An Staes

The paper uses proteomics to show increased ECM remodeling and complement activation in cardiac ATTR amyloidosis.

This paper introduces a high-throughput and ultrasensitive immunopeptidomics platform that identifies thousands of MHC I and II peptides from low-input samples.

The paper evaluates library-free DIA workflows for LiP-MS and introduces DIA-LiPA, a pipeline that improves structural interpretation of limited proteolysis data.

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

The paper compares DIA and DDA methods for immunopeptidomics, showing DIA improves detection of low-abundant bacterial epitopes from Listeria monocytogenes.

This paper introduces FibeRtypeR, a tool to estimate muscle fiber type proportions from bulk transcriptomics and proteomics data using single-fiber reference profiles.

The paper improves bacterial epitope discovery by integrating multiple search engines and rescoring, increasing peptide identification by 27% and detecting 18 new bacterial peptides.

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.

This study shows Olduvai domains suppress mitochondrial pathways, delaying cellular maturation and promoting brain size increase in humans.

The paper introduces a dual-column electrospray source for nano-flow proteomics to improve throughput while maintaining sensitivity in low-input samples.

CysQuant quantifies cysteine oxidation and protein abundance using DDA or DIA-MS, revealing redox changes in Arabidopsis exposed to light.

The paper investigates N-terminal proteoforms and finds they can engage in different protein complexes compared to their canonical counterparts.

This study benchmarks 12 DIA analysis workflows for shotgun proteomics samples, finding DIA-NN and Spectronaut in library-free mode offer highest sensitivity with good reproducibility and accuracy.

The paper investigates non-coding transcript translation in HEK293T cells, finding limited but potentially functional translation products using ribosome profiling and mass spectrometry.

The paper removes the dependency on DDA libraries in DIA by using predicted spectral libraries, making the workflow deterministic and improving standardization in clinical proteomics.