Julian Uszkoreit

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

This study benchmarks rescoring methods across proteomics search engines and datasets, finding that prediction-based approaches improve identification consensus and reduce variability.

pmultiqc generates metadata-aware QC reports for proteomics data using standardized metrics and integrates with existing workflows and cloud services.

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

This paper identifies NICA cells as a pathogen portal in CRC and shows how EBV and HERVs contribute to tumor progression through epigenetic and antiviral mechanisms.

WOMBAT-P benchmarks label-free proteomics workflows by comparing four analysis pipelines using standardized metrics and datasets.

This study analyzes bipartite peptide-protein graphs in proteomics, showing how graph structures vary with data type and organism, and highlights the challenge of quantifying proteins without unique peptides.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

The paper introduces PIA, a tool for protein inference in proteomics, highlights its support for PSI standards, and benchmarks it against a dataset for isoform detection.