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Kosuke Ogata @ogatkk.bsky.social · 28/05/2026

Our kinase-based Phospho-Labeler approach for structural proteomics has now been published in Cell Reports Methods.

Reposted by Kosuke Ogata

Pedro Beltrao @pedrobeltrao.bsky.social · 25/05/2026

new lab preprint - Protein function prediction is a well established problem but proteins exist in different post-translationally modified forms. Here, @julianvangerwen.bsky.social built a ML model to predict the biological process regulated by individual phosphosites www.biorxiv.org/content/10.6...

biorxiv.org

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Kosuke Ogata @ogatkk.bsky.social · 13/05/2025

We utilized protein kinases to probe substrate protein structures. The phosphate groups enabled selective extraction of labeled sites. Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler www.biorxiv.org/content/10.1...

biorxiv.org

Detecting Protein Higher-Order Structural Changes Using Kinase as a Phospho-Labeler

We developed an approach to detect protein conformational changes on a proteome-wide scale by labeling proteins with phosphate groups through in vitro kinase reactions. This structural proteomics appr...

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Reposted by Kosuke Ogata

Mann Lab @mannlab.bsky.social · 26/02/2025

In our latest @Nature review with Tiannan Guo & Judith Steen, we explore how technological breakthroughs are revolutionizing MS-based proteomics: From enhanced sensitivity enabling single-cell analysis to high-throughput plasma proteomics & AI-based data interpretation www.nature.com/articles/s41...

nature.com

Mass-spectrometry-based proteomics: from single cells to clinical applications - Nature

This Review summarizes advances in mass-spectrometry-based proteomics and explores the potential applications of these technologies in the clinic.

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Reposted by Kosuke Ogata

Vadim Demichev @vadim-demichev.bsky.social · 29/01/2025

DIA-NN 2.0 is released! We consider it the biggest step forward in the history of DIA-NN. On modern LC-MS almost all identifications are now peptidoform-confident, with major improvements e.g. for phospho. Some other cool things too: github.com/vdemichev/Di...

github.com

Release DIA-NN 2.0 · vdemichev/DiaNN

We are excited to announce DIA-NN 2.0, the most significant milestone in the history of DIA-NN development. Key Breakthroughs Proteoform Confidence mode: DIA-NN 2.0 solves the long-standing chall...

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Reposted by Kosuke Ogata

Alejandro Brenes @ajbrenes.com · 10/11/2024

#teamMassSpec here is a starting pack in case you just moved over, or in case you've been absent for a while. This is #proteomics or #massspec related. The pack is not comprehensive but it's a start. go.bsky.app/HH7kqEh

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Reposted by Kosuke Ogata

Alejandro Brenes @ajbrenes.com · 16/11/2024

Here's a new list for early career researchers (=not had your own lab for ages) in proteomics. Feel free to ask to be added or removed, I've tried to make a guess but could've got it wrong. I think it's good to also have an ECR network. #teamMassSpec go.bsky.app/Dp8PHX1

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