Protein List Comparator (ProLiC)
In the recent years, high throughput proteomics has been gained remarkable progress resulting in huge data sets of protein identifications obtained from different cells or tissues. This often heterogeneous and distributed information needs to be integrated and compared in order to achieve a more comprehensive understanding of the cell function.
However, a direct comparison of available data, i.e. the protein lists along with related information (e.g. accession numbers, amino acid sequences, the assigned peptide identifications etc.), is challenging. For example, protein accessions may be obtained from various databases with different nomenclature. Furthermore, even within the same database, accession numbers may change with different database versions. Therefore, matching of protein identifications with respect to accession numbers alone is usually unsatisfying.
Furthermore, the assignment of experimentally obtained spectrum information to peptide sequences and the subsequent protein inference, usually contains uncertainty (e.g. due to an incomplete sequence coverage or an ambiguous peptide pattern).
The Protein List Comparator (ProLiC) software addresses these issues. To this end, ProLiC includes different possibilities to solve the problem of protein list comparison:
In addition to a simple accession based comparison, which is still supported by the software, ProLiC permits a more reliable comparison of protein lists from different sources by considering measured sequence and/or peptide information. The above mentioned uncertainty is addressed by the development of a protein grouping algorithm along with an adequate definition of a protein similarity criteria. The protein grouping algorithm of ProLiC is highly customizable via parameter settings given in the configuration file of the software.
ProLiC is a tool that can be used from the command line, which enables incorporation of ProLiC comparisons in ordinary shell scripts. The software is open source, free of charge and can be downloaded using the download link below. The download also includes a detailed manual.
Michael Kohl (michael.kohl:at:rub.de)