Protein Inference Algorithms (PIA)
Most search engines for protein identification in MS/MS experiments return protein lists, although the actual search yields a set of peptide spectrum matches (PSMs). The step from PSMs to proteins is called “protein inference”. If a set of identified PSMs supports the detection of more than one protein in the searched database (“protein ambiguity”), usually only one representative accession is reported. These representatives may differ according to the used search engine and settings. Thus the protein lists of different search engines generally cannot be compared with one another. PSMs of complementary search engines are often combined to enhance the number of reported proteins or to verify the evidence of a peptide, which is improved by detection with distinct algorithms.
We developed an algorithm suite written in Java, including a fully parametrisable web-interface (using JavaServer Faces), which combines PSMs from different experiments and/or search engines, and reports consistent and thus comparable results. None of the parameters for the inference, like filtering or scoring, are fixed as in prior approaches, but held as flexible as possible, to allow for any adjustments needed by the user.
Link to publication