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

http://en.wikipedia.org/wiki/Metabolomics

METABOLOMICS TECHNOLOGIES

Separation DetectionSample Signal

•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)•…

NMR based detectionSample Signalnuclei spin resonance

METABOLOMICS TECHNOLOGIES NMR experiments is very quick NMR equipment is quite expensive MS is more sensitive than NMR MS spectra can be wider than NMR

METABOLOMICS - ESPECTRO

MS:m/zNMR:ppm

[con

cent

ratio

n]

Visualization: 1 – SampleExample: TIC – Total Ion Counter

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

ESPECTRO 3D

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

ESPECTRO 3D 2D

Processing methods for differential analysis of LC-MS profile data - katajamaa - Oresic - BMC Bioinf 2005

Σ

METABOLOMICS – 1 MUESTRA (RESULTADO)

MS:m/zNMR:ppm

[con

cent

ratio

n]

Visualization: 1 – SampleExample: TIC – Total Ion Counter

METABOLOMICS – VARIAS MUESTRAS

MS:m/zNMR:ppm

[con

cent

ratio

n]

Several Samples

Bins0 500 1500 19601000

Sam

ples

Sam

ples

BINS

METABOLOMICS DATA

METABOLOMICS - COMMON PROBLEMS Base line correction Phasing / Alignment Solvent Peak

NMR : TSP, …(3-trimethylsilylpropionic acid)

MS : Water Standard pH shifts Temperature Effects

0 200 400 600 800

05

1015

Index

data

.3[1

:800

, 1]

0 200 400 600 800

010

2030

4050

Index

data

.3[-(

1:80

0), 1

]

METABOLOMICS – PREPROCESAMIENTO DE DATOS

Base-Line Subtraction Suavizado

Moving Average Used for smoothing No data reduction Overlapping windows

Binning Used for smoothing… … and data reduction Non overlapping windows

window size

…

window size …

window size

Integración

METABOLOMICS – PREPROCESAMIENTO DE DATOS

Phase Alignment

Scale

METABOLOMICS PRE-PROCESAMIENTO1. Corrección de línea

base (remoción de background)

2. Suavizado (smoothing)

3. Binning (disminución de datos y suavizado)

4. Alineamiento de Picos

5. Normalización de Escala

COMMON METABOLOMICS METHODS

Hierarchical Clustering (similar to Transcriptomics but using only sample clustering)

PCA – Principal Component Analysis -

Que software ya conocido podemos usar? MeV

METABOLOMICS - PROTOCOLO

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