Andreas‐David Brunner

The obesity-linked peptide SP16 regulates adipocytes through GIP and insulin receptor

This study identifies SP16 as a novel GIP receptor agonist that promotes lipolysis and has metabolic benefits in diet-induced obese mice.

The social architecture of an in-depth cellular protein interactome

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

Robust dimethyl-based multiplex-DIA workflow doubles single-cell proteome depth via a reference channel

This paper introduces a multiplex-DIA workflow that enhances single-cell proteome depth using dimethyl labeling and a reference channel, achieving reliable quantification of nearly 4,000 proteins per cell.

AlphaViz: Visualization and validation of critical proteomics data directly at the raw data level

AlphaViz validates proteomics results by visualizing raw data and comparing with automated analysis outputs.

Ultra-high sensitivity mass spectrometry quantifies single-cell proteome changes upon perturbation

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.

AlphaMap: An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge

AlphaMap visually annotates proteomics data with sequence-specific knowledge, enabling integration of experimental results with UniProt annotations and proteolytic cleavage sites.

Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories toward type 2 diabetes

This study uses multi-omics analysis of pancreatic islet donors to show heterogeneous beta cell changes associated with type 2 diabetes progression.

Deep learning the collisional cross sections of the peptide universe from a million training samples

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

AI-driven Deep Visual Proteomics defines cell identity and heterogeneity

Pairing AI-driven image analysis with automated laser microdissection and sensitive mass spectrometry yields proteomes of single cells or nuclei chosen by their morphology, with tissue position retained.

Parallel accumulation - serial fragmentation combined with data-independent acquisition (diaPASEF): Bottom-up proteomics with near optimal ion usage

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.

Trapped ion mobility spectrometry (TIMS) and parallel accumulation - serial fragmentation (PASEF) enable in-depth lipidomics from minimal sample amounts

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 global targeting of more than 25,000 peptides

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

Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

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