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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · 4d

The counting statistics for single-cell MS support accurate estimates of protein abundance in single cells, which is essential for quantitative analysis.

Further, measuring and modeling protein degradation is key to biological interpretations.

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

Transformative Opportunities for Single-Cell Proteomics

Many pressing medical challenges, such as diagnosing disease, enhancing directed stem-cell differentiation, and classifying cancers, have long been hindered by limitations in our ability to quantify p...

pubs.acs.org

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · 5d

Earlier this year, @parallelsq.bsky.social hosted a research fest.

We began with a broad perspective:
◾️ A century of remarkable progress! Proteomics drove conceptual discoveries and medical treatments.

Listen to what's next!

Proteomics: The arc of progress
youtu.be/Sc2QLXb84XI?...

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Parallel Squared Technology Institute @parallelsq.bsky.social · 6d

Congrats to @e11bio.bsky.social on developing and showcasing PRISM for mapping brain wiring.

Andrew Payne @andrewcpayne.bsky.social · 7d

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.

Read more: e11.bio/blog/prism

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Parallel Squared Technology Institute @parallelsq.bsky.social · 6d

It's good to look back and see how far we have come since Research Fest took place almost six months ago.

Over the next few weeks, we will post some throwback videos from the presentations. Let's start with opening remarks by PTI's Director, @slavov-n.bsky.social:

youtu.be/Sc2QLXb84XI

Proteomics: The arc of progress | Nikolai Slavov

YouTube video by Parallel Squared Technology Institute

youtu.be

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Parallel Squared Technology Institute @parallelsq.bsky.social · 6d

Our large scale measurements of protein functions and conformations can help realize the potential of AI.

When developing AI models, we emphasize careful validation & rigorous benchmarking.

Nikolai Slavov @slavov-n.bsky.social · 6d

In this article, I shared my perspective on AI.

AI excels at supervised learning, and well annotated datasets can help unlock new AI capabilities.

🔗 www.nature.com/articles/s42...

OA 🔗 rdcu.be/eI4JW

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · 9d

I am looking forward to ICSB next week.

I will present:
1⃣ New technology from @parallelsq.bsky.social:
parallelsq.org/blog/proteom...

2⃣ New biology from @slavovlab.bsky.social
biorxiv.org/content/10.1...

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Parallel Squared Technology Institute @parallelsq.bsky.social · 15d

@jasonderks.bsky.social is presenting at iSCMS! Come by this Saturday afternoon around 2pm to hear his talk: "Increasing proteomics throughput by multiplexing in the mass and time domains".

singlecellms.org?page_id=442

Conference Program – iSCMS

singlecellms.org

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Parallel Squared Technology Institute @parallelsq.bsky.social · 17d

We developed approaches to increase the parallelization of proteomics in the mass and time domains and demonstrated 27x increased throughput.

They can scale further the throughput of the metabolic pulse proteomics demonstrated by @andrewleduc.bsky.social et al.

www.parallelsq.org/blog/proteom...

Proteomics: Greater than the sum of its parts - PTI - Parallel Squared Technology Institute

Over the past 2 years, PTI synergized advances in computational sciences, chemistry, biology and mass spectrometry to develop the next generation of applications and methods in single cell proteomics.

www.parallelsq.org

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Parallel Squared Technology Institute @parallelsq.bsky.social · 17d

Multiplexed DIA enabled multimodal proteomics of ~ 10³ single cells, including quant of protein synthesis & degradation rates.

Our technologies can increase the multiplexing along different dimensions (mass, time) and thus scale up throughput further to ~ 10⁴ - 10⁵ single cells.

🔽

Slavov Laboratory @slavovlab.bsky.social · 17d

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...

🧵

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Reposted by Parallel Squared Technology Institute

Slavov Laboratory @slavovlab.bsky.social · 17d

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...

🧵

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Parallel Squared Technology Institute @parallelsq.bsky.social · 19d

Science communication is a key part of our mission, so thank you @juliabauman.bsky.social for this video about PTI's single cell proteomics research!

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Parallel Squared Technology Institute @parallelsq.bsky.social · 22d

PTI is growing and we are looking for more scientists to join our team!

Neurodegenerative Disease Senior Scientist: jobs.lever.co/convergentre...

Computational Biologist: jobs.lever.co/convergentre...

Research Chemist: jobs.lever.co/convergentre...

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Parallel Squared Technology Institute @parallelsq.bsky.social · Sep 3

We share our technologies to maximize the benefit for the community.

PSMtags enable 9-plexDIA with better sequencing and multiplexing.

PSMtags support sensitive proteomic analysis of over 1,000 samples / day.

parallelsq.org/psmtags

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · Aug 25

The registration for SCP2026 is open !

Join us next July for the the 9th Single Cell Proteomics Conference.

single-cell.net/proteomics/s...

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · Aug 5

Scaling DNA sequencing is a notable success story.

Scaling protein analysis is harder since the proteome is a much taller mountain: www.nature.com/articles/s41...

@asimovpress.bsky.social writes about @parallelsq.bsky.social's approach to scale up proteomics.

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Parallel Squared Technology Institute @parallelsq.bsky.social · Jul 16

Increasing throughput is particularly helpful when it also increases data quality. 🚀

Nikolai Slavov @slavov-n.bsky.social · May 28

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...
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Parallel Squared Technology Institute @parallelsq.bsky.social · Jun 19

The talk by Dr. Kevin McDonnell at #SCP2025 is on YouTube:

JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains

youtu.be/qgqloCJJa1M?...

JMod: Joint modeling of mass spectra for enhanced multiplexing in the mass and time domains, SCP2025

YouTube video by Nikolai Slavov

youtu.be

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Parallel Squared Technology Institute @parallelsq.bsky.social · Jun 2

PTI will be represented at #ASMS2025 with with two posters (TP203 and ThP 533) and two talks (TOA 2:30 pm and WOA 8:30 am). Find us to hear about our PSMtag, and applications in Alzheimer's and aging biology!

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · May 31

🟦 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...

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · Jun 2

We developed multiple interdependent technologies.

Together, they are opening up new opportunities:

www.parallelsq.org/blog/proteom...

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Reposted by Parallel Squared Technology Institute

Devin Schweppe @dschweppe.bsky.social · Jun 2

#ASMS2025
Come here about the latest in real-time instrument control including applications to single cell proteomics (@parallelsq.bsky.social), #glycotime, and quantitative proteomics!

Nick Riley @nmriley.bsky.social · Jun 2

#ASMS2025 offers great evening workshops. If you are interested in real-time decision-making during MS data acquisition or still looking for one to join,

consider the Real time Mass Spectrometry Workshop featuring speakers and panelists Sarah Sipe, Aarthie Senathirajah, and Manuel Peris Diaz.

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · May 31

Find PTI's preprints at the PTI 𝑏𝑖𝑜𝑅𝑥𝑖𝑣 channel:

connect.biorxiv.org/relate/summa...

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · May 30

Furthermore, we identify sets of ubiquitin ligases whose levels robustly discriminate AD from non-AD samples. One subset exhibited consistent increases in AD, while another exhibited consistent decreases, revealing complex alterations to the ubiquitin system in AD.

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

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · May 30

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...

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Reposted by Parallel Squared Technology Institute

Nikolai Slavov @slavov-n.bsky.social · May 30

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.

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