Ivo Alexander Hendriks

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.

This study identifies ZATT/ZNF451 as a key factor in resolving stalled TOP2 cleavage complexes without relying on TDP2, proteolysis, or DSB repair pathways.

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.

This study resolves the structure of bacteriophage T4 at different stages, revealing mechanisms of genome delivery and superinfection exclusion.

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

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.

The paper reports the structure of a novel contractile injection system in Salmonella enterica subsp. salamae and identifies a new CIS cluster.

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.

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.

This study presents the cryo-EM structures of PlPVC1 in extended and contracted states, revealing structural features and contraction mechanism insights.

This study shows interferon induces ADP-ribosylation in p62 bodies via PARP14, requiring ubiquitin activation and proteasome activity.

The paper uses proteomics to analyze protein dynamics during replication origin firing in human cells, identifying NCAPH2 as a novel factor required for efficient origin firing.

The paper identifies TOPORS as a SUMO-targeted ubiquitin ligase (STUbL) essential for SUMO-dependent DNA-protein crosslink repair and stress responses, showing its cooperative function with RNF4.

The paper identifies 14,056 citrullination sites across 4,008 proteins using mass spectrometry, revealing widespread citrullination and its functional roles in histone marks and autoantigens.

This study reveals the structure and mechanism of the Zorya anti-phage defense system using cryo-EM and functional assays, showing how it detects phage invasion and activates defense.

The paper introduces UBIMAX, a method to profile ubiquitylation, and identifies Dbn1 as a novel DNA damage-induced ubiquitylation target regulated by SCFβTRCP.

This study identifies an N-terminal signal peptide that enables efficient loading of therapeutics into the Afp nano-injection system for targeted delivery.

This study identifies catalytic and non-catalytic functions of DNA polymerase kappa in translesion DNA synthesis using CRISPR screening and TLS analysis.

This paper identifies VCF1 as a novel p97 cofactor that enhances p97-UFD1-NPL4 interactions with ubiquitylated substrates, promoting proteasomal degradation.

The paper identifies DAXX as a novel histone chaperone pathway that deposits H3.3K9me3 before DNA deposition, expanding the histone chaperone network's role in heterochromatin assembly.

This study identifies the dual role of sumoylation in adipocyte differentiation by regulating gene expression and transcriptional network rewiring through SLAMseq and ChIPseq.

The paper identifies ADP-ribosylation sites regulated by HPF1 and ARH3 using proteomics, revealing widespread mono-ADP-ribosylation and challenges existing assumptions about PARP1 target residues.

The paper introduces AI-ETD for MS-based proteomics analysis of physiological ADP-ribosylation, identifying more ADPr sites than existing methods.

The paper introduces an advanced proteomics strategy using mass spectrometry to comprehensively profile ADP-ribosylation sites, identifying over 11,000 unique peptides and 7,000 sites in HeLa cells.