Parallel Squared Technology Institute (PTI)

Six years on from this perspective: science.org/doi/10.1126/sc… The technology has rapidly advanced and spread beyond a few pioneering labs. I am excited for the next phase, when the technology will increasingly enable mechanistic investigations & discoveries. 🚀

At the same time, some proteins are very long-lived. Some persist as long as the organism itself. Protein lifetimes range from minutes to decades: ⏹️ That's a dynamic range of ~6,000,000. Lifetimes vary across cell types & states, and these dynamics are essential to life! 2/

You can help enable the quantification of thousands of samples/day without sacrificing depth or accuracy. What makes this position special is that these technologies are directly and tightly integrated with biological discovery. 2/2 jobs.lever.co/convergentrese…

A special opportunity for lovers of mass spectrometry proteomics to join a like-minded team at PTI. Join a collaborative initiative to enable direct protein analysis at unprecedented scale, in partnership with leading instrument developers, academics, and industry leaders. 1/2

We’re testing conceptual hypotheses, dissecting disease progression, proteostasis, protein degradation, PTMs, and aggregation, all with focus on creative, rigorous data interpretation. If you want to do science that changes how we think, this is it. 👇 jobs.lever.co/convergentrese…

🔥 We’re hiring! A rare opportunity to rethink neurodegeneration: 🟦 Develop creative, rigorous approaches to data interpretation that move beyond descriptive analysis toward mechanistic insight. Join our team at Parallel Square Technology Institute (@ParallelSqTech) to study neurodegenerative disease using direct protein analysis at single-cell resolution. 1/2

I’m grateful to be named a Distinguished Professor by Northeastern University College of Engineering. This recognition reflects the support, collaboration, and creativity of many colleagues, students, and collaborators over the years. I’m thankful to be part of a community that values rigorous science, curiosity-driven research, and supportive mentorship.

Single-Cell Proteomic Technologies: Tools in the Quest for Principles Journal 🔗 annualreviews.org/content/journa… OA 🔗 slavovlab.net/Slavov-Lab-Pub… 2/2

This review reflects on a journey I’ve been lucky to witness closely: ◼️ The transformation of single-cell proteomics from a fragile idea into a powerful discipline. The technological progress towards deeper coverage and higher throughput is fast and exciting, but what excites me most is the biology: ◼️ the chance to move beyond associations and toward causal, mechanistic understanding built on direct protein measurements. None of this would exist without early pioneers who pushed the field forward when success was far from guaranteed, nor without sustained advances in instrumentation that dramatically improved ion utilization and sensitivity. I see this as a starting point, a promising start. The next phase of the field should focus on discovery: mechanisms, principles, and new quantitative and conceptual ways of thinking about cellular regulation. Onward. 🚀 1/2

Mass spectrometry proteomics now enables measuring not just protein abundance, but the birth, life, and degradation of proteins inside the single cells of living mice, moving us from static “snapshots” to dynamics of cellular proteomes. This shift opens the door to decoding how cellular proteomes are regulated over time and how control mechanisms shape cell identity and function. Dive into the science of measuring proteome dynamics in single cells: 2/2 🔗 blog.slavovlab.net/2025/11/19/in-…

Discussing research with the innovators beats scrolling a feed. If you’re in single-cell biology, proteomics, mass spec tech, or computational biology, join our next meeting this July. #SCP2026

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/scp…

Protein degradation is often considered a final step in gene expression regulation. It also regulates the first step: Transcription TFs (e.g. p53, HIF, Myc) are regulated by 𝐝𝐞𝐠𝐫𝐚𝐝𝐚𝐭𝐢𝐨𝐧-𝐠𝐚𝐭𝐞𝐝 𝐜𝐨𝐧𝐭𝐫𝐨𝐥: ⬛️ It confers advantages. blog.slavovlab.net/2025/08/16/pro…

We're delighted to have Mahlon Collins featured in an IonOpticks 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/fro…

The focussed research organizations enabled by @Convergent_FROs are driving forward an ambitious agenda ! A mission control for frontier technology youtu.be/L5W-lV1K_xQ?si…

@slavov_n We will host full day hands-on workshop that will take participants from biological samples through sample preparation to mass spectrometry data acquisition and analysis. #workshop" target="_blank" rel="nofollow noopener">single-cell.net/proteomics/scp…

#SCP2026 will be in July. I am looking forward to it !

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/fulltext/…

A reflection on 2025 🔬 Despite strong headwinds, 2025 brought much research progress. I enjoyed many research projects, especially the ones below: 📌 Research Highlights from Slavov Lab(@slavovLab): 🔹 Protein abundance regulation across individual cells: Our direct measurements of protein synthesis and degradation rates in single cells suggested principles underlying protein abundance variation in mammalian tissues at single-cell resolution. 🔹 Proteomic symmetry breaking in early development: We published our collaborative discovery on the roles of protein asymmetry in early developmental decisions: Protein abundance patterns diverge very early in development, revealing distinct cellular states emerging from the first divisions of the zygote and linking proteome dynamics with developmental fate decisions. 🔹 Protein degradation shapes proteomes: We quantified substantial contributions to protein degradation and growth-dependent dilution to protein abundance regulation across the proteome and across different organs and tissues, much larger than previously appreciated. 🔗 slavovlab.net/publications.h… 📌 Research Highlights from Parallel Squared Technology Institute (@ParallelSqTech): 🔹 PSMtags: new mass tags to boost multiplexing and sequencing PTI introduced PSMtags, a new class of mass tags that improves de novo sequencing, sensitive peptide identification, and enables higher multiplexing (up to 9 samples) by plexDIA. 🔹 timePlex: time-encoded sample multiplexing for combinatorial scaling PTI developed timePlex, which multiplexes samples using time offsets between injections, adding time as an orthogonal dimension to mass. Demonstrations include 3-timePlex × 9-plexDIA = 27-plex, supporting 27 samples/run. timePlex opens an avenue for further growth to come in 2026 and beyond. 🔹 JMod: joint decoding software for highly multiplexed DIA spectra PTI released JMod, open-source software for joint modeling/decoding of complex DIA spectra, explicitly handling overlaps as linear superpositions. This strengthens analysis of multiplexed DIA data in both mass and time domains and helps unlock the throughput enabled by new chemistries and acquisition schemes. 🔹 UPS dysregulation in Alzheimer’s disease and its impact on the proteome. Using plexDIA protein analysis of human cortex (AD vs. non-AD), PTI reported widespread dysregulation, with a prominent signal being decreased abundance and coordination of 20S proteasome subunits, pointing to protein-quality-control mechanisms that contribute to increased protein levels in AD pathology. 🔗 parallelsq.org/blog/proteomic… We’re grateful for the collective effort of students, collaborators, and partners who helped advance technologies and biology in ways that open new doors for discovery.

A mission control for frontier technology An ambitious perspective on technological innovation and scaling by @Convergent_FROs youtu.be/L5W-lV1K_xQ?si…

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/10.110…