Hannah Boekweg

Improved detection of differentially abundant proteins through FDR-control of peptide-identity-propagation

The paper introduces PIP-ECHO, a method to control false discovery rate in peptide-identity-propagation, showing it outperforms existing tools in FDR control and differential protein abundance detection.

Pushing the Isotopic Envelope: When carrier channels pollute their neighbors signals

The paper investigates how impurities in isobaric labeling reagents can cause contamination in single-cell proteomics, leading to inaccurate quantification when carrier channels are overused.

Features of peptide fragmentation spectra in single cell proteomics

This study examines how peptide fragmentation spectra differ between single cell and bulk proteomics, identifying key changes that affect peptide identification.

Benchmarking PSM identification tools for single cell proteomics

This study benchmarks peptide spectrum match identification tools for single cell proteomics and finds MetaMorpheus performs best at 1% FDR, with post-processing ML improving results by up to 40%.

Temporal variation in lymphocyte proteomics

This study investigates proteomic changes in CLL during the asymptomatic stage using small sample sizes and highlights the need for larger control populations sampled over time.

Simplified and unified access to cancer proteogenomic data

The paper introduces a Python package, cptac, that provides unified access to processed cancer proteogenomic data from the CPTAC consortium for analysis and education.

Calculating sample size requirements for temporal dynamics in single cell proteomics

The paper calculates the sample size requirements for detecting proteome dynamics in single cell proteomics time course experiments.