Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata

MOTIVATION Experimental spatial proteomics, i.e. the high-throughput assignment of proteins to sub-cellular compartments based on quantitative proteomics data, promises to shed new light on many biological processes given adequate computational tools. RESULTS Here we present pRoloc, a complete infrastructure to support and guide the sound analysis of quantitative mass-spectrometry-based spatial proteomics data. It provides functionality for unsupervised and supervised machine learning for data exploration and protein classification and novelty detection to identify new putative sub-cellular clusters. The software builds upon existing infrastructure for data management and data processing.