Richard A. Scheltema

An optimized SP3 sample processing workflow for in-depth and re-producible phosphoproteomics

This study presents an optimized phosphoproteomics workflow using SP3 beads with improved phosphopeptide identification and detection of multiply phosphorylated peptides in HEK-293T cells.

Structure of an oxygen-induced tubular nanocompartment in Pyrococcus furiosus

The paper identifies oxygen-induced tubular nanocompartments in Pyrococcus furiosus using proteomics and cryo-EM, revealing their structure and role in ROS protection.

Towards a structurally resolved human protein interaction network

The paper uses AlphaFold2 to predict structures for 65,484 human protein interactions, identifying high confidence models and disease-related mutations.

Xlink Mapping and AnalySis (XMAS) - Smooth Integrative Modeling in ChimeraX

A ChimeraX bundle loads crosslinking mass spectrometry hits from several search engines, draws the distance constraints on structures, filters them by replicate, and feeds HADDOCK.

Notch-Jagged signaling complex defined by an interaction mosaic

The paper identifies five interaction regions between Notch1 and Jagged1 using XL-MS and SAXS, revealing a backfolded architecture that redefines the activation mechanism of Notch-Jagged signaling.

Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

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