Martin Wühr

Proteome-wide quantification of protein turnover in frog and fly embryos reveals divergent strategies of maternal inheritance

The paper quantifies protein turnover in frog and fly embryos using 18O-water labeling and proteomics, revealing divergent strategies of maternal proteome inheritance.

Transitions in the proteome and phospho-proteome during early embryonic development in Xenopus

The paper analyzes proteome and phospho-proteome changes during Xenopus embryonic development, identifying key transitions in protein expression and phosphorylation patterns.

Expanding Targeted Instrumentation for Discovery Applications: Complement Reporter Ion Quantification with a Quadrupole-Ion Trap Instrument

This paper demonstrates that a quadrupole-ion trap instrument can perform multiplexed shotgun proteomics with accuracy comparable to a dedicated tribrid instrument, offering a cost-effective alternative.

Synergistic Arg-C Ultra and Lys-C Digestion for Quantitative Proteomics

This paper introduces a synergistic Lys-C/Arg-C Ultra digestion strategy to improve proteome coverage and quantitative reproducibility in shotgun proteomics.

Robustness of mitochondrial biogenesis and respiration explain aerobic glycolysis

The paper explains aerobic glycolysis as a result of mitochondrial respiration saturation and decoupling of mitochondrial biogenesis from other cellular processes.

Quantitative proteome dynamics across embryogenesis in a model chordate

The paper presents a proteome atlas of Ciona covering eight developmental stages and ~7,000 genes, showing maximal divergence during mid-developmental stages contrary to the hourglass model.

Super-resolution mass spectrometry enables rapid, accurate, and highly-multiplexed proteomics at the MS2-level

The paper demonstrates that super-resolution mass spectrometry with least-squares fitting enables highly-multiplexed, accurate, and precise shotgun proteomics at the MS2 level.

Differential nuclear import sets the timing of protein access to the embryonic genome

The paper identifies that differential nuclear import timing controls gene expression onset in early embryonic development by regulating protein access to the genome.

Gut bacterial nutrient preferences quantified in vivo

The paper quantifies nutrient preferences of gut bacteria in mice using isotope tracing and finds dietary fiber, protein, and host-derived metabolites drive microbial growth.

Proteome capacity constraints favor respiratory ATP generation

The paper shows mitochondrial respiration is more proteome-efficient than aerobic glycolysis in yeast and mammals, with flexibility arising from maintaining a fermentation-capable proteome.

Global Protein-Turnover Quantification in Escherichia coli Reveals Cytoplasmic Recycling under Nitrogen-Limitation

The paper quantifies protein turnover in E. coli under 12 conditions, revealing cytoplasmic protein recycling under nitrogen limitation and identifying unknown proteolysis pathways.

Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes

This study evaluates the Arrhenius equation's ability to predict temperature dependence in complex developmental processes like frog and fruit fly embryogenesis, finding it provides a good approximation despite deviations at extreme temperatures.

TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level

This paper introduces TMTProC, an optimized complementary ion quantification method for TMTPro tags, improving sensitivity and accuracy in multiplexed proteomics.

Precise temporal regulation of post-transcriptional repressors is required for an orderly Drosophila maternal-to-zygotic transition

The paper shows that precise degradation of post-transcriptional repressors during the Drosophila MZT is essential for orderly transition to zygotic gene control.

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-Statistics with Peptide Quantification Concordance

The paper introduces BACIQ, a method to calculate confidence intervals for multiplexed proteomics data by integrating peptide signal and measurement agreement, improving the detection of subcellular protein movement.

The protein repertoire in early vertebrate embryogenesis

The paper presents a comprehensive characterization of protein dynamics in Xenopus laevis early development and provides a web-based resource for data exploration.

Accurate, Sensitive, and Precise Multiplexed Proteomics using the Complement Reporter Ion Cluster

The paper introduces TMTc+, a proteomics method that improves accuracy, sensitivity, and precision of multiplexed measurements compared to existing approaches.

Proteomics of phosphorylation and protein dynamics during fertilization and meiotic exit in the Xenopus egg

The paper quantifies protein and phospho-site dynamics during fertilization and meiotic exit in Xenopus eggs using mass spectrometry-based proteomics, revealing limited degradation and extensive dephosphorylation.