The regulation of nuclear-encoded mitochondrial proteins is fascinating. They are synthesized in a fully eukaryotic manner, with introns, splicing, and cytosolic ribosomes. Yet, they are degraded by proteases that look and act bacterial. blog.slavovlab.net/2025/09/23/m...

Some proteins are primarily regulated by one mechanism: RNA abundance, translation, or clearance. The regulation of most proteins is dominated by different regulatory mechanisms across cell types. Gratifyingly, this complex regulation defines simple rules ⬇️ www.biorxiv.org/content/10.1...

We quantified mRNA abundance, translation, protein abundance, protein degradation and cell growth across thousands of single cells from a mammalian tissue. The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles: www.biorxiv.org/content/10.1... 🧵

A key mechanism controlling mitosis is the precise timing of over 32,000 phosphorylation events. Below are some of the key regulators of mitosis.

Proteins self-organize to build large structures, 100,000-fold larger then the proteins. It's elegantly dynamic ! Proteins constantly self-assemble and disassemble to build skeletal structures in our cells, shaping and orchestrating life.

𝐓𝐨𝐝𝐚𝐲 𝐦𝐚𝐫𝐤𝐬 𝐨𝐮𝐫 𝟏𝟎𝐭𝐡 𝐚𝐧𝐧𝐢𝐯𝐞𝐫𝐬𝐚𝐫𝐲 🎉 A decade of pushing the boundaries in proteomics, systems biology, and data-driven discovery. 🔬 Thank you to our collaborators, alumni & supporters!

Our findings (now published in @narjournal.bsky.social‬) identify the first metazoan RNase MRP-specific protein subunits. We also define the RNA-targeting repertoire of this essential enzyme in mammalian cells. academic.oup.com/nar/article/...

The registration for SCP2026 is open ! Join us next July for the the 9th Single Cell Proteomics Conference. single-cell.net/proteomics/s...

Neighboring gene effects account for much of the observed phenotypes of gene deletions. This is a crucial factor to consider in knockout experiments. Phenotypic similarity is exponentially related to chromosomal proximity in both yeast & human genomes. Human Data 🔽

The epitranscriptome formed by the growing number of modifications occurring within mRNA transcripts.

Protein synthesis is among the most energy demanding processes in a cell. 𝐖𝐡𝐲 𝐚𝐫𝐞 𝐭𝐡𝐞𝐧 𝐬𝐨𝐦𝐞 𝐩𝐫𝐨𝐭𝐞𝐢𝐧𝐬 𝐜𝐨𝐧𝐭𝐢𝐧𝐮𝐨𝐮𝐬𝐥𝐲 𝐬𝐲𝐧𝐭𝐡𝐞𝐬𝐢𝐳𝐞𝐝 𝐚𝐧𝐝 𝐢𝐦𝐦𝐞𝐝𝐢𝐚𝐭𝐞𝐥𝐲 𝐝𝐞𝐠𝐫𝐚𝐝𝐞𝐝 ? blog.slavovlab.net/2025/08/16/p...

Spliceosome Dynamics During splicing, stepwise assembly is one principle by which spliceosomes on the one hand ensure the faithful recognition of splice sites and on the other hand become susceptible to regulatory inputs to implement alternative splicing.

Quantitative protein assays on Illumina chips. A creative use of the impressive imaging capabilities developed for DNA sequencing by synthesis. ◼️ It allowed quantifying binding and enzyme catalysis 🧵

Recently, I presented technological progress in single-cell proteomics & the biological analysis that it enables: 𝐒𝐢𝐧𝐠𝐥𝐞-𝐜𝐞𝐥𝐥 𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬: 𝐅𝐫𝐨𝐦 𝐏𝐫𝐨𝐭𝐞𝐢𝐧 𝐕𝐚𝐫𝐢𝐚𝐭𝐢𝐨𝐧 𝐭𝐨 𝐁𝐢𝐨𝐥𝐨𝐠𝐢𝐜𝐚𝐥 𝐅𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐬 youtu.be/8nhjKSTqeOs?...

Cell size varies by many orders of magnitude. The mechanisms that generate and maintain this extraordinary diversity of sizes remain incompletely understood.

Our first plenary session starts with @slavov-n.bsky.social telling us about single cell proteomics and moving it to biological function

Many developmental processes are regulated post-transcriptionally. Such regulation can now be analyzed by robust single-cell mass spectrometry methods. Here are some ideas ▶️ journals.biologists.com/dev/article/...

A succinct and clear presentation of multiplexing proteomic technologies that we developed at PTI.

The talk by @andrewleduc.bsky.social at #SCP2025 is on YouTube: 𝐐𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐨𝐟 𝐠𝐞𝐧𝐞 𝐞𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐜𝐨𝐧𝐭𝐫𝐨𝐥 𝐢𝐧 𝐚 𝐦𝐚𝐦𝐦𝐚𝐥𝐢𝐚𝐧 𝐭𝐢𝐬𝐬𝐮𝐞 𝐚𝐭 𝐬𝐢𝐧𝐠𝐥𝐞 𝐜𝐞𝐥𝐥 𝐫𝐞𝐬𝐨𝐥𝐮𝐭𝐢𝐨𝐧 youtu.be/adkY6txDyqs?...

We developed multiple interdependent technologies. Together, they are opening up new opportunities: www.parallelsq.org/blog/proteom...

🟦 Label-free single-cell proteomics (blue bars). 🟧 Multiplexed single-cell proteomics affords higher throughput (orange bars). ⬛️ Proteome depth & quantitative accuracy are comparable. We aim to make the 🟧 bars taller. www.parallelsq.org/psmtags www.biorxiv.org/content/10.1...

More evidence for the role of protein degradation in significantly shaping the proteome of brain tissue!

Leading these (and many ongoing) projects has been demanding, exhilarating & rewarding. They required highly coordinated collaborations among diverse experts within PTI, MIT, MGH and beyond. 1/2

Alzheimer's disease (AD) is associated with numerous proteome changes. We find large & consistent decrease in the abundance and stoichiometry of 20S proteasome subunits. ⬛️ It leads to abnormal accumulation of 20S substrate proteins. 🧵 biorxiv.org/content/10.1...

I am very enthusiastic for improving fragmentation spectra & the research this empowers. This means increasing the sensitive and scope of sequencing the immunopeptidome ==> better cell therapies. biorxiv.org/content/10.1... 1/2

We just released JMod: an open source software supporting multiplexed DIA. It supports parallelization in both the mass domain (plexDIA) using small mass offsets and in the time domain (timePlex). It enabled 27-plex DIA & opens the door to further scaling 🚀 www.biorxiv.org/content/10.1...

~ 30,000 protein data points / run from single-cell level proteomes is a boost for the field ! It's exciting to think of the capabilities afforded by these scalable approaches.

A new dimension for multiplexing mass spec analysis -- time -- is enabling scaling up throughput at new levels. We demonstrate 27-plex DIA enabling over 500 samples / day. We project that timePlex will enable throughputs exceeding 1,000 samples / day. www.biorxiv.org/content/10.1...

A highlight of our recent research article by @andrewleduc.bsky.social et al. www.azolifesciences.com/news/2025051...

Tune in to hear me give a talk on our work quantifying mechanisms protein abundance regulation in single cells from primary tissues!

𝐓𝐨 𝐮𝐧𝐝𝐞𝐫𝐬𝐭𝐚𝐧𝐝 𝐭𝐡𝐞 𝐛𝐫𝐚𝐢𝐧, we need to understand what shapes its molecular composition. What are the contributions of protein synthesis and degradation rates to determining protein abundance in the brain ? www.biorxiv.org/content/10.1...

Single-cell proteomics is gaining momentum. It can analyze the proteomes of ~ 1,000 single cells / day, and we need to ensure high quality cell isolation and sample preparation: ⬛️ These approaches can help: nature.com/articles/s41...

To be more accessible, #SCP2025 will offer a remote broadcast. Attending virtually is free but requires registration: single-cell.net/proteomics/s...

An alternative to tSNE & UMAP for more accurate data visualization: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data. The trees are constructed to accurately represent true distances between the objects in the high-dimensional space.

As we get ready for the British Society for Proteome Research annual meeting in Liverpool (July 7-9th), we will start highlighting our amazing speakers. First is @slavov-n.bsky.social who will talk to us about Biological and technological frontiers for single-cell proteomics.

Our paper on the impact of protein leakage due to loss of membrane integrity for single cell proteomic sample prep is out in @natcomms.nature.com! We analyze thousands of primary single cells from murine tracheal tissue and record membrane permeability (sytox-green)🧵 www.nature.com/articles/s41...

These papers triumphed over their rejections blog.slavovlab.net/2014/08/15/p...

Alternative splicing (AS) is common, but its impact on the proteome remains debated, especially in primary cells. What determines which AS isoforms result in abundant proteins ? We find that proteoform-specific ... 🧵 www.biorxiv.org/content/10.1...

Protein samples can be multiplexed to increase throughput. In 2023, PTI set out to make tags (barcodes) that not only increase throughput but also enhance peptide sequence identifications: pubs.acs.org/doi/10.1021/... We will share results soon: www.parallelsq.org/workshops-an...

In vitro cell lines grow fast and protein abundance variation is explained largely by protein synthesis rate: RNA abundance & translation efficiency In contrast, protein degradation is a major - sometimes dominant - factor in differentiated cells from tissues. Why ? 👇

Updated preprint: Cell growth rate strongly impacts the mechanisms controlling variation in protein concentrations. We report larger than previously appreciated contributions of protein degradation to protein variation, both across proteoforms and tissue types. www.biorxiv.org/content/10.1...

Exciting time for scaling up sensitive & specific proteomics. Looking forward to higher-plex DIA and improved amino acid sequence identification.

Be courageous to be creative.

We received detailed, thoughtful & constructive reviews. Thanks to the peer reviewers !

Two more weeks to submit an abstract! single-cell.net/proteomics/s...

I have long advocated for scaling up protein analysis, but such scaling should focus on quality & specificity and expand the spectrum of direct measurements. Experimental questions & designs are key to scientific progress. . www.mcponline.org/article/S153...

Check out our work on the role of protein degradation! Importantly, we demonstrate not only the importance of degradation in regulating expression, but also that rates varies across conditions! This motivates making these measurements across many contexts, like single cells ;)

pre-rRNA is cleaved into rRNA by a 500 kDa ribonucleoprotein, RNase MRP. Why is such a large complex needed for a simple cleavage ? We show how specific protein subunits distinguish RNase MRP from related enzymes and define its catalytic repertoar. www.biorxiv.org/content/10.1...

What determines protein abundance variation ? For many proteins, abundance variation is dominated by clearance (degradation and dilution) variation. Globally, clearance variation across tissues explains ~ 40 % of protein abundance variation. www.biorxiv.org/content/10.1...

What explains the divergence between RNA and protein levels ? Protein degradation is a HUGE factor. It accounts for up to 50 % of protein variation across proteins & tissue types. www.biorxiv.org/content/10.1... 🧵