Machine learning and network analysis using mathematical optimisation in mass spectrometry bioinformatics.

In this work we develop and present a set of novel computational techniques which address the problems of ICR-FT-MS data mining. The described methodology focuses mainly on two scopes of biogeochemical research, namely the analysis of natural organic matter (NOM) and metabolomics. The development of our approaches focuses on the fields of graph theory, machine learning, and combinatorics. Detailed results of our methods are produced, presented, and evaluated within their corresponding sections

Development of an Intermodal Journey Planner for the Visitors of Athens

240 σ.Εθνικό Μετσόβιο Πολυτεχνείο--Μεταπτυχιακή Εργασία. Διεπιστημονικό-Διατμηματικό Πρόγραμμα Μεταπτυχιακών Σπουδών (Δ.Π.Μ.Σ.) "Γεωπληροφορική"Η Εργασία αποτελεί την Διπλωματική Εργασία για το Μεταπτυχιακό Πρόγραμμα Σπουδών "Γεωπληροφορική" του Εθνικού Μετσόβιου Πολυτεχνείου. Αντικείμενο της Εργασίας ήταν η δημιουργία ενός Σχεδιαστή Ταξιδίων Με Μέσα Μαζικής Μεταφοράς (Intermodal Journey Planner), που να απευθύνεται κατά κύριο λόγο στους επισκέπτες της πόλης. Για τον λόγο αυτό η σχετική εφαρμογή σχεδιάστηκε ώστε να είναι αρκετά απλή στην χρήση και να μπορεί να δίνει με λίγα βήματα και γρήγορα μια πολύ καλή καθοδήγηση, ενώ ως γλώσσα του περιβάλλοντος χρήσης επιλέχθηκε η Αγγλική. Η εφαρμογή παρέχεται μέσω ενός web interface και στηρίζεται σε open source εργαλεία. Η δημιουργία της στάθηκε ως πλαίσιο για την απόκτηση γνώσης σχετικά με την γλώσσα προγραμματισμού Java, την δημιουργία web sites και εφαρμογών, την πλοήγηση με χρήση γράφων, όπως επίσης και με την λογική της ανάπτυξης λογισμικού ανοικτού κώδικα και των μεθοδολογιών λειτουργίας μιας κοινότητας ανάπτυξης τέτοιου λογισμικού.The Project is a Thesis for the "Geoinformatics" Postgraduate Studies Programme of the National Technical University of Athens. Goal of the Project was the implementation of an Intermodal Journey Planner for Athens‘ region, targeting its foreign visitors. Thus, the service was designed to be easy in use and capable to provide a good routing solution with only a few steps. Additionally, the language of the user interface is English. The service is provided by a web interface and is based mainly on open source tools. Its development was the frame for the acquisition of knowledge regarding Java, Web Sites‘ Creation, Rich Internet Applications, Routing, Data Manipulation, as also regarding open source software development and team collaboration.Μιχαήλ Δ. Τζιώτη

Kendrick-analogous network visualisation of ion cyclotron resonance Fourier transform mass spectra: Improved options for the assignment of elemental compositions and the classification of organic molecular complexity.

Here, we propose a novel computational and visual approach for the analysis of high field Fourier transform ion cyclotron resonance mass spectra (FTICR/MS) based on successive and multiple atomic and Kendrick analogous mass difference analyses. Compositional networks based on elemental compositions and functional networks based on selected functional groups equivalents enable improved assignment options of elemental composition and classification of organic complexity with tunable validation windows. The approach is demonstrated through the analysis of a 12T FTICR mass spectrum of an intricate water soluble extract of a secondary organic aerosol with a previously established abundance in CHNOS molecules

Ultrahigh resolution mass spectrometry based non-targeted microbial metabolomics.

© 2012 Springer Science+Business Media, LLC. All rights are reserved. Microbial metabolomes gain more and more attention due to the fact that microorganisms are ubiquitous and important in environment and health. Some are involved in basic environmental processes and govern element cycles in the entire ecosystem; others have relevance for animals and human (as commensal or pathogens) and have the potential to be used in biotechnology. The tools of Metabolomics have been used for many years in microbial research and the paradigm is changing from studies on single species cultures to multispecies communities, like in biofilms or environmental and human microbiomes. These changes lead to a new variety of metabolomic tools (metametabolomics) adapted to the study of multiple organisms systems. In addition the needs in high-resolution instrumentation are changing to analytical platforms that enable to deal with the yet unknown compounds. ICR-FT/MS is a promising ultrahigh resolution mass spectrometry approach mastering the challenge in non-targeted metabolomics. This chapter presents an introduction to the current state of the art in microbial metabolomics, the importance of ICR-FT/MS in this field and is describing solutions for non-targeted metabolomics with a focus on bacterial samples

Dissolved organic matter in sea spray: a transfer study from marine surface water to aerosols

Atmospheric aerosols impose direct and indirect effects on the climate system, for example, by absorption of radiation in relation to cloud droplets size, on chemical and organic composition and cloud dynamics. The first step in the formation of Organic primary aerosols, i.e. the transfer of dissolved organic matter from the marine surface into the atmosphere, was studied. We present a molecular level description of this phenomenon using the high resolution analytical tools of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR). Our experiments confirm the chemoselective transfer of natural organic molecules, especially of aliphatic compounds from the surface water into the atmosphere via bubble bursting processes. Transfer from marine surface water to the atmosphere involves a chemical gradient governed by the physicochemical properties of the involved molecules when comparing elemental compositions and differentiating CHO, CHNO, CHOS and CHNOS bearing compounds. Typical chemical fingerprints of compounds enriched in the aerosol phase were CHO and CHOS molecular series, smaller molecules of higher aliphaticity and lower oxygen content, and typical surfactants. A non-targeted metabolomics analysis demonstrated that many of these molecules corresponded to homologous series of oxo-, hydroxy-, methoxy-, branched fatty acids and mono-, di- and tricarboxylic acids as well as monoterpenes and sugars. These surface active biomolecules were preferentially transferred from surface water into the atmosphere via bubble bursting processes to form a significant fraction of primary organic aerosols. This way of sea spray production leaves a selective biological signature of the surface water in the corresponding aerosol that may be transported into higher altitudes up to the lower atmosphere, thus contributing to the formation of secondary organic aerosol on a global scale or transported laterally with possible deposition in the context of global biogeocycling

Using ultrahigh resolution mass spectrometry to unravel the chemical space of complex natural product mixtures.

Complex environmental and biological samples contain an enormous pool of abiotic and biotic low-molecular-weight natural products. The analysis of the entity of metabolites, in general referred to as metabolomics, is an important step toward the discovery of novel molecular structures in any type of organism as well as to improve the understanding of cellular regulation and adaption processes. Natural product analysis by means of metabolomics benefits from recent improvements in sampling and separation technologies such as solid-phase extraction (SPE), ultraperformance liquid chromatography (UPLC), and multidimensional chromatography, as well as from improved resolution and sensitivity in organic structural spectroscopy, namely infrared (IR) and Raman spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and especially mass spectrometry. A combination of pathway mapping, statistical analysis, and mass defect filtering can be applied to focus on most important compounds or series of structurally related natural products