Sami Pietilä

PhosPiR automates phospho-proteomic analysis by integrating multiple R packages to provide data cleaning, statistical testing, enrichment analysis, and visualization for high-dimensional mass spectrometry data.

The paper introduces a DIA-only metaproteomics approach that improves peptide yields and reduces data requirements compared to DDA-assisted methods.

This study introduces data-independent acquisition mass spectrometry for metaproteomics, showing improved reproducibility in characterizing microbial function.