Parallel Squared Technology Institute
@parallelsq.bsky.social
A nonprofit research institute for advancing protein research in human health and disease | parallelsq.org
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...
www.youtube.com/watch?v=WUU1...
November 13, 2025 at 7:02 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...
www.youtube.com/watch?v=WUU1...
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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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 !
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
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.
1/2
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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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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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
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.
1/n
Our team, led by Jason Derks, enabled combinatorial-scaling of mass spec proteomics throughput by developing multiplexing in the time domain, timePlex.
1/n
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
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?...
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
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
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
youtu.be/UD8uSIfg7WY
@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...
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
@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...
www.youtube.com/watch?v=2rLB...
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...
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
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...
www.youtube.com/watch?v=plK4...
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...
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
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...
Watch on YouTube: www.youtube.com/watch?v=jA2I...
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/...
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
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/...
Further, measuring and modeling protein degradation is key to biological interpretations.
pubs.acs.org/doi/10.1021/...
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?...
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
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?...
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?...
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
Read more: e11.bio/blog/prism
October 2, 2025 at 11:00 PM
Congrats to @e11bio.bsky.social on developing and showcasing PRISM for mapping brain wiring.
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
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
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
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
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.
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
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
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.
When developing AI models, we emphasize careful validation & rigorous benchmarking.
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...
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
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...
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...
@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
singlecellms.org?page_id=442
Conference Program – iSCMS
singlecellms.org
September 23, 2025 at 6:21 PM
@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
singlecellms.org?page_id=442
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.
🔽
Our technologies can increase the multiplexing along different dimensions (mass, time) and thus scale up throughput further to ~ 10⁴ - 10⁵ single cells.
🔽
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...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
September 21, 2025 at 1:38 PM
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.
🔽
Our technologies can increase the multiplexing along different dimensions (mass, time) and thus scale up throughput further to ~ 10⁴ - 10⁵ single cells.
🔽
Reposted by Parallel Squared Technology Institute
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...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
September 21, 2025 at 11:07 AM
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...
🧵
The results revealed 𝐜𝐨𝐦𝐩𝐥𝐞𝐱 regulation & 𝐬𝐢𝐦𝐩𝐥𝐞 organizing principles:
www.biorxiv.org/content/10.1...
🧵
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!
September 19, 2025 at 3:10 PM
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!
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...
Neurodegenerative Disease Senior Scientist: jobs.lever.co/convergentre...
Computational Biologist: jobs.lever.co/convergentre...
Research Chemist: jobs.lever.co/convergentre...
September 16, 2025 at 2:30 PM
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...
Neurodegenerative Disease Senior Scientist: jobs.lever.co/convergentre...
Computational Biologist: jobs.lever.co/convergentre...
Research Chemist: jobs.lever.co/convergentre...
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
PSMtags enable 9-plexDIA with better sequencing and multiplexing.
PSMtags support sensitive proteomic analysis of over 1,000 samples / day.
parallelsq.org/psmtags
September 3, 2025 at 1:33 PM
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
PSMtags enable 9-plexDIA with better sequencing and multiplexing.
PSMtags support sensitive proteomic analysis of over 1,000 samples / day.
parallelsq.org/psmtags
Reposted by Parallel Squared Technology Institute
The registration for SCP2026 is open !
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
August 25, 2025 at 11:13 AM
The registration for SCP2026 is open !
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
Join us next July for the the 9th Single Cell Proteomics Conference.
single-cell.net/proteomics/s...
Reposted by Parallel Squared Technology Institute
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.
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.
August 5, 2025 at 12:45 PM
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.
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.
Increasing throughput is particularly helpful when it also increases data quality. 🚀
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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This means increasing the sensitive and scope of sequencing the immunopeptidome ==> better cell therapies.
biorxiv.org/content/10.1...
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July 16, 2025 at 2:24 PM
Increasing throughput is particularly helpful when it also increases data quality. 🚀
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
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
June 19, 2025 at 11:35 AM
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
youtu.be/qgqloCJJa1M?...
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!
June 2, 2025 at 8:33 PM
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!