Summary: The discovery of functionally related groups in a set of significantly abundant proteins from a mass spectrometry experiment is an important step in a proteomics analysis pipeline. Here we describe NetWeAvers (NetworkWeighted Averages) for analyzing groups of regulated proteins in a network context, e.g. as defined by clusters of protein-protein interactions. NetWeAvers is an R package that provides a novel method for analyzing proteomics data integrated with biological networks. The method includes an algorithm for finding dense clusters of proteins and a permutation algorithm to calculate cluster P-values. Optional steps include summarizing quantified peptide values to single protein values and testing for differential expression, such that the data input can simply be a list of identified and quantified peaks.

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Journal Bioinformatics
McClellan, E.A, Moerland, P.D, van der Spek, P.J, & Stubbs, A. (2013). NetWeAvers: An R package for integrative biological network analysis with mass spectrometry data. Bioinformatics, 29(22), 2946–2947. doi:10.1093/bioinformatics/btt513