Jonathan R. Krieger

This paper optimizes diagonal-PASEF mass spectrometry with retention time down-sampling, improving identifications and quantification in proteomics.

The paper introduces uMetaP, an ultra-sensitive metaproteomic method that enhances detection of the gut dark metaproteome and identifies drug targets in intestinal inflammatory diseases.

TIMS2Rescore is a data-driven rescoring pipeline optimized for DDA-PASEF data that improves protein identification in proteomics analyses.

The paper benchmarks dia-PASEF with timsTOF HT for high-throughput proteome analysis in a multi-center study, showing consistent protein and peptide identification across laboratories.

The paper introduces midiaPASEF, a DIA scan mode that enhances information content in proteomics, enabling precise precursor m/z determination and efficient automated processing.

This paper introduces an immunopeptidomics workflow using PEAKS XPro to identify HLA-I ligands and neoantigens without relying on standard databases, revealing diverse peptides and mutations in colorectal cancer.

The paper demonstrates that Evosep One technology enables faster quantitative proteome analysis with comparable coverage to conventional methods.