Applied Proteomics and Interactomics external website

The Applied Proteomics and Interactomics group focus on developing mass spectrometry-based omics technologies for biomolecular research under the IBAR service facility for chromatography and mass spectrometry analysis (Protein Chemistry Facility - PCF) performing protein, peptide, proteome and subproteome analysis. The facility was established in 2012 by a EU funded grant PROCERA (POSCCE-A2-O2.2.1-2009-4) in the Department of Bioinformatics and Structural Biochemistry (IBAR-DBSB).

Its main research topics are closely related with the focus-area of other groups and departments of IBAR: proteome and subproteome characterization in melanoma, protein-protein interactions in biological systems, co- and post-translational modification analysis with a special focus on glycosylation, imunopeptidome investigation, identification of specific protein interactors. Another priority is the study of protein phosphorylation, a dynamic process that implies the complementary activities of protein kinases and protein phosphatases. Mass spectrometric analysis of the samples implies the use of CID, HCD and ETD fragmentation methods. Data analysis and interpretation of results is made using Thermo Scientific™ Proteome Discoverer™ software. For phosphosite localization, besides the automated analysis (PhosphoRS Node in Proteome Discoverer) a manual inspection of the raw tandem mass spectra of the peptide is often made.

As a service unit the facility can provide the following methods of analysis:

• analytical and preparative HPLC of small molecules and biomolecules
• nanoHPLC separation of peptides
• low-/high-resolution mass spectrometry (MS) and tandem MS
• sample preparation of proteins and peptides for LC/MS analysis (spectrophotometric -UV-VIS, fluorimetric and electrophoretic methods -SDS-PAGE)
• bioinformatic MS data analysis
• batch or column fast protein chromatography