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Parallel Squared Technology Institute
@parallelsq.bsky.social
A nonprofit research institute for advancing protein research in human health and disease | parallelsq.org
Reposted by Parallel Squared Technology Institute
During his graduate studies, Mahlon Collins worked with ALS patients who underwent painful spinal taps to donate CSF for his biomarker research. Now, he leads neurodegenerative disease research at @parallelsq.bsky.social.

Learn more about Mahlon's journey: bit.ly/3NoKX4g
From patient donations to cellular insights: Mahlon Collins on single-neuron proteomics and the future of Alzheimer’s research
Mahlon Collins leads neurodegenerative disease research at the Parallel Squared Technology Institute (PTI). A neurobiologist by training, he has witnessed firsthand the tremendous burden these disease...
bit.ly
January 12, 2026 at 11:29 PM
Reposted by Parallel Squared Technology Institute
Single-cell proteomics is moving past descriptive snapshots to quantitative models of cellular regulation and biological mechanisms.

Come to #Boston this July to shape the next chapter and have your voice heard.

Abstract deadline: Apr 1, 2026.

single-cell.net/proteomics/s...
January 20, 2026 at 1:48 PM
We're delighted to have Mahlon Collins featured in an @ionopticks.bsky.social article! The article goes over Mahlon's work on AD research, with a focus on advancing single-neuron proteomics at PTI.

ionopticks.com/2026/01/09/f...
January 13, 2026 at 2:10 PM
The focussed research organizations enabled by @convergentresearch.bsky.social are driving forward an ambitious agenda !

youtu.be/L5W-lV1K_xQ?...
Convergent Research: A mission control for frontier technology
YouTube video by Convergent Research
youtu.be
January 6, 2026 at 1:13 PM
Reposted by Parallel Squared Technology Institute
Biology’s earliest decisions are written in proteins.

Using single-cell proteomics, we discovered protein (and functional) symmetry breaking in mammalian embryos long before major transcriptome differences are detectable.

cell.com/cell/fulltex...
January 6, 2026 at 1:06 PM
Single-cell proteomics enables discoveries!

It illuminates the frontiers of biomedical research.
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...
December 8, 2025 at 5:13 PM
Reposted by Parallel Squared Technology Institute
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...
December 8, 2025 at 2:10 PM
To facilitate technology dissemination, we will host a workshop in our laboratory. Register to secure a spot!

Workshop participation is free with in-person conference registration but requires an advanced registration. To facilitate interactions and hands-on experience, participation is limited.
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...
December 1, 2025 at 12:41 PM
Research Fest highlighted PTI's scientific achievements to date as well as the team that made it all happen. We are thankful for the members on our team and the community who support our work, and wish everyone a Happy Thanksgiving.

youtu.be/YFfeJqHC3tM
Panel Discussion with Nikolai Slavov, Harrison Specht, Sarah Sipe, and Kevin McDonnell
YouTube video by Parallel Squared Technology Institute
youtu.be
November 26, 2025 at 4:01 PM
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.
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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...
November 20, 2025 at 2:44 PM
Reposted by Parallel Squared Technology Institute
More excellent work from @parallelsq.bsky.social ! So proud to be part of this team #TeamMassSpec #proteomics
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...
November 19, 2025 at 1:44 PM
No one is immune to aging but what exactly happens to our immune system as it ages? @thibaultcolombani.bsky.social takes a molecular dive into the immune system and talks about understanding age-induced immune altercations through single-cell proteomics.

www.youtube.com/watch?v=WUU1...
November 13, 2025 at 7:02 PM
Proteoforms matter:
Protein functions change due to sequence variants and diverse modifications regulating their activities.

𝐓𝐨 𝐬𝐞𝐞 𝐛𝐢𝐨𝐥𝐨𝐠𝐲 (𝐚𝐧𝐝 𝐝𝐢𝐬𝐞𝐚𝐬𝐞) 𝐜𝐥𝐞𝐚𝐫𝐥𝐲, 𝐰𝐞 𝐧𝐞𝐞𝐝 𝐩𝐫𝐨𝐭𝐞𝐨𝐟𝐨𝐫𝐦-𝐥𝐞𝐯𝐞𝐥 𝐪𝐮𝐚𝐧𝐭𝐢𝐟𝐢𝐜𝐚𝐭𝐢𝐨𝐧 𝐚𝐭 𝐬𝐜𝐚𝐥𝐞.

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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 !
November 8, 2025 at 3:02 PM
Reposted by Parallel Squared Technology Institute
𝐶𝑜𝑚𝑏𝑖𝑛𝑎𝑡𝑜𝑟𝑖𝑎𝑙 scaling may unlock a new level of throughput. This is enabling a long-awaited experiment !

Our team, led by Jason Derks, enabled combinatorial-scaling of mass spec proteomics throughput by developing multiplexing in the time domain, timePlex.

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November 1, 2025 at 4:59 PM
Reposted by Parallel Squared Technology Institute
Combining this time domain multiplexing with mass domain multiplexing (plexDIA), we demonstrated combinatorial scaling of throughput. You can read about it www.biorxiv.org/content/10.1... and hear Jason describe it at the Parallel Squared Technology Institute Research Fest: youtu.be/2rLBk4IaZpk?...
Increasing Mass spectrometry throughput using time encoded sample multiplexing | Jason Derks
YouTube video by Parallel Squared Technology Institute
youtu.be
November 1, 2025 at 4:59 PM
Mahlon Collins is leading our discoveries in profiling the proteome of single neurons from Alzheimer's disease patients. He presents this research journey in a talk, "Discovering Alzheimer's disease protein dysfunctions with high throughput proteomics".

youtu.be/UD8uSIfg7WY
Discovering Alzheimers disease protein dysfunctions with high throughput proteomics | Mahlon Collins
YouTube video by Parallel Squared Technology Institute
youtu.be
October 31, 2025 at 6:11 PM
@jasonderks.bsky.social presents "Increasing Mass spectrometry throughput using time encoded sample multiplexing" at Research Fest in Boston, MA on April 22, 2025.

www.youtube.com/watch?v=2rLB...
Increasing Mass spectrometry throughput using time encoded sample multiplexing | Jason Derks
YouTube video by Parallel Squared Technology Institute
www.youtube.com
October 23, 2025 at 6:38 PM
And, we are back with another presentation from this year's Research Fest. PTI's Senior Computational Scientist, Kevin McDonnell, talks about developing joint modeling (aka JMod) of mass spectra for empowering multiplexed DIA proteomics.

www.youtube.com/watch?v=plK4...
Jmod: Joint modeling of mass spectra for empowering mulitplexed DIA proteomics | Kevin McDonnell
YouTube video by Parallel Squared Technology Institute
youtu.be
October 16, 2025 at 6:49 PM
Throwback Thursday continues with a presentation by Maddy Yeh and Mark Adamo from Research Fest: "Tags for improving peptide sequencing and throughput in sensitive proteomics".

Watch on YouTube: www.youtube.com/watch?v=jA2I...
Tags for improving peptide sequencing and throughput in sensitive proteomics | Maddy Yeh, Mark Adamo
YouTube video by Parallel Squared Technology Institute
www.youtube.com
October 9, 2025 at 6:00 PM
Reposted by Parallel Squared Technology Institute
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
October 4, 2025 at 1:06 PM
Reposted by Parallel Squared Technology Institute
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?...
October 3, 2025 at 10:59 AM
Congrats to @e11bio.bsky.social on developing and showcasing PRISM for mapping brain wiring.
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
October 2, 2025 at 11:00 PM
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
October 2, 2025 at 5:38 PM
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.
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
October 2, 2025 at 2:09 PM
Reposted by Parallel Squared Technology Institute
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...
September 29, 2025 at 12:25 PM