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Metabolomics

Bioinformatics – Functional Genomics – Dr. Víctor Treviño. Metabolomics. El metaboloma Representa la colección de todos los metabolitos de un organismo biológico Productos de función y expresión genética. Metabolomics. http://en.wikipedia.org/wiki/Metabolomics.

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Metabolomics

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  1. Bioinformatics – Functional Genomics – Dr. Víctor Treviño Metabolomics

  2. El metaboloma • Representa la colección de todos los metabolitos de un organismobiológico • Productos de funciónyexpresióngenética Metabolomics http://en.wikipedia.org/wiki/Metabolomics

  3. Metabolomics Technologies Sample Signal Separation Detection • Gas chromatography (GC) • High performance liquid chromatography (HPLC) • Capillary electrophoresis (CE) • Ultra-high pressure liquid chromatography (UPLC) • Ion mobility • Matrix-assisted laser desorption/ionization (MALDI) • … • Mass Spectrometry(mass-to-charge ratio) • Fourier transform ion cyclotron resonance (FTMS) • … Sample NMR based detection Signal nuclei spin resonance

  4. NMR experiments is very quick NMR equipment is quite expensive MS is more sensitive than NMR MS spectra can be wider than NMR Metabolomics Technologies

  5. Metabolomics - Espectro Visualization: 1 – Sample Example: TIC – Total Ion Counter [concentration] MS:m/z NMR:ppm

  6. Metabolomics –Identificación de Metabolitos – Interpretación Espectro • Los tiempos de retención de muchos metabolitos son conocidos • Otros se pueden aislar apartir del “pico” y luego estudiar para identificar

  7. Espectro 3D The Handbook of Metabonomics and Metabolomics (2007) – JeremyK. Nicholson, Elaine Holmes and John C. Lindon

  8. Espectro 3D  2D Σ Processing methods for differential analysis of LC-MS profile data - katajamaa - Oresic - BMC Bioinf 2005

  9. Metabolomics – 1 Muestra (Resultado) Visualization: 1 – Sample Example: TIC – Total Ion Counter [concentration] MS:m/z NMR:ppm

  10. Metabolomics – VariasMuestras Several Samples [concentration] MS:m/z NMR:ppm

  11. Samples Samples BINS  0 500 1000 1500 1960 Bins

  12. Metabolomics Data

  13. Base line correction • Phasing / Alignment • Solvent Peak • NMR : TSP, …(3-trimethylsilylpropionic acid) • MS : Water • Standard • pH shifts • Temperature Effects Metabolomics - Common Problems

  14. Base-Line Subtraction • Suavizado • Moving Average • Used for smoothing • No data reduction • Overlapping windows • Binning • Used for smoothing… • … and data reduction • Non overlapping windows Metabolomics – Preprocesamiento de datos window size … window size … window size Integración

  15. Phase Alignment • Scale Metabolomics – Preprocesamiento de datos

  16. Metabolomics pre-procesamiento • Corrección de línea base (remoción de background) • Suavizado (smoothing) • Binning (disminución de datos y suavizado) • Alineamiento de Picos • Normalización de Escala

  17. Hierarchical Clustering (similar to Transcriptomics but using only sample clustering) • PCA – Principal Component Analysis - • Que software yaconocidopodemosusar? • MeV Common Metabolomics Methods

  18. Metabolomics - Protocolo Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry - De Vos - Hall - Nat Prot 2007

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