete risky propositions in gaining large-scale support.

Some of the coolest reactions sustaining our lives are catalyzed by this molecule. Its cobalt ion can shuttle between +1, +2, and +3 oxidation states, enabling the versatile chemistry of vitamin B12. Research on B12 has been recognized by multiple Nobel Prizes, including Dorothy Hodgkin's in 1964.

Accurate predictions of the effects of amino acid substitutions will be extremely useful. This has motivated numerous prediction models. Yet, their predictions remain scattered & inconsistent. This is an area with great potential for models to improve 🚀

A striking trend in the willingness of peers to review. What are the underlying causes ?

Great accomplishments often involve risk. Thus, meaningful progress requires learning to live with the right kinds of risk. I think of it as pursuing the real-world projections of our ideals, even when the path is uncertain. nikolai.slavovlab.net/Idealism/

Among all proteome changes in Alzheimer’s disease (AD), 20S proteasomes stand out. ⬛️ Their abundance strongly declines in AD patients. => This decline parallels a reduction in 20S substrate proteins and leads to abnormal protein accumulation in AD. biorxiv.org/content/10.1...

A 5cm TIMS device achieves ion separation corresponding to effective flight length of a 10m (1,000cm) drift tube. 𝑀𝑎𝑠𝑠 𝑠𝑝𝑒𝑐 𝑡𝑒𝑐ℎ 𝑖𝑠 𝑐𝑜𝑜𝑙 ! This animation shows how Trapped Ion Mobility Spectrometry (TIMS) works.

Our latest article is out in Cell ! Together with the Zernicka-Goetz lab, we show that fertilization triggers proteomic asymmetry in mammalian zygotes, giving rise to alpha vs. beta 2-cell blastomeres with distinct developmental potential. cell.com/cell/fulltex...

I remember fondly how much fun we had with the data analysis, especially when we first identified the consistent proteomic differences between sister blastomeres. Our results exemplify why direct protein analysis is key to discovering and understanding biological mechanisms.

In a few milliseconds, these ions travel the height of a ten-story building. 𝑀𝑎𝑠𝑠 𝑠𝑝𝑒𝑐 𝑡𝑒𝑐ℎ 𝑖𝑠 𝑐𝑜𝑜𝑙 ! This animation shows how ions travel in Astral mass spectrometer.

𝗔𝗯𝘀𝘁𝗿𝗮𝗰𝘁 𝘀𝘂𝗯𝗺𝗶𝘀𝘀𝗶𝗼𝗻 𝗶𝘀 𝗼𝗽𝗲𝗻 ! The 9th Single Cell Proteomics Conference (#SCP2026) will take place in #Boston, July 2026. The Single Cell Proteomics Conference focuses on providing opportunities for scientific discussions, interactions and community development. single-cell.net/proteomics/s...

The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts. We have been mapping mRNA modifications for over a decade. => Characterizing their functions -- especially on translation -- is a research frontier.

This figure is embarrassing. What's more concerning is that similar AI 'results' are harder to detect in text and analysis. How do we limit such superficial & distorting AI use in scientific research ? www.nature.com/articles/s41...

The interview covers the trajectory from early, high-risk ideas to robust, scalable workflows. Much has changed, and progress continues unabated.

Increased exon-10 inclusion elevates tau with 4 microtubule-binding repeats (4R) and contributes to neuronal degeneration. In addition to 4R, many other tau proteoforms are associated with Alzheimer’s and other neurodegenerative disorders. 𝐏𝐫𝐨𝐭𝐞𝐨𝐟𝐨𝐫𝐦 𝐝𝐲𝐬𝐫𝐞𝐠𝐮𝐥𝐚𝐭𝐢𝐨𝐧 𝐢𝐬 𝐜𝐞𝐧𝐭𝐫𝐚𝐥 𝐭𝐨 𝐩𝐚𝐭𝐡𝐨𝐥𝐨𝐠𝐲.

An inspirational example of 𝐬𝐜𝐢𝐞𝐧𝐭𝐢𝐟𝐢𝐜 𝐜𝐫𝐞𝐚𝐭𝐢𝐯𝐢𝐭𝐲, 𝐨𝐫𝐢𝐠𝐢𝐧𝐚𝐥𝐢𝐭𝐲 𝐚𝐧𝐝 𝐫𝐢𝐠𝐨𝐫: Chemiosmosis remains one of the most striking examples of originality in modern biology. At a time when biochemical dogma insisted on high-energy intermediates, Peter Mitchell proposed & rigorously articulated the radical ...

Thanksgiving reminds me how fortunate I am to collaborate with research teams (@parallelsq.bsky.social, @slavovlab.bsky.social) who combine rigor, imagination, and openness. I’m grateful for the blue-sky thinking that fuels discovery, and for the spirit of sharing that makes progress possible.

A question relevant to mRNA-based virtual models: Are protein and phosphorylation levels predictable from genomic and transcriptomic data ? This study concluded: "The performance of even the best-performing model was modest, ..."

miRNA have multiple functions beyond their role in modulating translation.

Which is the most misguided editorial in a high-profile journal ? I will nominate the first suggestion. 1/2

The time is ripe to advance our understanding of the complex world of translation. We can profile the diverse pool of modified tRNAs and a wider spectrum of amino acid incorporation into proteins: www.biorxiv.org/content/10.1... The synergy of these developments will exciting ❗️ 1/2

Missing data are common in all omics data. But they are not one thing. They can have very different generative mechanisms. Successful analysis starts with understanding their origin and continues with missing aware analysis. youtu.be/KwprNYv5Pp0?...

A wonderful visualization of the importance of perspective. Keep it in mind the next time you do dimensionality reduction.

The multiplexing approaches that we are developing allow scaling up such rate measurements. timePlex, PSMtags, and JMod can all support increased throughput for 𝑖𝑛 𝑣𝑖𝑣𝑜 metabolic pulse experiments, and thus make dynamic protein analysis more scalable. Quote

Single-cell omics methods are mighty but bound to static snapshot when analyzing 𝑖𝑛 𝑣𝑖𝑣𝑜 tissues. Mass spec offers a solution. ⬛️ It enables omics scale quantification of the rates of macromolecule synthesis and degradation in a living organism. blog.slavovlab.net/2025/11/19/i...

I added "𝑇ℎ𝑒 𝑠𝑡𝑟𝑒𝑛𝑔𝑡ℎ 𝑜𝑓 𝑤𝑒𝑎𝑘 𝑡𝑖𝑒𝑠". It was rejected. The rejection so dispirited its author, that he did not resubmit it for years. Now, it's a cornerstone having shaped a field. It's been cited 78,352 times. blog.slavovlab.net/2014/08/15/p...

Among all proteome changes in Alzheimer’s disease (AD), 20S proteasomes stand out. ⬛️ Their abundance strongly declines in AD patients. => This decline parallels a reduction in 20S substrate proteins and leads to abnormal protein accumulation in AD. www.biorxiv.org/content/10.1...

Protein regulation varies across single cells, cell types, tissues, and organs. The brain proteome is highly sculpted by protein degradation. Why ? This is our model: biorxiv.org/content/10.1...

How do plants orient towards light ? In the absence of obvious physical sensing organs like lenses, how do plants work out the precise direction from which light is coming ?

Fitness influencers promote super-high-protein diets, and protein-fortified foods and protein supplements form a market worth tens of billions of USD. Yet, studies show there’s only so much protein the body can use.

Dimensionality reduction can see structures that do not exist and miss structures that exist. 𝐓𝐡𝐞 𝐬𝐢𝐦𝐩𝐥𝐞𝐬𝐭 𝐞𝐱𝐩𝐥𝐚𝐧𝐚𝐭𝐢𝐨𝐧 𝐢𝐬𝐧’𝐭 𝐚𝐥𝐰𝐚𝐲𝐬 𝐭𝐡𝐞 𝐛𝐞𝐬𝐭 𝐨𝐧𝐞. 1/n

Current efforts focus on predicting transcriptional responses to gene silencing. Even if spectacularly successful, they leave open key questions: ◾️Functions of genetic mutations & polymorphisms ◾️Proteoform functions ◾️Protein abundance regulation Biology is complex.

The protein and mRNA abundance voronoi diagrams offer remarkably different perspectives. Each tile in the maps represents a gene product; its size is proportional to the fraction of the gene product in hepatocytes.

A reminder that the abundance of 'housekeeping' proteins varies significantly across cells and tissues. GAPDH is often slandered as a 'housekeeping' protein, and its abundance varies significantly across human tissues. How do you define a 'housekeeping' protein ?

The protein concentration in the cytoplasm is so high that the average protein has a water hydration shell with a thickness of only ≈ 10 water molecules separating it from the adjacent protein hydration shell. 1/2

"Some participants have already found a way to hack the score, exposing fundamental flaws in how bio-foundation models are evaluated." 𝐄𝐯𝐚𝐥𝐮𝐚𝐭𝐢𝐧𝐠 𝐦𝐨𝐝𝐞𝐥𝐬 𝐢𝐬 𝐡𝐚𝐫𝐝. 𝐈𝐭 𝐧𝐞𝐞𝐝𝐬 𝐦𝐨𝐫𝐞 𝐚𝐭𝐭𝐞𝐧𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐫𝐞𝐬𝐨𝐮𝐫𝐜𝐞𝐬. 1/2

Protein degradation plays major roles in aging physiology & pathology. We can start analyzing it quantitatively at higher resolution & scale. A promising new direction for aging research 🚀

#Proteomics Tutorial drop! Had fun writing this, ping me if interested in other search engines. #TeamMassSpec www.parallelsq.org/blog/fantast...

A beautiful example illustrating a difference between plasma protein analysis by different technologies. Peptides from some proteoforms correlate better to epitope-based measurements (Olink) than others. The measurements differ because they reflect different proteoforms !