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Prague, Czech Republic

Krasny L.,Institute Of Microbiology Vvi | Hoffmann F.,Friedrich - Schiller University of Jena | Ernst G.,Friedrich - Schiller University of Jena | Trede D.,SCiLS GmbH | And 10 more authors.
Journal of the American Society for Mass Spectrometry | Year: 2014

Matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI MSI) is a well-established analytical technique for determining spatial localization of lipids in biological samples. The use of Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometers for the molecular imaging of endogenous compounds is gaining popularity, since the high mass accuracy and high mass resolving power enables accurate determination of exact masses and, consequently, a more confident identification of these molecules. The high mass resolution FT-ICR imaging datasets are typically large in size. In order to analyze them in an appropriate timeframe, the following approach has been employed: the FT-ICR imaging datasets were spatially segmented by clustering all spectra by their similarity. The resulted spatial segmentation maps were compared with the histologic annotation. This approach facilitates interpretation of the full datasets by providing spatial regions of interest. The application of this approach, which has originally been developed for MALDI-TOF MSI datasets, to the lipidomic analysis of head and neck tumor tissue revealed new insights into the metabolic organization of the carcinoma tissue. © 2014 American Society for Mass Spectrometry. Source

Kavan D.,Institute Of Microbiology Vvi | Kavan D.,Charles University | Kuzma M.,Institute Of Microbiology Vvi | Lemr K.,Institute Of Microbiology Vvi | And 4 more authors.
Journal of the American Society for Mass Spectrometry | Year: 2013

We have developed a de novo sequencing software tool (CYCLONE) and applied it for determination of cyclic peptides. The program uses a non-redundant database of 312 nonribosomal building blocks identified to date in bacteria and fungi (more than 230 additional residues in the database list were isobaric). The software was used to fully characterize the tandem mass spectrum of several cyclic peptides and provide sequence tags. The general strategy of the script was based on fragment ion pre-characterization to accomplish unambiguous b-ion series assignments. Showcase examples were a cyclic tetradepsipeptide beauverolide, a cyclic hexadepsipeptide roseotoxin A, a lasso-like hexapeptide pseudacyclin A, and a cyclic undecapeptide cyclosporin A. The extent of ion scrambling in smaller peptides was as low as 5 % of total ion current; this demonstrated the feasibility of CYCLONE de novo sequencing. The robustness of the script was also tested against database sets of various sizes and isotope-containing data. It can be downloaded from the http://ms.biomed.cas.cz/ MSTools/ website. [Figure not available: see fulltext.] © 2013 American Society for Mass Spectrometry. Source

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