Philipp Emanuel Geyer

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

This study evaluates bead-based and conventional plasma proteomics workflows, finding bead methods enhance low-abundance protein detection but are prone to contamination bias, while perchloric acid-based methods resist contamination better.

This study evaluates whether chromatographic performance affects proteome coverage under high-speed data acquisition, finding that proteome depth is now more influenced by mass spectrometry than chromatography.

This paper introduces Transposon-Display, a method to identify and optimize AI-designed protein binders for intracellular use, enabling controlled protein manipulation in human cells.

The paper quantifies the human liver proteome at cell-type resolution across multiple conditions, revealing proteome changes in disease states and providing a web-based resource for exploration.

The Clinical Knowledge Graph (CKG) links over 16 million nodes and 220 million relationships with statistical and machine learning workflows to accelerate proteomics data analysis and clinical biomarker interpretation.

The paper provides considerations and recommendations for designing and analyzing plasma proteomics studies to improve translational applications in clinical settings.