Lutz Fischer

KlinkPPI provides a unified interface to retrieve and compare protein-protein interaction data from multiple databases without merging or consensus.

RapCluster provides an interactive web platform with 11 clustering algorithms to improve transparency and reproducibility in clustering analysis.

MetaXtract extracts structured metadata from Thermo Fisher raw files to enhance FAIR data practices and workflow efficiency.

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.

Prosit-XL improves cross-linked peptide identification by predicting fragment intensities, enhancing protein-protein interaction discovery and interactome mapping.

The paper identifies issues in crosslinking mass spectrometry analysis where heuristic methods can distort error estimation, leading to false protein-protein interaction discoveries and proposes ways to correct this.

xiView is a platform for analyzing and visualizing Crosslinking Mass Spectrometry data, supporting multiple datasets and using coordinated visualization techniques.

The paper uses AI to predict protein complex structures in Bacillus subtilis using crosslinking and cofractionation mass spectrometry data.

The paper introduces an MS3-trigger algorithm that improves the sensitivity and specificity of MS3-based crosslinker identification in crosslinking mass spectrometry.

The paper evaluates MS-cleavable crosslinkers, finding that improved peptide backbone fragmentation, not mass resolution, is the main advantage of DSSO.

The paper demonstrates a reliable false-discovery rate estimation method for protein-protein interactions identified by crosslinking mass spectrometry using Escherichia coli cell lysate.

The paper identifies non-covalently-associated peptides in mass spectrometry that can mislead crosslink analysis and proposes methods to distinguish them from true crosslinks.

The paper introduces iRAP, a method to identify RNA-binding sites across the proteome, finding 1331 sites in 324 yeast proteins, many outside known domains.

The paper introduces Xi-MPA, a method for in-search assignment of monoisotopic peaks in cross-linking mass spectrometry, which improves peptide identification without compromising accuracy.

The paper evaluates the impact of using a correct false discovery rate formula for heterobifunctional cross-linkers and finds minimal practical advantages.

This study develops QCLMS to detect protein conformational changes by analyzing cross-linking yields and introduces methods to distinguish minor and major changes.

The paper introduces an updated MaxQuant workflow for quantitative cross-linking/mass spectrometry (QCLMS) that improves cross-link quantification accuracy and reliability through automation and label-swap replicas.

This paper determines the structure of C3(H2O) using quantitative cross-linking/mass spectrometry and modeling, revealing domain rearrangements compared to C3 and C3b.

This paper evaluates cross-linking/mass spectrometry for protein structure prediction through a blind test in CASP11, identifying limitations in link distribution and structural definition.