Peter Cimermančič

Integrating Narrow-Window DIA with AI-Powered Search Enables Deep and Reliable Functional Proteomics

The paper benchmarks nDIA and related proteomics methods, showing nDIA with DIA-NN and Tesorai Search provides high coverage and reliable results in proteomic analysis.

Rapid Mechanistic Bridging of an Alzheimer's Disease Plasma Protein Staging Panel Across Brain Proteomics Cohorts

The paper evaluates a seven-protein plasma panel across brain proteomics cohorts to show its association with AD proteomic changes.

Single-cell foundation models benefit from cross-modal training: adding proteomics data beats parameter scaling

The paper shows that adding proteomics data to a single-cell RNA-seq model improves its performance beyond increasing model size.

Functional diversification of the cephalopod proteome by RNA-editing

This study investigates how RNA editing in cephalopods alters protein function through proteomics and biochemical assays, revealing its impact on protein stability, localization, and interactions.

Back to Basics: Spectrum and Peptide Sequence are Sufficient for Top-tier Mass Spectrometry Proteomics Identification

This paper introduces a deep learning-based approach for peptide identification in mass spectrometry proteomics that outperforms existing tools by using spectra and peptide sequences directly.