Publication: Desarrollo de herramientas bioinformáticas para estudios de proteómica a gran escala de "Candida albicans"
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2016-08-10
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Universidad Complutense de Madrid
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Abstract
El concepto de Proteómica, acuñado en analogía al de Genómica, fue usado por primera vez por Marc Wilkins a mediados de los años 90 para describir al conjunto total de proteínas que se expresan por los genes de una célula, tejido u organismo. Anteriormente, a finales de los 80, el desarrollo de las técnicas de ionización suave, como la Ionización por Electrospray, ESI (Electrospray Ionization) o la Desorción Suave por Láser, SLD (Soft Laser Desorption), permitió ionizar grandes biomoléculas como los péptidos y proteínas manteniéndolas relativamente intactas. Esto sentó las bases de la espectrometría de masas aplicada a la proteómica. En la proteómica shotgun (el término inglés está muy asentado), el primer paso del experimento generalmente consiste en la digestión de las proteínas de la muestra en péptidos por acción de una enzima proteolítica como la tripsina. Esto incrementa notablmente el rendimiento en términos de número de proteínas que pueden ser identificadas en un sólo experimento comparado con los experimentos basados en gel. Sin embargo, tiene el coste asociado de provocar una gran complejidad de la mezcla de péptidos y el problema añadido de la inferencia de las proteínas originarias. Los péptidos son separados por cromatografía líquida e ionizados para entrar a continuación en el espectrómetro de masas donde son separados en función de la proporción entre su masa y su carga (m/z) y los valores obtenidos son registrados en un espectro MS1. En la espectrometría de masas en tándem (MS/MS), los péptidos con mayor intensidad son seleccionados para ser fragmentados de modo que se generan espectros MS/MS, colecciones de valores m/z y de intensidad para cada precursor y sus fragmentos...
The concept of Proteomics, a term coined in analogy to Genomics, was first used by Marc Wilkins in the mid 90s to describe the total set of proteins being expressed by the genes of a cell, tissue or organism. Earlier, in the late 80s, the development of soft ionizations techniques, such as Electrospray Ionization (ESI) and Soft Laser Desorption (SLD) enabled the ability to ionize large bio-molecules such as peptides and proteins while keeping them relatively intact. This settled the foundation upon which mass spectrometry was applied to what would later become modern proteomics. In shotgun proteomics, the first step of the experiment usually consists of a digestion of the sample proteins into peptides by means of a proteolytic enzyme such as trypsin. This greatly increases performance in terms of the number of proteins that can be detected in a single LC-MS/MS run compared to gel-based approaches, but comes at the cost of a great complexity at the peptide level and the protein inference problem. Peptides are then separated by liquid chromatography, then ionized and eventually enter the mass spectrometer where they are separated as a function of their mass-to-charge (m/z ) ratio and then recorded in the MS1 spectrum. In tandem mass spectrometry (MS/MS) peptides with higher intensities are selected to be fragmented so MS/MS spectra, a collection of m/z values and intensities of the precursor and product ions, are produced...
The concept of Proteomics, a term coined in analogy to Genomics, was first used by Marc Wilkins in the mid 90s to describe the total set of proteins being expressed by the genes of a cell, tissue or organism. Earlier, in the late 80s, the development of soft ionizations techniques, such as Electrospray Ionization (ESI) and Soft Laser Desorption (SLD) enabled the ability to ionize large bio-molecules such as peptides and proteins while keeping them relatively intact. This settled the foundation upon which mass spectrometry was applied to what would later become modern proteomics. In shotgun proteomics, the first step of the experiment usually consists of a digestion of the sample proteins into peptides by means of a proteolytic enzyme such as trypsin. This greatly increases performance in terms of the number of proteins that can be detected in a single LC-MS/MS run compared to gel-based approaches, but comes at the cost of a great complexity at the peptide level and the protein inference problem. Peptides are then separated by liquid chromatography, then ionized and eventually enter the mass spectrometer where they are separated as a function of their mass-to-charge (m/z ) ratio and then recorded in the MS1 spectrum. In tandem mass spectrometry (MS/MS) peptides with higher intensities are selected to be fragmented so MS/MS spectra, a collection of m/z values and intensities of the precursor and product ions, are produced...
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Tesis inédita de la Universidad Complutense de Madrid, Facultad de Farmacia, Departamento de Microbiología II, leída el 15-01-2016