Fränze Müller

pyXLMS simplifies crosslinking mass spectrometry analysis by integrating search engine results with downstream tools, enabling non-experts to perform comprehensive analyses.

This paper introduces DIA-QCLMS, a framework for quantitative crosslinking mass spectrometry that improves confidence assessment and integrates structural features, showing improved reproducibility in analyzing protein dynamics.

This study identifies a DDK/CDK-12/DNA-2 signaling axis that promotes meiotic DNA end resection in C. elegans, preventing aberrant recombination outcomes.

This study compares the performance of Orbitrap Astral and Eclipse mass spectrometers in CLMS, finding the Astral provides higher sensitivity and more unique residue pairs.

This paper introduces a new cleavable crosslinker, DiSPASO, for in-cell crosslinking and evaluates its performance in different model systems.

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.

This study improves an in vivo crosslinking workflow to identify protein-protein interactions, finding 56 novel nuclear PPIs and showing increased crosslinking of low-abundance proteins.

The paper introduces an algorithm for non-cleavable crosslink identification in MS Annika, revealing the structure of the C. elegans Box C/D complex and enabling proteome-wide analysis.

The paper introduces a synthetic peptide library and tool to benchmark cross-linking mass spectrometry workflows and demonstrates the importance of algorithm choice for improving identification rates and FDR.