A Bioconductor workflow for processing and analysing spatial proteomics data.

ABSTRACT: Spatial proteomics is the systematic study of protein sub-cellular localisation. In this workflow, we describe the analysis of a typical quantitative mass spectrometry-based spatial proteomics experiment using the MSnbase and pRoloc Bioconductor package suite. To walk the user through the computational pipeline, we use a recently published experiment predicting protein sub-cellular localisation in pluripotent embryonic mouse stem cells. We describe the software infrastructure at hand, importing and processing data, quality control, sub-cellular marker definition, visualisation and interactive exploration. We then demonstrate the application and interpretation of statistical learning methods, including novelty detection using semi-supervised learning, classification, clusterin

SUBMITTER: Breckels LM 

PROVIDER: S-EPMC6053703 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature