Karl Mechtler

This paper combines TMT and DIA proteomics techniques to improve low-input proteomics, showing how to overcome co-isolation interference and enabling TMT quantification with DIA-focused software.

This study identifies MAST1 and 14-3-3 as regulators of Tau phosphorylation in the developing cortex through interactions and phosphorylation events.

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

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

TripleToolWF improves immunopeptide identification and quantification by combining three search engines, increasing results by 6-25% and enhancing confidence in bacterial immunopeptide binding.

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 evaluates DIA search engines, high-load libraries, and instrumentation platforms for single-cell proteomics across different cell types.

This study identifies CANE1 as a regulator of autophagosome size in Arabidopsis thaliana under phosphate starvation, linking it to ER stress and autophagy.

This study introduces bacSCP, a single-cell proteomics protocol for bacteria, demonstrating its ability to quantify proteins and reveal stress-response heterogeneity in Bacillus subtilis.

This paper shows that lowering FAIMS resolution improves peptide identification in low-load and single-cell proteomics by increasing ion transmission and sensitivity.

The paper uses single cell proteomic analysis to identify distinct functional states of neutrophils in human glioblastoma, revealing clusters with pathogenic and anti-tumorigenic properties not detectable by scRNA-seq.

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.

This paper introduces a high-throughput single-cell proteomics workflow achieving 5300 protein groups per cell with high accuracy, enabling the study of cellular heterogeneity and lineage differentiation.

This study harmonizes quality controls across proteomics core facilities to improve data comparability and reliability through a 4-year longitudinal dataset and common processing software.

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 develops a causal model to assess and correct ratio compression caused by ion interference in multiplex proteomics data.

The paper shows that different promoter classes use distinct PIC compositions and mechanisms, leading to focused or dispersed transcription initiation patterns in Drosophila.

The paper integrates transcriptome and proteome data from human brain organoids to uncover posttranscriptional regulation of ribosomal genes during corticogenesis.

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.

This study shows MSX2 regulates syncytiotrophoblast fate in human trophoblast stem cells by directly controlling gene expression and interacting with the SWI/SNF complex.

The paper investigates how PTMs on H2A variants in Arabidopsis affect cell functions and DNA damage response through motif-specific cross-talk.

This study identifies Ski7 as a post-transcriptional regulator that maintains low transcript levels of specific genes during the zebrafish oocyte-to-embryo transition, impacting fertility and redox processes.

This study identifies the role of the SFiNX complex dimerization in enabling co-transcriptional silencing via molecular condensate formation in Drosophila.

The paper benchmarks crosslinking mass spectrometry search engines using synthetic peptide libraries, revealing significant variation in false discovery rates across different validation strategies.

This study identifies SFiNX, a complex required for Piwi-mediated co-transcriptional silencing in Drosophila, revealing its role in piRNA-guided heterochromatin formation.

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