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Our annual single-cell proteomics workshop was fun & productive. Stay tuned for video recordings & the next workshop! parallelsq.org/blog/pti-hosts…

Excited to share my PhD work investigating the regulation of my favorite X- and Y-chromosome genes! Page Lab

A new preprint: While analyzing proteomes of cells from mammalian tissues, Andrew Leduc identified protein leakage from permeabilized cells. We identified clear patterns that can be used to detect & mitigate this issue: biorxiv.org/content/10.110…

Check out our work on identifying and providing solutions for protein leakage artifacts associated with sample preparation. It all started out with our struggle to explain a strange bi-clustering pattern in our data.

We report many proteins not predicted by the genetic code. They are stable & abundant O( 10³ ) copies / cell. Generative mechanisms include codon-anticodon mismatches & RNA modifications. Their abundance depends on codon frequency & protein stability. biorxiv.org/content/10.110…

We have released DIA-NN 2.1.0, download link github.com/vdemichev/DiaN…, release notes github.com/vdemichev/DiaN…. It is a minor update, main highlights are: - Built-in support for Thermo .raw (Windows + Linux) - New QC metrics in PDF report & visualising trends across the experiment

Protein samples can be multiplexed to increase throughput. In 2023, Parallel Squared Technology Institute (PTI) set out to make tags (barcodes) that not only increase throughput but also enhance peptide sequence identifications: pubs.acs.org/doi/10.1021/ac… We will share results soon: parallelsq.org/workshops-and-…

Our paper on the impact of protein leakage due to loss of membrane integrity for single cell proteomic sample prep is out in Nature Communications! We analyze thousands of primary single cells from murine tracheal tissue and record membrane permeability🧵 nature.com/articles/s4146…

We just released JMod: an open source software supporting multiplexed DIA. It supports parallelization in both the mass domain (plexDIA) using small mass offsets and in the time domain (timePlex). It enabled 27-plex DIA & much further scaling 🚀 biorxiv.org/content/10.110…

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!