Sander R. Piersma

EGFR upregulation drives signaling reactivation during EGFR inhibition in glioblastoma without broad kinome rewiring

This study shows that EGFR inhibition in glioblastoma does not lead to broad kinome rewiring but instead results in increased EGFR abundance and partial restoration of EGFR signaling.

HOOK2 downregulation compromises the tumorigenic and stemness properties of ovarian cancer cells by increasing endoplasmic reticulum stress

This study shows that reducing HOOK2 levels in ovarian cancer cells decreases tumor growth, migration, and stemness by increasing endoplasmic reticulum stress and cell death.

Phosphoproteomics of Hypertrophic Cardiomyopathy Patient Myocardium and Novel hiPSC-CM Model Reveal Protein Kinase A as a Modulator of Microtubule Repolymerization

The paper identifies altered microtubule post-translational modifications in hypertrophic cardiomyopathy and shows protein kinase A modulates microtubule repolymerization in patient-derived hiPSC-CMs.

Boosting the speed and accuracy of protein quantification algorithms in mass spectrometry-based proteomics

The paper introduces a new data structure and fragment weighting method to improve the speed and accuracy of protein quantification in mass spectrometry-based proteomics.

Integrated Multi-Omics Mapping of Mitochondrial Dysfunction and Substrate Preference in Barth Syndrome Cardiac Tissue

This study analyzes heart tissue from BTHS patients using integrated omics to identify metabolic and mitochondrial changes associated with the disease.

NUAK1 regulates contraction in vascular smooth muscle cells derived from abdominal aortic aneurysm patients

This study identifies NUAK1 as a regulator of vascular smooth muscle cell contraction in abdominal aortic aneurysm patients, showing its role in modulating MYPT1 activity and contraction-related proteins.

DPHL v2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

DPHL v2 improves upon DPHL v1 by including semi-tryptic peptides and protein isoforms, increasing identified and dysregulated proteins in colorectal cancer analysis.

Feasibility of phosphoproteomics on leftover samples after RNA extraction with guanidinium thiocyanate

The paper evaluates AGPC-based extraction for phosphoproteomics on limited samples, showing comparable results to urea-based methods and enabling multi-omics analysis.

Standardization and Harmonization of Distributed Multi-National Proteotype Analysis supporting Precision Medicine Studies

This paper standardizes a proteotype analysis workflow across multiple international sites to enable distributed, reproducible proteomic data generation for precision medicine.

DPHL: A pan-human protein mass spectrometry library for robust biomarker discovery using Data-Independent Acquisition and Parallel Reaction Monitoring

The paper introduces DPHL, a pan-human protein mass spectrometry library built using DIA and PRM, and demonstrates its utility in identifying differentially expressed proteins in prostate cancer and DLBCL.

INKA, an integrative data analysis pipeline for phosphoproteomic inference of active phosphokinases

INKA identifies active phosphokinases in cancer by integrating kinase and substrate phosphorylation data from phosphoproteomics.