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Reposted by @kmcdonnell.bsky.social

Nikolai Slavov @slavov-n.bsky.social · 01/09/2026

Accurately quantifying over 700K precursors in a single 9-plexDIA set of 20ng proteomes is a new milestone. JMod achieves high quantitative accuracy over a 32-fold dynamic range of proteome spiked-in ratios across single-cell and bulk sample sizes. 1/ doi.org/10.1101/2025...

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 24/10/2025

Our new preprint outlining how to make 1000-plex mass tags!

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Reposted by @kmcdonnell.bsky.social

Jason Derks @jasonderks.bsky.social · 28/05/2025

We are excited to introduce ‘time’ as a new domain for proteomics multiplexing! It enables: -Label-free multiplexing -Combinatorial multiplexing with plexDIA Using combined 9-plexDIA and 3-timePlex we demonstrate 27-plex DIA 🚀

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Reposted by @kmcdonnell.bsky.social

Harrison Specht @harrisons.bsky.social · 28/05/2025

🧪 Transforming biomedical discovery needs proteomics that is specific and accurate, but also faster and cheaper @parallelsq.bsky.social is proud to introduce 9-plex PSMtags: a new mass tag that improves sequencing and increases throughput in sensitive proteomics 👇 www.biorxiv.org/content/10.1...

biorxiv.org

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

JMod is open source and available on GitHub. If you are interested in collaborating or contributing to the project, please feel free to reach out! 7/7 github.com/ParallelSqua...

github.com

GitHub - ParallelSquared/JMod: Joint modeling of DIA spectra

Joint modeling of DIA spectra. Contribute to ParallelSquared/JMod development by creating an account on GitHub.

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

We would also like to thank everyone at PTI for contributing to the project, it has been a huge team effort and a wonderful environment to work in! 6/7

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

JMod also uniquely supports multiplexing in the time domain as demonstrated in timePlex [link] by Derks et al. This orthogonal dimension can be combined with plexDIA, providing multiplicative increases in throughput! 5/7 www.biorxiv.org/content/10.1...

biorxiv.org

Increasing mass spectrometry throughput using time-encoded sample multiplexing

Liquid chromatography-mass spectrometry (LC-MS) can enable precise and accurate quantification of analytes at high-sensitivity, but the rate at which samples can be analyzed remains limiting. Throughp...

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

JMod can also provide highly accurate quantitation for these highly multiplexed samples, regardless of isotopic overlap 4/7

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

In the context of plexDIA, JMod uniquely supports channel offsets of <4 Da. Using 2 Da offsets, it enables almost 2-fold more throughput for any given tag. We demonstrate this using PSMtag, which was newly developed here at PTI, enabling 9-plexDIA! 3/7 www.biorxiv.org/content/10.1...

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

By modeling both MS1 and MS2 spectra as linear superpositions of library precursors, JMod can identify and quantify highly similar precursors within the same spectrum as well as deconvolve overlapping isotopes introduced by plexDIA. 2/7

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kmcdonnell.bsky.social @kmcdonnell.bsky.social · 28/05/2025

Increasing throughput in mass spec proteomics requires new ways to model the increased complexity of the spectra. We are delighted to share JMod, our new open source software developed at @parallelsq.bsky.social , which enables new multiplexing approaches. 1/7 www.biorxiv.org/content/10.1...

biorxiv.org

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