Michael R. Hoopmann

The paper develops a deep learning-enhanced fragment ion indexing method to reduce memory usage in tandem mass spectrometry searches while maintaining search accuracy and speed.

This paper expands structural surfaceomics to identify cancer-specific protein conformations across multiple tumor models, revealing potential immunotherapy targets through crosslinking mass spectrometry and structural modeling.

Nova is a C# library for handling mass spectrometry data, offering native support and extensibility for real-time analysis and instrument control applications.

The paper audits error control in twelve crosslinking mass spectrometry pipelines using ground-truth designs, finding some pipelines exceed false discovery rates by up to 29-fold.

The paper summarizes recent developments in the Crux toolkit for analyzing bottom-up proteomics data, including speedups, new features, and tools.

PTMProphet provides localization confidence for post-translational modifications in proteomics data, improving accuracy for downstream analysis.

This paper summarizes current XL-MS practices, compares strategies, and proposes common protocols to establish best practice guidelines for accurate and reproducible results.

The paper introduces a protein standard with shared peptides to benchmark protein inference algorithms, showing that methods excluding shared peptides provide more accurate error estimates.