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The 'net4pg' package     allows to assess and handle ambiguity of protein identifications. It     implements methods for two main applications. First, it allows to represent    and quantify ambiguity of protein identifications by means of graph     connected components (CCs). In graph theory, CCs are defined as the largest    subgraphs in which any two vertices are connected to each other by a path     and not connected to any other of the vertices in the supergraph. Here,     proteins sharing one or more peptides are thus gathered in the same CC     (multi-protein CC), while unambiguous protein identifications constitute CCs     with a single protein vertex (single-protein CCs). Therefore, the proportion    of single-protein CCs and the size of multi-protein CCs can be used to    measure the level of ambiguity of protein identifications. 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