Isotopic envelope identification by analysis of the spatial distribution of components in MALDI-MSI data

One of the significant steps in the process leading to the identification of proteins is mass spectrometry, which allows for obtaining information about the structure of proteins. Removing isotope peaks from the mass spectrum is vital and it is done in a process called deisotoping. There are different algorithms for deisotoping, but they have their limitations, they are dedicated to different methods of mass spectrometry. Data from experiments performed with the MALDI-ToF technique are characterized by high dimensionality. This paper presents a method for identifying isotope envelopes in MALDI-ToF molecular imaging data based on the Mamdani-Assilan fuzzy system and spatial maps of the molecular distribution of peaks included in the isotopic envelope. Several image texture measures were used to evaluate spatial molecular distribution maps. The algorithm was tested on eight datasets obtained from the MALDI-ToF experiment on samples from the National Institute of Oncology in Gliwice from patients with cancer of the head and neck region. The data were subjected to pre-processing and feature extraction. The results were collected and compared with three existing deisotoping algorithms. The analysis of the obtained results showed that the method for identifying isotopic envelopes proposed in this paper enables the detection of overlapping envelopes by using the approach oriented to study peak pairs. Moreover, the proposed algorithm enables the analysis of large data sets

Method for mass spectrometry spectrum deisotoping based on fuzzy inference systems

Celem niniejszego artykułu jest omówienie zaproponowanego algorytmu do identyfikacji obwiedni izotopowych, opartego na teorii systemów rozmytych. Obecnie proteomika jest ściśle powiązana z chorobami nowotworowymi. Dlatego też bardzo ważne jest precyzyjne zidentyfikowanie białek znajdujących się w obszarze raka; stosowana jest w tym celu spektrometria masowa. Jedną z technik spektrometrii masowej jest MALDI. Otrzymane dane będące widmem masowym składają się ze stosunku masy do ładunku jonów oraz intensywnosci pików. W celu przetworzenia danych, usunięcia szumu, linii bazowej etc. stosuje się przetwarzanie wstępne. Identyfikacja obwiedni izotopowych jest częścią procesu przetwarzania wstępnego w proteomice. Polega ona na identyfikacji izotopów wchodzących w skład obwiedni izotopowej, a także pozwala na zredukowanie wymiaru danych. Istnieje wiele algorytmów do identyfikacji obwiedni izotopowej, jednak każdy z nich dedykowany jest dla innego rodzaju techniki spektrometrii masowej (MALDI, LC-MS, ESI, etc.) bądź dla konkretnego rodzaju cząsteczek. Dlatego też zaproponowany algorytm został oparty na teorii systemów rozmytych, a reguły wnioskowania zostały oparte na wieloletnich doświadczeniach eksperta w dziedzinie spektrometrii masowej. Przetestowany był on na danych uzyskanych z Instytutu Onkologii im. Marii Skłodowskiej-Curie w Gliwicach, pochodzących z badań nad rakiem głowy i szyi dla losowo wybranej grupy peptydów i lipidów. Wyniki autorskiego algorytmu do identyfikacji obwiedni izotopowych porównano z jedną z istniejących metod do identyfikacji obwiedni izotopowych.Nowadays, mass spectrometry is widely used in proteomics for confident and precise identification of the protein. One of the most important steps in the signal analysis is deisotoping because some peaks in the spectrum are not the unique compound, but there are members of an isotopic envelope. Although the mass spectrometry is present in proteomics for a long time already, the problem of isotope peaks identification is not solved yet. The existing algorithms, usually designed for the particular type of spectrometer, are semi-supervised and do not give satisfactory results. We propose a new algorithm based on fuzzy inference systems that can accurately identify the isotopic envelopes in the spectrum of the complex structure

An efficient 3D cell culture method on biomimetic nanostructured grids.

Current techniques of in vitro cell cultures are able to mimic the in vivo environment only to a limited extent, as they enable cells to grow only in two dimensions. Therefore cell culture approaches should rely on scaffolds that provide support comparable to the extracellular matrix. Here we demonstrate the advantages of novel nanostructured three-dimensional grids fabricated using electro-spinning technique, as scaffolds for cultures of neoplastic cells. The results of the study show that the fibers allow for a dynamic growth of HeLa cells, which form multi-layer structures of symmetrical and spherical character. This indicates that the applied scaffolds are nontoxic and allow proper flow of oxygen, nutrients, and growth factors. In addition, grids have been proven to be useful in in situ examination of cells ultrastructure

Socio-economic costs of continuing the status-quo of mercury pollution

Mercury is considered a global pollutant and it has been concluded that a significant portion of humans and wildlife throughout the world are exposed to methyl mercury at levels of concern. The Governing Council of UNEP has concluded that long-term international action is required. Most of the measures needed to reduce emissions will lead to costs to society. However, mercury pollution also results in costs to society including for example damage costs from negative impacts on human health and the environment, loss of income from reduced commercial fisheries, administrative costs for scientific research and development, control and risk communication. The aim of this report is to present an estimate of the socio-economic costs of continued mercury contamination of the environment as an input to the global considerations on what international long-term action should be taken. The study contains an analysis of the damage costs of continuing mercury pollution without any further measures until 2020. The analysis has mainly focussed on IQ losses due to the exposure to methyl mercury via ingestion of contaminated fish. Other human health, social and environmental damages are also discussed as are costs of controlling mercury emissions. Furthermore, societal benefits of reducing mercury emissions are presented for two emission reduction scenarios

HeLa cells stained with Hoechst 33342 and propidium iodide after 24 (A), 48 (B) and 72 (C) hours of 3D culture on the nanostructure grids.

<p>Original magnification x200. A fragment of the spherical 3D structure of cell growing on nanostructured grids visualized after 48 hours. Original magnification x400 (D).</p

Light microscopy image of nanostructured grid.

<p>Original magnification x200 (A). Scanning electron microscopy image of nanostructured microfiber. Original magnification x500 (B).</p

Cells growing on the scaffold visualized using light microscopy after 48 hours of incubation.

<p>Original magnification x200 (A). Scanning electron microscopy image of HeLa cells on the nanostructured grid fibers after 48 hours of incubation. Original magnification x100 (B).</p

Transmission electron microscopy images of HeLa cells on the nanostructure grid fibers after 48 h culture.

<p>Original magnification x6000.</p