IDM: a data management system for high-throughput proteomics

Advanced proteomic research needs the use of high level informatics tools that allow the effective analysis of large quantities of differing types of data originating from very complex samples [1]. However such informatics tools are numerous, expensive and employ the use of several steps with high time-consuming. Here we present a user-friendly bioinformatics platform, named IDentification Mass (IDM), able to cross huge amount of transcriptomic and proteomic data. First of all IDM is able to simultaneously translate thousands of nucleotide sequences in corresponding six frame amino acid sequences in order to create a custom protein database. This step is required for protein identification in case of non-model organisms and allows to correlate mass spectrometric protein data with the corresponding amino acidic sequence. Protein identification by IDM is possible with both approaches: Peptide Mass Finger Print and Sequence Tag identification. Starting from the protein database, the software can in-silico digest all the amino acid sequences and compare the virtual mass peak list with the experimental one generated by mass spectrometry analysis. In the same time, it is possible to search in custom database amino acid sequences identified by MS/MS analysis of peptides obtained by protein enzymatic digestion. In order to validate the software, proteome analysis of a parasitoid insect (Eupelmus urozonus) venom was performed. ESI direct injection in FTICR-MS of twenty two-dimensional gel electrophoresis (2DE) trypsinized protein spots of E. urozonus venom was performed. Among tryptic mixture, the most intense peptides were subjected to Collision Induced Dissociation (CID) in order to determine the amino acid sequences [2]. By IDM platform, it was possible to identify unequivocally fifteen proteins of E. urozonus venom. Among the identified proteins, we found putative serpin, apyrase, serine protease, gamma-glutamyltranspeptidase, endopeptidase, metallo-beta-lactamase. Additionally, the IDM platform was able to identify post-translational modifications, such as phosphorylation. Many of these proteins were already found in other parasitoid venoms such as Nasonia vitripennis [3]. Moreover some of these proteins affect the immune system of host, other inhibit the host physiological activity such as reproduction and coagulation [4].