Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions.

ABSTRACT: By determining protein-protein interactions in normal, diseased and infected cells, we can improve our understanding of cellular systems and their reaction to various perturbations. In this protocol, we discuss how to use data obtained in affinity purification-mass spectrometry (AP-MS) experiments to generate meaningful interaction networks and effective figures. We begin with an overview of common epitope tagging, expression and AP practices, followed by liquid chromatography-MS (LC-MS) data collection. We then provide a detailed procedure covering a pipeline approach to (i) pre-processing the data by filtering against contaminant lists such as the Contaminant Repository for Affinity Purification (CRAPome) and normalization using the spectral index (SIN) or normalized spectral abundance f

SUBMITTER: Morris JH 

PROVIDER: S-EPMC4332878 | biostudies-literature | 2014 Nov

REPOSITORIES: biostudies-literature