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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/10.110… 1/2

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…

#SCP2025 continues with a hands-on workshop at PTI Parallel Squared Technology Institute (PTI) single-cell.net/proteomics/scp…

We performed global and systematic proteome analysis of Alzheimer's disease (AD). Our results suggest that decreased ubiquitin-proteasome system capacity and impaired clearance of proteins contribute substantially to proteopathic burden in AD. biorxiv.org/content/10.110…

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/10.110…

Furthermore, we identify coherent sets of ubiquitin system enzymes, proteins that target substrates for proteasomal degradation, whose levels robustly discriminate AD from non-AD samples. One subset exhibited consistent increases in AD, while another exhibited consistent

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. 1/2

Find PTI's preprints at the PTI bioRxiv channel: connect.biorxiv.org/relate/summary…

🟦 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. parallelsq.org/psmtags biorxiv.org/content/10.110…

The next generation plexDIA tags are looking promising !

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!