Head: Professor Michał Dadlez
Staff: M.Sc. Jacek Olędzki, M.Sc. Jacek Sikora, M.Sc. Magdalena Bakun, M.Sc. Agnieszka Fabijańska, M.Sc. Janusz Dębski, M.Sc. Agata Malinowska, M.Sc. Piotr Zarębski, M.Sc. Marta Tkaczyk, Michał Kistowski
Mass Spectrometry Laboratory acitivity is measuring the molecular masses of biologically relevant molecules. Based on molecular masses of protein tryptic fragments protein identification is carried out, including the posttranslational modifications. Also, mass spectrometry allows for relative and absolute quantification of the species, even in the context of complex mixtures. The laboratory operates using the cutting edge molecular mass measurements (MS) technology: Q-ToF Premier, LTQ FTICR, Orbitrp Velos spectrometers. Samples supplied by intramural and extramural research groups are analysed in terms of molecular masses of peptides, proteins, oligonucleotides etc. Most often the proteomic contents of polyacrylamide gel bands or spots is being analysed, but also, using coupled liquid chromatography and MS procedures, the protein contents of complex sets of proteins are being studied. For this purpose new informatic tools for MS data analysis are being worked out in the Laboratory. On average 240 protein identification analyses and 100 mass measurement analyses are being carried out each month in the last two years. In addition to protein identification the technology enables us to identify and localise posttranslational modifications. Many research groups, from different areas of biomedical sciences, are carrying out the proteomic analyses in the Laboratory. Currently, Laboratory participates in several projects, financed by Polish Ministry of Education and Science and EU. Laboratory organises proteomic lectures and courses for IBB and University of Warsaw students.
During last two years the Laboratory focused on establishing universal protocols for routine differential proteomics (DP) of a variety of biological samples. DP aims at characterizing the differences in terms of protein abundance between biological states of interest by listing proteins of different abundance in these states. When overlayed on the existing knowledge of protein interaction nets (systems biology approach) the results of the DP experiment may lead to better understanding of the phenomena under study at systems level. For example the synaptosomal proteome of WT and transgenic mouse models of Alzheimer’s disease is being studied by DP By combining peptide isoelectrofocusing and HPLC separation techniques, isotopic labeling of peptides and high sensitivity mass spectrometry we are able to monitor the levels of > 2000 proteins in a single experiment. The same approach is being used to study a proteomic fingerprint of spherocytosis in erythrocyte membranes, or different renal diseases in human urea proteome with the aim of establishing new diagnostic tools for these pathologies.
MS can also be applied for protein structure studies. We are using hydrogen-deuterium exchange to elucidate structural properties of different proteins and their complexes, like for instance the receptor for advanced glycation-end products (RAGE) and its ligands and keratin8 in complex with NBD domain of CFTR.