Jesper Velgaard Olsen

Deciphering molecular mechanisms of synergistic growth reduction in kinase inhibitor combinations

This study investigates synergistic effects of kinase inhibitor combinations by analyzing phosphoproteomics and transcriptomics data to identify molecular mechanisms and pathway interactions.

An auto-generated ADP-ribosyl-cysteine degron drives DTX2-dependent turnover of PARP7

This study identifies an ADP-ribosyl-cysteine degron in PARP7 that is recognized by DTX2, leading to PARP7 degradation and affecting AR signaling in prostate cancer.

High-fidelity bispecific protease KRysin for deeper plasma proteomics and phosphoproteomics

KRysin, a bispecific protease, improves plasma and phosphoproteomics by enhancing digestion completeness and PTM coverage compared to trypsin.

Pulsed-SILAC in single mouse embryos reveals early embryonic protein synthesis dynamics and phosphosite regulation

The paper uses pulsed-SILAC in single mouse embryos to study protein synthesis dynamics and phosphosite regulation during early embryogenesis, revealing active maternal proteome synthesis and post-translational regulation.

Mapping the human sperm proteome across compartments, donors and individual cells

This study maps the human sperm proteome across compartments, donors, and individual cells, revealing conserved and variable proteins and linking mitochondrial dysfunction to male infertility.

Tethering-mediated recruitment of pioneer factors by NuRD enables signal dependent gene activation and protects cell identity

The paper identifies NuRD's role in tethering pioneer factors like SOX2 to transcription sites, enhancing ERK-dependent gene activation and maintaining cell identity.

A chemogenetic CRISPR knockout screen identifies a ubiquitin-mediated calcineurin-BMP pathway relay in T cell activation

Near-Zero Missed Cleavages with a High-Fidelity Recombinant Arg-C Zero for Mass Spectrometry-Based Proteomics

This paper introduces Arg-C Zero, a high-fidelity protease with near-zero missed cleavages, demonstrating its utility in proteomics, especially for analyzing post-translational modifications.

Deciphering cytokine-driven ADP-ribosylation signaling networks via Af1521-based mass spectrometry analysis of labile Glu/Asp-linkages

The paper develops an MS-based workflow to detect Glu/Asp-ADPr modifications, identifies over 600 sites in cytokine-stimulated cells, and reveals residue-specific ADPr dynamics in immune signaling.

The proteomics and phosphoproteomics landscape of melanoma under T cell attack

This study profiles the proteomics and phosphoproteomics of melanoma cells under T cell attack to identify immune checkpoint targets and therapeutic vulnerabilities.

Improved peptide search for identification of SUMO and sequence-based modifications, in MaxSBM

The paper introduces MaxSBM, a MaxQuant module for identifying sequence-based modifiers like SUMO, improving peptide identification rates and spectral annotation.

Molecular basis of the Druantia anti-phage defense system

This study investigates the molecular mechanism of the Druantia anti-phage defense system, showing that DruH-E provides robust immunity and revealing its DNA unwinding and regulation by ATP.

Composition variations in archaeological human bone proteomes

The paper compares proteome composition and modification in different bone types from archaeological human skeletons, finding cortical bone better preserves proteins than trabecular bone and petrous bone has the most complex proteomes.

The HSP90-CDC37 Chaperone System Orchestrates RAF1 Kinase Activation Through a Pre-Dimerization Mechanism

This study reveals the HSP90-CDC37 chaperone system's role in RAF1 activation through pre-dimerization and asymmetric folding, showing its active regulatory role in MEK signaling and cell proliferation.

Archaeological preservation of amelogenesis pathways

The paper analyzes archaeological dental enamel proteomes to study the effects of amelogenesis on protein digestion and phosphorylation, and introduces a new marker for estimating genetic sex.

Glucocorticoid-induced proteome and phosphoproteome changes in breast cancer cell lines

This study uses mass spectrometry to analyze proteome and phosphoproteome changes in breast cancer cell lines after glucocorticoid treatment, revealing GR-dependent responses and noncanonical TFs and kinases involved in metastasis.

Comparison of extracellular vesicles and mechanically induced vesicles for structure determination of membrane proteins

This study compares extracellular vesicles (EVs) and mechanically induced vesicles (MVs) for membrane protein structure determination, finding that MVs provide better structural representation of HER2 in native environments.

Early Identification of At-Risk Patients: ProteomicSignature Predicts Progression to DecompensatedCirrhosis

This paper identifies a four-protein proteomic signature that predicts progression to decompensated cirrhosis with high accuracy in both training and external validation cohorts.

Quantitative proteomics and phosphoproteomics reveal glucocorticoid stimulation of TLR and Rho GTPase signaling in neutrophil-like cells

The paper uses proteomics and phosphoproteomics to show GCs activate TLR and Rho GTPase signaling in neutrophil-like cells, leading to abnormal activation and aging.

Higher-Throughput Proteome Profiling Enabled by Parallelized Pre-Accumulation and Optimized Ion Processing in the Orbitrap Astral Zoom Mass Spectrometer

Orbitrap Astral Zoom upgrades enable 270 Hz DIA scanning, identifying 7184 protein groups at 500 samples/day and >12,000 proteins from fractionated HEK293 in 2.7 h.

Acute IFN-γ elicits long-term proteomic IFN-γ signature in melanoma cells

The paper shows that a short IFN-γ pulse induces a long-term proteomic signature in melanoma cells, challenging assumptions about cytokine signaling duration.

Comparative Analysis of Lysine-Specific Peptidases for Optimizing Proteomics Workflows

This study compares three LysC homologues for proteomics, finding A. lyticus LysC provides better peptide identification and digestion efficiency than others.

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

Identification and removal of contamination in palaeoproteomic analysis of dental enamel

The paper investigates contamination in palaeoproteomic analysis of dental enamel and finds that simple water or bleach washes before demineralization effectively remove contamination without harming endogenous proteins.

Meteorin resolves nociceptive hypersensitivity by reducing connexin-mediated coupling in satellite glial cells

This study shows meteorin reduces nociceptive hypersensitivity by decreasing connexin-mediated coupling in satellite glial cells, with long-lasting therapeutic effects in pain models.

The Human Cell Line Phosphoproteome Atlas: A Deep Empirical Resource Revealing Kinase Activity Landscapes

The paper presents a comprehensive human phosphoproteome atlas with over 200,000 phosphosites, improving phosphoproteomics speed and accuracy, and identifies kinase activity patterns linked to drug sensitivity.

From HeLa to human blood: extending single-cell proteomics to the smallest immune cells

This paper develops a high-sensitivity single-cell proteomics platform and applies it to analyze small immune cells, achieving deep proteome coverage and identifying key markers in PBMCs.

High-Throughput Spatial Proteomics at Cellular and Subcellular Resolution via a Hanging Droplet Workflow

This paper introduces a high-throughput spatial proteomics workflow for FFPE samples, enabling efficient processing and analysis of subcellular regions with high resolution.

Benchmarking enrichment and depletion methods for quantitative plasma proteomics in different plasma types and the correlation to clinical routine assays.

This study benchmarks enrichment and depletion methods for plasma proteomics across different plasma types and evaluates their correlation with clinical assays.

New methods on the block: Taxonomic identification of archaeological bones in resin-embedded sediments through palaeoproteomics

This paper demonstrates the successful retrieval of palaeoproteomic data from bone fragments in resin-impregnated sediment blocks, enabling microstratigraphic taxonomic identification of Pleistocene faunal remains.