Karl Mechtler

Making the Impossible Possible: Uniting TMT and DIA for Scalable Low-Input-Proteomics

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.

A complex of MAST1 and 14-3-3 regulates Tau phosphorylation in the developing cortex

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

Unified down-stream analysis of crosslinking mass spectrometry results with pyXLMS

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

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

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

Digging deeper into the immunopeptidome with TripleToolWF

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

A DIA-based quantitative crosslinking mass spectrometry framework for dynamic structural proteomics

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.

Dbf4-dependent kinase promotes meiotic DNA end resection through cyclin-dependent kinase 12 and DNA-2 in Caenorhabditis elegans

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

The Single Cell Proteomic blueprint, navigating instrumentation platforms, software tools and high-load libraries in neutrophils, RKO and A549 cells

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

CANE1-mediated autophagosome size regulation fine-tunes phosphate starvation tolerance in Arabidopsis thaliana

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

Pushing the limits of SCP: bacSCP, a proof-of-concept study to investigate heterogeneity of bacteria by single cell proteomics.

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.

Low-resolution FAIMS for increased peptide coverage in low-load and single-cell proteomics

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

Single cell proteomic analysis defines discrete neutrophil functional states in human glioblastoma

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.

Breaking Barriers in Crosslinking Mass Spectrometry: Enhanced Throughput and Sensitivity with the Orbitrap Astral Mass Analyzer

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.

A journey towards developing a new cleavable crosslinker reagent for in-cell crosslinking

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

A community audit of error control in crosslinking mass spectrometry

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.

In vivo crosslinking and effective 2D enrichment for interactome studies of the nucleosome.

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.

A multi-year longitudinal harmonization of quality controls in mass spectrometry proteomics core facilities

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.

Proteome-wide non-cleavable crosslink identification with MS Annika 3.0 reveals the structure of the C. elegans Box C/D complex

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.

A causal model of ion interference enables assessment and correction of ratio compression in multiplex proteomics

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

Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns

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

Integrated transcriptome and proteomeanalysis in human brain organoids revealsposttranscriptional regulation of ribosomalgenes.

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

Mimicked synthetic ribosomal protein complex for benchmarking cross-linking mass spectrometry workflows

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.

MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells

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

Crosstalk between H2A variant-specific modifications impacts vital cell functions

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

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

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.

The molecular principles of Piwi-mediated co-transcriptional silencing through the dimeric SFiNX complex

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

A synthetic peptide library for benchmarking crosslinking mass spectrometry search engines

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

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation

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

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.