Paolo Nanni

qg generates reproducible, configuration-driven acquisition queues for mass spectrometry with QC control and vendor-specific file output.

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

prolfquapp simplifies differential expression analysis in quantitative proteomics by providing a command-line tool with dynamic HTML reports and integration with existing analysis tools.

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.

prolfqua provides an R package for proteomics differential expression analysis with quality control, normalization, and statistical modeling, showing sensitive and specific results.

The paper characterizes breast cancer cell responses to metabolic drugs using proteomics and computational models, showing heterogeneous effects and pathway-level flux changes.