Joshua Klein

ibaqpy computes iBAQ values for proteomics data using SDRF metadata, improving scalability and reproducibility in large-scale experiments.

The paper introduces the Universal Spectrum Identifier (USI) to standardize referencing mass spectra in proteomics repositories, enabling transparent traceability of spectral evidence in publications.

The paper improves N-glycopeptide identification using fragmentation prediction and glycome network smoothing, demonstrating performance gains on existing datasets.

The paper demonstrates the use of GlycReSoft to analyze site-specific glycosylation of the SARS-CoV-2 spike protein from glycoproteomics data.