Tobias Schmidt

Unifying the analysis of bottom-up proteomics data with CHIMERYS

CHIMERYS deconvolves chimeric spectra in proteomic data, enabling unified analysis across DDA, DIA, and PRM experiments by accurately identifying and quantifying multiple peptides per spectrum.

Koina: Democratizing machine learning for proteomics research

Koina provides an open-source, accessible ML/DL prediction service for proteomics, improving integration with existing tools like FragPipe.

Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

The paper introduces a web-based tool for cross-resource peptide spectrum comparison and visualization, with a focus on integration and retrieval from spectral databases.

Generating high-quality libraries for DIA-MS with empirically-corrected peptide predictions

This paper introduces a method to generate high-quality DIA-MS libraries using peptide predictions and empirical refinement, demonstrating its effectiveness in non-model organisms and non-canonical databases.

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues

The paper creates a proteome and transcriptome atlas of 29 human tissues, revealing differences in mRNA-protein abundance and challenges in proteogenomics.