Jürgen Cox

This study shows that different stress types cause distinct plasma proteomic and metabolic responses in humans, with physical stress having the strongest effect.

The paper introduces MaxSBM, a MaxQuant module for identifying sequence-based modifiers like SUMO, improving peptide identification rates and spectral annotation.

The paper identifies a bimodal distribution of peptide collision cross sections, showing two stable conformations, and proposes a two-valued predictor to improve peptide identification in proteomics.

pmultiqc generates metadata-aware QC reports for proteomics data using standardized metrics and integrates with existing workflows and cloud services.

This paper introduces metadata integration in MaxQuant to standardize and simplify proteomics data analysis and reuse.

This study uses enamel proteomics to determine biological sex and assess intraspecific variation in Paranthropus robustus from South Africa, supporting the idea that morphological variation may reflect taxonomic diversity.

ProteoPlotter is a visualization tool for proteomics data that complements Perseus, offering enhanced features for data analysis and interpretation.

The paper updates MaxQuant for isobaric labeling data, showing improved accuracy and reduced batch effects using weighted median normalization.

This paper introduces a deep learning-based approach for peptide identification in mass spectrometry proteomics that outperforms existing tools by using spectra and peptide sequences directly.

MaxLynx improves XL-MS analysis by automating cross-linked peptide identification with enhanced scoring and filtering, outperforming existing tools on synthetic and proteome-wide datasets.

MaxNovo is a de-novo peptide sequencing algorithm that outperforms existing methods in high-sensitivity range, using expert knowledge rather than machine learning.

This study identifies three archaeal ESCRT-based cell division mechanisms and suggests an evolutionary link between archaea and eukaryotes through ESCRT similarity.

The paper introduces two algorithms in MaxQuant that improve reporter ion-based quantification by addressing normalization issues and missing values in isobaric labeling.

The paper introduces an enhanced MaxQuant software for ion mobility shotgun proteomics, improving quantification accuracy and coverage using 4D data analysis.

The paper systematically detects amino acid substitutions in proteomes using mass spectrometry data and reveals that translation errors are primarily caused by codon-anticodon mispairing, with patterns influenced by ribosome velocity and evolutionary constraints.

PerseusNet, a new module for the Perseus software, enables proteome interaction graph analysis through statistical methods and tools for network generation and exploration.

MaxQuant.Live enables real-time global targeting of over 25,000 peptides by combining shotgun and targeted proteomics approaches.

The paper introduces the timsTOF Pro instrument with online PASEF, achieving high sensitivity and reproducibility in proteomics.

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