Pierre Sabatier

It is my great honor to announce that registration for the 7th ESCP Single Cell Proteomics Conference is now open: lnkd.in/e4iyiQjf
With around 250 participants, it is one of the largest SCP conferences worldwide. We are also proud to announce that there is no participation fee for our conference.

New preprint from Uppsala Univ. & Univ. of Copenhagen: Single-cell proteomics with Whisper Zoom 40 SPD quantifies >4,000 proteins/sample, revealing cell-type differences, mRNA–protein discrepancies & markers for future T1DM studies.
Learn more: www.biorxiv.org/content/10.1...

DIA-NN 2.2.0 is released! The new DIA-NN 2.2.0 Enterprise achieves up to ~1.6x median speedup on 64-cores under Windows (please see benchmark below). Release notes: github.com/vdemichev/Di..., download (Academia): github.com/vdemichev/Di...

Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma Neutrophils are vital innate immune cells shown to infiltrate glioblastomas, however we currently lack the molecular understanding of their functional states within the tumour niche. Neutrophils are k...

Happy to share our latest preprint doing low cell number (mini-bulk) and single cell #proteomics on tumour associated neutrophils from human glioblastoma where we find multiple functional states that would be invisible to scRNAseq, some showing pro-tumoural states with potential therapeutic value

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.

That's the only valid reason 🤩
It should be a good timing with all your spatial work piling up!

I will have to skip it unfortunately 😔
Are you going?

Pumped to finally show off our spatial proteomics work presented a few weeks ago at the EAS Congress @eassociety.bsky.social and now live on @biorxivpreprint.bsky.social 🥳

Time for a science thread! #TeamMassSpec #SpatialProteomics #AtheroSky 🧵

www.biorxiv.org/content/10.1...

Great work, congrats!!

🦷 Excited to share how proteomics is pushing the boundaries of palaeoanthropology!
We used proteomics on Paranthropus robustus fossils from South Africa (~2 million years old) to get insights into biological sex and variation.
A great example of how LC-MS/MS can uncover new transformative info👇

Ok this is just insane. Such an amazing application of DVP. Having collaborated on some mitosis related projects I had dreamed of doing exactly this kind of experiment. AI/ML segmentation + laser capture has so many unique applications. This is the tip of the iceberg.

I can imagine 😅
Looking forward to it!!

Thanks!And congrats on your very nice preprint!!

Any single-cell data coming from the SILAC mouse analysis?
That would be mind-blowing!

Global analysis of protein turnover dynamics in single cells The SC-pSILAC method enables single-cell measurement of both protein abundance and turnover, providing notable advances in the depth and versatility of proteomic technologies.

🚀 Excited to share our latest article in #singlecell proteomics published in Cell!
We've developed SC-pSILAC to simultaneously measure protein turnover and abundance in single cells, unlocking the first large-scale, 2D proteomic insights at single-cell resolution!

www.cell.com/cell/fulltex...

A Nature Communications study from the Olsen group demonstrates the potential of Evosep One in high-throughput drug target identification through an optimized Thermal Proteome Profiling (TPP) and PISA assay workflow.

Read full study here: www.nature.com/articles/s41...

HEY PROTEOMICS PEOPLE! Can you comment here where you learned to do proteomics? I started putting up a survey but based on just the 64 people on our podcast there are too many options for a multiple choice survey effectively. Thank you!

The theory at the Proteomics Master in Lille, and the practice during my PhD at Roman Zubarev's lab!

Really nice results from the Olsen group, evaluating the pre-accumulation method, which multiplies Orbitrap duty cycle at short transients and allows >70 Hz repetition rates.

They then combined it with PhiSDM spectral processing, mitigating the resolution sacrifice.
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...

🧵

Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis Mass spectrometry-based single-cell proteomics (SCP) is gaining momentum but remains limited to a few laboratories due to the high costs and specialized expertise required. The ability to send samples to specialized core facilities would benefit nonspecialist laboratories and popularize SCP for biological applications. However, no methods have been tested in SCP to “freeze” the proteome state while maintaining cell integrity for transfer between laboratories or prolonged sorting using fluorescence-activated cell sorting (FACS). This study evaluates whether short-term formaldehyde (FA) fixation can maintain the cell states. We demonstrate that short-term FA fixation does not substantially affect protein recovery, even without heating and strong detergents, and maintains analytical depth compared with classical workflows. Fixation also preserves drug-induced specific perturbations of the protein abundance during cell sorting and sample preparation for SCP analysis. Our findings suggest that FA fixation can facilitate SCP by enabling sample shipping and prolonged sorting, potentially democratizing access to SCP technology and expanding its application in biological research, thereby accelerating discoveries in cell biology and personalized medicine.

🚨 More research on single-cell proteomics!
We evaluated how formaldehyde-based fixation preserve proteome state, drug response and cell integrity. Ultimately, cell fixation can facilitate access to #singlecell by enabeling sample shiping and prolonged sorting 📦

pubs.acs.org/doi/10.1021/...

Release DIA-NN 2.0 · vdemichev/DiaNN We are excited to announce DIA-NN 2.0, the most significant milestone in the history of DIA-NN development. Key Breakthroughs Proteoform Confidence mode: DIA-NN 2.0 solves the long-standing chall...

DIA-NN 2.0 is released! We consider it the biggest step forward in the history of DIA-NN. On modern LC-MS almost all identifications are now peptidoform-confident, with major improvements e.g. for phospho. Some other cool things too: github.com/vdemichev/Di...

A multi-tissue longitudinal proteomics study to evaluate the suitability of post-mortem samples for pathophysiological research - Communications Biology Longitudinal proteomics study identifies variability in proteome alterations in different tissues, reveals distinct consensus semitryptic motives in different organs and provides criteria for designin...

I am excited to share our latest paper on post-mortem multi-organ protein changes in a clinically relevant mouse model! www.nature.com/articles/s42...

A huge shoutout to my amazing co-authors for their incredible contributions!

Key highlights in replies (1/n)

Roman Zubarev and Muriel Priault's 4th Edition of the "Janeiro na Madeira" meeting starts this Sunday

23 talks freely accessible, Zoom link on the website.

jnm-2025.mozellosite.com

Jean-Pierre Changeux (allosteric proteins)
en.wikipedia.org/wiki/Jean-Pi...
kicks off at 17:00 GMT

#teammasspec

Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics - Nature Methods Chip-Tip is a label-free quantification-based single-cell proteomics workflow for deep single-cell proteomics, which identifies over 5,000 proteins and 40,000 peptides in single HeLa cells.

🚨 Our #singlecell article is out! We describe the Chip-Tip label-free SCP workflow quantifying >5000 proteins in single HeLa cells. With high scalability, increased depth and throughput we can now envision large-scale LFQ-SCP biomedical studies!
www.nature.com/articles/s41...

Identification numbers and FDR control of Spectronaut 18 vs DIA-NN 1.9 as benchmarked by Jesper Olsen and colleagues (Nature Methods) www.nature.com/articles/s41...

Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics - Nature Methods Chip-Tip is a label-free quantification-based single-cell proteomics workflow for deep single-cell proteomics, which identifies over 5,000 proteins and 40,000 peptides in single HeLa cells.

Thrilled to have this article out at last!
We describe a label-free single-cell proteomics workflow that enables great depth (>4500 proteins in stem cells) and higher throughput of up to 120 SPD, allowing reliable quantification of key cell markers.
www.nature.com/articles/s41...

Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics www.nature.com/artic...

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#proteomics #prot-paper

Enhanced sensitivity and scalability with a Chip-Tip workflow enables deep single-cell proteomics Nature Methods - Chip-Tip is a label-free quantification-based single-cell proteomics workflow for deep single-cell proteomics, which identifies over 5,000 proteins and 40,000 peptides in single...

We are excited to share our new Nature Methods paper describing the Chip-Tip workflow for single-cell proteomics identifying >5,000 proteins in single cells, enabling PTM analysis without enrichment and throughput of up to 120 single cell samples per day: rdcu.be/d6qJe

DIA-NN 2.0 release is almost ready, will come with some big news. One is scanning methods support, at the moment doing some tuning of the algorithm using Synchro-PASEF data :) Turns out, 'Q1 information' is really helpful for gaining peptidoform confidence. Likely also channel-confidence in plexDIA.

diaTracer enables spectrum-centric analysis of diaPASEF proteomics data - Nature Communications Data-independent acquisition advances proteomics quantification. Here, the authors present diaTracer, a spectrum-centric tool for diaPASEF data that supports broad proteomics applications, enabling di...

Sitting at Pike Place Market in Seattle at 7am in the morning, sipping coffee with my son, a long layover on the way home from Taipei. Otherwise I would do a long post. DiaTracer in #FragPipe work really well, making library-free analysis of any diaPASEF data possible. www.nature.com/articles/s41...