Panalyzer: a software tool to tackle the protein inference problem

Protein identification by shotgun proteomics is a peptide-centric approach where there is no straightforward way to restore the link between proteolytic products and their protein antecedents. The same peptide sequence can belong to multiple protein sequences, therefore ambiguities in determining the identity of the proteins present in the sample can occur. This issue becomes especially problematic in the case of complex samples of higher eukaryotes where large protein families and multiple protein isoforms are present. At the moment, most search engines do not provide effective tools to filter and sort identified proteins in large datasets and in many publications many protein identifications with no real evidence are reported.