Sam van Puyenbroeck

This study establishes quality control standards for single-cell proteomics through inter-laboratory benchmarking, identifying software and technical factors affecting data reliability.

InstaNovo-P improves phosphorylated peptide detection and site localization in phosphoproteomics by using a transformer-based model fine-tuned on phosphoproteomics data.

MLMarker computes tissue similarity scores for proteomics data, identifies tissue origins in biofluids, and provides interpretable predictions using a Random Forest model.

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

This study benchmarks eight de novo peptide sequencing models on proteomics datasets to evaluate their performance and identify limitations in resolving sequence ambiguity.