J. Krijgsveld

Degradome analysis to identify direct protein substrates of small-molecule degraders

The paper introduces a method to identify direct protein substrates of small-molecule degraders using degradome analysis and mass spectrometry.

A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens

The paper introduces a single-sample workflow, MTBE-SP3, for simultaneous proteomic and metabolomic analysis, showing it reduces technical variation and enables consistent results across biological matrices.

Chromosome 8 gain drives cancer progression by hijacking the translation factor 4E-BP1 sensitizing for targeted CDK4/6 inhibition

This study identifies chr8 gains and 4E-BP1 expression as prognostic markers in Ewing sarcoma, showing they drive cancer progression by promoting proliferation and sensitizing to CDK4/6 inhibitors.

Lipid Droplets Fuel Small Extracellular Vesicle Biogenesis

This study shows that lipid droplets are linked to small extracellular vesicle biogenesis and that manipulating lipid droplets can affect sEV secretion and cargo.

Translational Activity Controls Ribophagic Flux and Turnover of Distinct Ribosome Pools

The paper investigates ribosome turnover in human cells, showing distinct subunit pools with different turnover rates and demonstrating that translation inhibition increases 80S ribosome pool size and induces ribophagy.

Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

This study evaluates pre-analytical factors affecting plasma and serum proteome and metabolome stability, recommending standardized protocols for clinical use.

DEAD-box RNA Helicases Act as Nucleotide Exchange Factors for Casein Kinase 2

The paper shows DDX proteins act as nucleotide exchange factors for CK22, enhancing kinase activity and revealing a new regulatory mechanism for protein kinases.

Multi-layered chromatin proteomics identifies cell vulnerabilities in DNA repair

This study uses multi-layered chromatin proteomics to identify cell vulnerabilities in DNA repair by analyzing chromatin dynamics and repair protein interactions.

An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein

The paper introduces an efficient, selection-free, and scalable CRISPR/Cas9-based pipeline for epitope tagging in mammalian stem cells, achieving knock-in efficiencies of 5-30%.