Bart Van Puyvelde

This paper introduces a normalization framework to decouple protocol and instrument effects in multicenter proteomics studies, demonstrating its application to the PME13 dataset.

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

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

The paper develops a targeted LC-MS method to quantify SARS-CoV-2 spike protein expression and enables proteome profiling of infected cells.

The paper presents a comprehensive benchmark dataset for evaluating label-free quantification methods across various proteomics acquisition strategies.

The paper introduces a web-based tool for cross-resource peptide spectrum comparison and visualization, with a focus on integration and retrieval from spectral databases.

The paper provides a roadmap for selecting a bottom-up mass spectrometry protocol for histone analysis by comparing four methods and introducing a new enzyme.

The paper removes the dependency on DDA libraries in DIA by using predicted spectral libraries, making the workflow deterministic and improving standardization in clinical proteomics.

The paper introduces ion-networks, a data format for DIA MS that captures full data integrity by representing reproducible fragment ions and their consistent co-elution across runs.