Florian Meier

EXCRETE improves exoproteome identification in cyanobacteria, revealing 85% of predicted secreted proteins and highlighting key functions in cell envelope maintenance and nutrient acquisition.

AlphaPept is an open-source framework for efficient processing of large MS-based proteomics datasets, achieving significant speed improvements using Python and machine learning.

The paper develops a high-throughput AP-MS method to map a comprehensive yeast interactome, doubling the number of proteins and tripling reliable interactions.

The paper investigates how 22 post-translational modifications affect peptide collision cross sections using ion mobility spectrometry, finding sequence- and modification-specific effects.

μPhos is a phosphoproteomics platform that enables the identification of 5,000 phosphorylation sites from 5 µg of sample, supporting extensive perturbation experiments.

This study demonstrates the application of dia-PASEF with TIMS to achieve high-throughput phosphoproteomics with short gradients, quantifying over 12,000 phosphopeptides in one hour.

The paper quantifies the human liver proteome at cell-type resolution across multiple conditions, revealing proteome changes in disease states and providing a web-based resource for exploration.

The paper develops a high-sensitivity mass spectrometry workflow to quantify single-cell proteome changes upon perturbation, revealing a stable core proteome despite transcriptomic variability.

The paper measures CCS values for a million peptides across five organisms and develops a method to predict CCS for any peptide and organism.

The paper introduces a new DIA scan mode that improves peptide precursor ion sampling and identification specificity using ion mobility, achieving high proteome coverage and accuracy.

This paper develops a high-sensitivity lipidomics workflow using TIMS and PASEF, enabling deeper lipid analysis from minimal samples with improved speed and coverage.

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.